Last edit: 05-09-15 Graham Wideman
| Last edit: 05-09-15 Graham Wideman |
Brain |
| AFNI -- All Helps on One Page Article created: 2003-01-20 |
The NIMH AFNI home site provides a listing of the results of the -help option for all approx 230 AFNI programs, which is an excellent service. I wanted them all on one page for quick browsing, searching en masse etc, which is what is assembled here.
Special Request: If you anticipate using this page frequently, please save me some bandwidth, and yourself some time, by saving the page on your local computer. (File > Save As or similar).
| Topic | Discussion |
| Version | See bottom line of each help output where "auto-generated" date indicates date that this info was produced by the AFNI team. Note that I do not recreate this page frequently. |
| Listing Order | The listing order is alphabetical, ignoring case, and ignoring initial "@" character on some AFNI commands/scripts. |
| Improved handling of brackets | In a few cases this listing is slightly improved over the AFNI site: some AFNI programs emit help with angle brackets (greater-than/less-than ) as part of their "Usage" line. Where these should appear in the web version of AFNI documentation, these fool browsers into reading the brackets and enclosed text as unknown HTML tags, causing the browser not to show that text (eg: as in SUMA_AlignToExperiment <EXPERIMENT Anatomy> <SURFACE Anatomy> ). The listing below handles this problem by translating these brackets to their "character entity" form. |
| 1dcat |
Usage: 1dcat a.1D b.1D ...
where each file a.1D, b.1D, etc. is an ASCII file of numbers
arranged in rows and columns.
The row-by-row catenation of these files is written to stdout.
TIMESERIES (1D) INPUT
---------------------
A timeseries file is in the form of a 1D or 2D table of ASCII numbers;
for example: 3 5 7
2 4 6
0 3 3
7 2 9
This example has 3 rows and 4 columns. Each column is considered as
a timeseries in AFNI. The convention is to store this type of data
in a filename ending in '.1D'.
When specifying a timeseries file to an command-line AFNI program, you
can select a subset of columns using the '[...]' notation:
'fred.1D[5]' ==> use only column #5
'fred.1D[5,9,17]' ==> use columns #5, #9, and #12
'fred.1D[5..8]' ==> use columns #5, #6, #7, and #8
'fred.1D[5..13(2)]' ==> use columns #5, #7, #9, #11, and #13
Sub-brick indexes start at 0. You can use the character '$'
to indicate the last sub-brick in a dataset; for example, you
can select every third sub-brick by using the selection list
'fred.1D[0..$(3)]' ==> use columns #0, #3, #6, #9, ....
Similarly, you select a subset of the rows using the '{...}' notation:
'fred.1D{0..$(2)}' ==> use rows #0, #2, #4, ....
You can also use both notations together, as in
'fred.1D[1,3]{1..$(2)}' ==> columns #1 and #3; rows #1, #3, #5, ....
You can also input a 1D time series 'dataset' directly on the command
line, without an external file. The 'filename' for such input has the
general format
'1D:n_1@val_1,n_2@val_2,n_3@val_3,...'
where each 'n_i' is an integer and each 'val_i' is a float. For
example
-a '1D:5@0,10@1,5@0,10@1,5@0'
specifies that variable 'a' be assigned to a 1D time series of 35,
alternating in blocks between values 0 and value 1.
This page auto-generated on Thu Aug 25 16:49:35 EDT 2005
|
| 1ddot |
Usage: 1ddot [options] 1Dfile 1Dfile ... - Prints out correlation matrix of the 1D files and their inverse correlation matrix. - Output appears on stdout. Options: -one = Make 1st vector be all 1's.This page auto-generated on Thu Aug 25 16:49:35 EDT 2005 |
| 1deval |
Usage: 1deval [options] -expr 'expression'
Evaluates the expression and writes the result to stdout.
Any single letter from a-z can be used as the independent
variable in the expression.
Options:
-del d = Use 'd' as the step for the variable in the
expression [default = 1.0]
-num n = Evaluate the expression 'n' times.
If -num is not used, then the length of an
input time series is used. If there are no
time series input, then -num is required.
-a q.1D = Read time series file q.1D and assign it
to the symbol 'a' (as in 3dcalc).
-index i.1D = Read index column from file i.1D and
write it out as 1st column of output.
This option is useful when working with
surface data.
Examples:
1deval -expr 'sin(2*PI*t)' -del 0.01 -num 101 > sin.1D
1deval -expr 'a*b*x' -a fred.1D -b ethel.1D > x.1D
TIMESERIES (1D) INPUT
---------------------
A timeseries file is in the form of a 1D or 2D table of ASCII numbers;
for example: 3 5 7
2 4 6
0 3 3
7 2 9
This example has 3 rows and 4 columns. Each column is considered as
a timeseries in AFNI. The convention is to store this type of data
in a filename ending in '.1D'.
When specifying a timeseries file to an command-line AFNI program, you
can select a subset of columns using the '[...]' notation:
'fred.1D[5]' ==> use only column #5
'fred.1D[5,9,17]' ==> use columns #5, #9, and #12
'fred.1D[5..8]' ==> use columns #5, #6, #7, and #8
'fred.1D[5..13(2)]' ==> use columns #5, #7, #9, #11, and #13
Sub-brick indexes start at 0. You can use the character '$'
to indicate the last sub-brick in a dataset; for example, you
can select every third sub-brick by using the selection list
'fred.1D[0..$(3)]' ==> use columns #0, #3, #6, #9, ....
Similarly, you select a subset of the rows using the '{...}' notation:
'fred.1D{0..$(2)}' ==> use rows #0, #2, #4, ....
You can also use both notations together, as in
'fred.1D[1,3]{1..$(2)}' ==> columns #1 and #3; rows #1, #3, #5, ....
You can also input a 1D time series 'dataset' directly on the command
line, without an external file. The 'filename' for such input has the
general format
'1D:n_1@val_1,n_2@val_2,n_3@val_3,...'
where each 'n_i' is an integer and each 'val_i' is a float. For
example
-a '1D:5@0,10@1,5@0,10@1,5@0'
specifies that variable 'a' be assigned to a 1D time series of 35,
alternating in blocks between values 0 and value 1.
This page auto-generated on Thu Aug 25 16:49:35 EDT 2005
|
| 1dfft |
Usage: 1dfft [options] infile outfile
where infile is an AFNI *.1D file (ASCII list of numbers arranged
in columns); outfile will be a similar file, with the absolute
value of the FFT of the input columns. The length of the file
will be 1+(FFT length)/2.
Options:
-ignore sss = Skip the first 'sss' lines in the input file.
[default = no skipping]
-use uuu = Use only 'uuu' lines of the input file.
[default = use them all, Frank]
-nfft nnn = Set FFT length to 'nnn'.
[default = length of data (# of lines used)]
-tocx = Save Re and Im parts of transform in 2 columns.
-fromcx = Convert 2 column complex input into 1 column
real output.
-hilbert = When -fromcx is used, the inverse FFT will
do the Hilbert transform instead.
-nodetrend = Skip the detrending of the input.
Nota Bene:
* Each input time series has any quadratic trend of the
form 'a+b*t+c*t*t' removed before the FFT, where 't'
is the line number.
* The FFT length will be a power-of-2 times at most one
factor of 3 and one factor of 5. The smallest such
length >= to the specified FFT length will be used.
* If the FFT length is longer than the file length, the
data is zero-padded to make up the difference.
* Do NOT call the output of this program the Power Spectrum!
That is something else entirely.
* If 'outfile' is '-', the output appears on stdout.
This page auto-generated on Thu Aug 25 16:49:35 EDT 2005
|
| 1dgrayplot |
Usage: 1dgrayplot [options] tsfile
Graphs the columns of a *.1D type time series file to the screen,
sort of like 1dplot, but in grayscale.
Options:
-install = Install a new X11 colormap (for X11 PseudoColor)
-ignore nn = Skip first 'nn' rows in the input file
[default = 0]
-flip = Plot x and y axes interchanged.
[default: data columns plotted DOWN the screen]
-sep = Separate scales for each column.
-use mm = Plot 'mm' points
[default: all of them]
-ps = Don't draw plot in a window; instead, write it
to stdout in PostScript format.
N.B.: If you view this result in 'gv', you should
turn 'anti-alias' off, and switch to
landscape mode.
TIMESERIES (1D) INPUT
---------------------
A timeseries file is in the form of a 1D or 2D table of ASCII numbers;
for example: 3 5 7
2 4 6
0 3 3
7 2 9
This example has 3 rows and 4 columns. Each column is considered as
a timeseries in AFNI. The convention is to store this type of data
in a filename ending in '.1D'.
When specifying a timeseries file to an command-line AFNI program, you
can select a subset of columns using the '[...]' notation:
'fred.1D[5]' ==> use only column #5
'fred.1D[5,9,17]' ==> use columns #5, #9, and #12
'fred.1D[5..8]' ==> use columns #5, #6, #7, and #8
'fred.1D[5..13(2)]' ==> use columns #5, #7, #9, #11, and #13
Sub-brick indexes start at 0. You can use the character '$'
to indicate the last sub-brick in a dataset; for example, you
can select every third sub-brick by using the selection list
'fred.1D[0..$(3)]' ==> use columns #0, #3, #6, #9, ....
Similarly, you select a subset of the rows using the '{...}' notation:
'fred.1D{0..$(2)}' ==> use rows #0, #2, #4, ....
You can also use both notations together, as in
'fred.1D[1,3]{1..$(2)}' ==> columns #1 and #3; rows #1, #3, #5, ....
You can also input a 1D time series 'dataset' directly on the command
line, without an external file. The 'filename' for such input has the
general format
'1D:n_1@val_1,n_2@val_2,n_3@val_3,...'
where each 'n_i' is an integer and each 'val_i' is a float. For
example
-a '1D:5@0,10@1,5@0,10@1,5@0'
specifies that variable 'a' be assigned to a 1D time series of 35,
alternating in blocks between values 0 and value 1.
This page auto-generated on Thu Aug 25 16:49:35 EDT 2005
|
| 1dnorm |
Usage: 1dnorm infile outfile where infile is an AFNI *.1D file (ASCII list of numbers arranged in columns); outfile will be a similar file, with each column being L2 normalized.This page auto-generated on Thu Aug 25 16:49:35 EDT 2005 |
| 1dplot |
Usage: 1dplot [options] tsfile ...
Graphs the columns of a *.1D type time series file to the screen.
Options:
-install = Install a new X11 colormap.
-sep = Plot each column in a separate sub-graph.
-one = Plot all columns together in one big graph.
[default = -sep]
-dx xx = Spacing between points on the x-axis is 'xx'
[default = 1]
-xzero zz = Initial x coordinate is 'zz' [default = 0]
-nopush = Don't 'push' axes ranges outwards.
-ignore nn = Skip first 'nn' rows in the input file
[default = 0]
-use mm = Plot 'mm' points [default = all of them]
-xlabel aa = Put string 'aa' below the x-axis
[default = no axis label]
-ylabel aa = Put string 'aa' to the left of the y-axis
[default = no axis label]
-stdin = Don't read from tsfile; instead, read from
stdin and plot it. You cannot combine input
from stdin and tsfile(s). If you want to do
so, see program 1dcat.
-ps = Don't draw plot in a window; instead, write it
to stdout in PostScript format.
N.B.: If you view this result in 'gv', you should
turn 'anti-alias' off, and switch to
landscape mode.
-xaxis b:t:n:m = Set the x-axis to run from value 'b' to
value 't', with 'n' major divisions and
'm' minor tic marks per major division.
For example:
-xaxis 0:100:5:20
Setting 'n' to 0 means no tic marks or labels.
-yaxis b:t:n:m = Similar to above, for the y-axis. These
options override the normal autoscaling
of their respective axes.
-ynames aa bb ... = Use the strings 'aa', 'bb', etc., as
labels to the right of the graphs,
corresponding to each input column.
These strings CANNOT start with the
'-' character.
-volreg = Makes the 'ynames' be the same as the
6 labels used in plug_volreg for
Roll, Pitch, Yaw, I-S, R-L, and A-P
movements, in that order.
You may also select a subset of columns to display using
a tsfile specification like 'fred.1D[0,3,5]', indicating
that columns #0, #3, and #5 will be the only ones plotted.
For more details on this selection scheme, see the output
of '3dcalc -help'.
Example: graphing a 'dfile' output by 3dvolreg, when TR=5:
1dplot -volreg -dx 5 -xlabel Time 'dfile[1..6]'
You can also input more than one tsfile, in which case the files
will all be plotted. However, if the files have different column
lengths, the shortest one will rule.
The colors for the line graphs cycle between black, red, green, and
blue. You can alter these colors by setting Unix environment
variables of the form AFNI_1DPLOT_COLOR_xx -- cf. README.environment.
You can alter the thickness of the lines by setting the variable
AFNI_1DPLOT_THIK to a value between 0.00 and 0.05 -- the units are
fractions of the page size.
TIMESERIES (1D) INPUT
---------------------
A timeseries file is in the form of a 1D or 2D table of ASCII numbers;
for example: 3 5 7
2 4 6
0 3 3
7 2 9
This example has 3 rows and 4 columns. Each column is considered as
a timeseries in AFNI. The convention is to store this type of data
in a filename ending in '.1D'.
When specifying a timeseries file to an command-line AFNI program, you
can select a subset of columns using the '[...]' notation:
'fred.1D[5]' ==> use only column #5
'fred.1D[5,9,17]' ==> use columns #5, #9, and #12
'fred.1D[5..8]' ==> use columns #5, #6, #7, and #8
'fred.1D[5..13(2)]' ==> use columns #5, #7, #9, #11, and #13
Sub-brick indexes start at 0. You can use the character '$'
to indicate the last sub-brick in a dataset; for example, you
can select every third sub-brick by using the selection list
'fred.1D[0..$(3)]' ==> use columns #0, #3, #6, #9, ....
Similarly, you select a subset of the rows using the '{...}' notation:
'fred.1D{0..$(2)}' ==> use rows #0, #2, #4, ....
You can also use both notations together, as in
'fred.1D[1,3]{1..$(2)}' ==> columns #1 and #3; rows #1, #3, #5, ....
You can also input a 1D time series 'dataset' directly on the command
line, without an external file. The 'filename' for such input has the
general format
'1D:n_1@val_1,n_2@val_2,n_3@val_3,...'
where each 'n_i' is an integer and each 'val_i' is a float. For
example
-a '1D:5@0,10@1,5@0,10@1,5@0'
specifies that variable 'a' be assigned to a 1D time series of 35,
alternating in blocks between values 0 and value 1.
This page auto-generated on Thu Aug 25 16:49:35 EDT 2005
|
| 1dsum |
Usage: 1dsum [options] a.1D b.1D ... where each file a.1D, b.1D, etc. is an ASCII file of numbers arranged in rows and columns. The sum of each column is written to stdout. Options: -ignore nn = skip the first nn rows of each file -use mm = use only mm rows from each fileThis page auto-generated on Thu Aug 25 16:49:35 EDT 2005 |
| 1dsvd |
Usage: 1dsvd [options] 1Dfile 1Dfile ...
- Computes SVD of the matrix formed by the 1D file(s).
- Output appears on stdout; to save it, use '>' redirection.
Options:
-one = Make 1st vector be all 1's.
-cond = Only print condition number (ratio of extremes)
-sing = Only print singular values
-1Dright = Only output right eigenvectors, in a .1D format
This can be useful for reducing the number of
columns in a design matrix. The singular values
are printed at the top of each vector column.
This page auto-generated on Thu Aug 25 16:49:35 EDT 2005
|
| 1dtranspose |
Usage: 1dtranspose infile outfile where infile is an AFNI *.1D file (ASCII list of numbers arranged in columns); outfile will be a similar file, but transposed. You can use a column subvector selector list on infile, as in 1dtranspose 'fred.1D[0,3,7]' ethel.1D * This program may produce files with lines longer than a text editor can handle. * If 'outfile' is '-' (or missing entirely), output goes to stdout.This page auto-generated on Thu Aug 25 16:49:35 EDT 2005 |
| 24swap |
Usage: 24swap [options] file ...
Swaps bytes pairs and/or quadruples on the files listed.
Options:
-q Operate quietly
-pattern pat 'pat' determines the pattern of 2 and 4
byte swaps. Each element is of the form
2xN or 4xN, where N is the number of
bytes to swap as pairs (for 2x) or
as quadruples (for 4x). For 2x, N must
be divisible by 2; for 4x, N must be
divisible by 4. The whole pattern is
made up of elements separated by colons,
as in '-pattern 4x39984:2x0'. If bytes
are left over after the pattern is used
up, the pattern starts over. However,
if a byte count N is zero, as in the
example below, then it means to continue
until the end of file.
N.B.: You can also use 1xN as a pattern, indicating to
skip N bytes without any swapping.
N.B.: A default pattern can be stored in the Unix
environment variable AFNI_24SWAP_PATTERN.
If no -pattern option is given, the default
will be used. If there is no default, then
nothing will be done.
N.B.: If there are bytes 'left over' at the end of the file,
they are written out unswapped. This will happen
if the file is an odd number of bytes long.
N.B.: If you just want to swap pairs, see program 2swap.
For quadruples only, see program 4swap.
N.B.: This program will overwrite the input file!
You might want to test it first.
Example: 24swap -pat 4x8:2x0 fred
If fred contains 'abcdabcdabcdabcdabcd' on input,
then fred has 'dcbadcbabadcbadcbadc' on output.
This page auto-generated on Thu Aug 25 16:49:35 EDT 2005
|
| 2dImReg |
Program: 2dImReg
Initial Release: 04 Feb 1998
Latest Revision: 02 Dec 2002
This program performs 2d image registration. Image alignment is
performed on a slice-by-slice basis for the input 3d+time dataset,
relative to a user specified base image.
Usage:
2dImReg
-input fname Filename of input 3d+time dataset to process
-basefile fname Filename of 3d+time dataset for base image
(default = current input dataset)
-base num Time index for base image (0 <= num)
(default: num = 3)
-nofine Deactivate fine fit phase of image registration
(default: fine fit is active)
-fine blur dxy dphi Set fine fit parameters
where:
blur = FWHM of blurring prior to registration (in pixels)
(default: blur = 1.0)
dxy = Convergence tolerance for translations (in pixels)
(default: dxy = 0.07)
dphi = Convergence tolerance for rotations (in degrees)
(default: dphi = 0.21)
-prefix pname Prefix name for output 3d+time dataset
-dprefix dname Write files 'dname'.dx, 'dname'.dy, 'dname'.psi
containing the registration parameters for each
slice in chronological order.
File formats:
'dname'.dx: time(sec) dx(pixels)
'dname'.dy: time(sec) dy(pixels)
'dname'.psi: time(sec) psi(degrees)
-dmm Change dx and dy output format from pixels to mm
-rprefix rname Write files 'rname'.oldrms and 'rname'.newrms
containing the volume RMS error for the original
and the registered datasets, respectively.
File formats:
'rname'.oldrms: volume(number) rms_error
'rname'.newrms: volume(number) rms_error
-debug Lots of additional output to screen
This page auto-generated on Thu Aug 25 16:49:35 EDT 2005
|
| 2swap |
Usage: 2swap [-q] file ... -- Swaps byte pairs on the files listed. The -q option means to work quietly.This page auto-generated on Thu Aug 25 16:49:35 EDT 2005 |
| 3dAFNIto3D |
Usage: 3dAFNIto3D [options] dataset
Reads in an AFNI dataset, and writes it out as a 3D file.
OPTIONS:
-prefix ppp = Write result into file ppp.3D;
default prefix is same as AFNI dataset's.
-bin = Write data in binary format, not text.
-txt = Write data in text format, not binary.
NOTES:
* At present, all bricks are written out in float format.
This page auto-generated on Thu Aug 25 16:49:35 EDT 2005
|
| 3dAFNItoANALYZE |
Usage: 3dAFNItoANALYZE [-4D] [-orient code] aname dset
Writes AFNI dataset 'dset' to 1 or more ANALYZE 7.5 format
.hdr/.img file pairs (one pair for each sub-brick in the
AFNI dataset). The ANALYZE files will be named
aname_0000.hdr aname_0000.img for sub-brick #0
aname_0001.hdr aname_0001.img for sub-brick #1
and so forth. Each file pair will contain a single 3D array.
* If the AFNI dataset does not include sub-brick scale
factors, then the ANALYZE files will be written in the
datum type of the AFNI dataset.
* If the AFNI dataset does have sub-brick scale factors,
then each sub-brick will be scaled to floating format
and the ANALYZE files will be written as floats.
* The .hdr and .img files are written in the native byte
order of the computer on which this program is executed.
Options
-------
-4D [30 Sep 2002]:
If you use this option, then all the data will be written to
one big ANALYZE file pair named aname.hdr/aname.img, rather
than a series of 3D files. Even if you only have 1 sub-brick,
you may prefer this option, since the filenames won't have
the '_0000' appended to 'aname'.
-orient code [19 Mar 2003]:
This option lets you flip the dataset to a different orientation
when it is written to the ANALYZE files. The orientation code is
formed as follows:
The code must be 3 letters, one each from the
pairs {R,L} {A,P} {I,S}. The first letter gives
the orientation of the x-axis, the second the
orientation of the y-axis, the third the z-axis:
R = Right-to-Left L = Left-to-Right
A = Anterior-to-Posterior P = Posterior-to-Anterior
I = Inferior-to-Superior S = Superior-to-Inferior
For example, 'LPI' means
-x = Left +x = Right
-y = Posterior +y = Anterior
-z = Inferior +z = Superior
* For display in SPM, 'LPI' or 'RPI' seem to work OK.
Be careful with this: you don't want to confuse L and R
in the SPM display!
* If you DON'T use this option, the dataset will be written
out in the orientation in which it is stored in AFNI
(e.g., the output of '3dinfo dset' will tell you this.)
* The dataset orientation is NOT stored in the .hdr file.
* AFNI and ANALYZE data are stored in files with the x-axis
varying most rapidly and the z-axis most slowly.
* Note that if you read an ANALYZE dataset into AFNI for
display, AFNI assumes the LPI orientation, unless you
set environment variable AFNI_ANALYZE_ORIENT.
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|
| 3dAFNItoMINC |
Usage: 3dAFNItoMINC [options] dataset
Reads in an AFNI dataset, and writes it out as a MINC file.
OPTIONS:
-prefix ppp = Write result into file ppp.mnc;
default prefix is same as AFNI dataset's.
-floatize = Write MINC file in float format.
NOTES:
* Multi-brick datasets are written as 4D (x,y,z,t) MINC
files.
* If the dataset has complex-valued sub-bricks, then this
program won't write the MINC file.
* If any of the sub-bricks have floating point scale
factors attached, then the output will be in float
format (regardless of the presence of -floatize).
* This program uses the MNI program 'rawtominc' to create
the MINC file; rawtominc must be in your path. If you
don't have rawtominc, you must install the MINC tools
software package from MNI. (But if you don't have the
MINC tools already, why do you want to convert to MINC
format anyway?)
* At this time, you can find the MINC tools at
ftp://ftp.bic.mni.mcgill.ca/pub/minc/
You need the latest version of minc-*.tar.gz and also
of netcdf-*.tar.gz.
-- RWCox - April 2002
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|
| 3dAFNItoNIFTI |
++ Program 3dAFNItoNIFTI: AFNI version=AFNI_2005_08_24_1751
Usage: 3dAFNItoNIFTI [options] dataset
Reads an AFNI dataset, writes it out as a NIfTI-1.1 (.nii) file.
NOTES:
* The nifti_tool program can be used to manipulate
the contents of a NIfTI-1.1 file.
* The input dataset can actually be in any input format
that AFNI can read directly (e.g., MINC-1).
* There is no 3dNIFTItoAFNI program, since AFNI programs
can directly read .nii files. If you wish to make such
a conversion anyway, one way to do so is like so:
3dcalc -a ppp.nii -prefix ppp -expr 'a'
OPTIONS:
-prefix ppp = Write the NIfTI-1.1 file as 'ppp.nii'.
Default: the dataset's prefix is used.
If you want a compressed file, try
using a prefix like 'ppp.nii.gz'.
-verb = Be verbose = print progress messages.
Repeating this increases the verbosity
(maximum setting is 3 '-verb' options).
-float = Force the output dataset to be 32-bit
floats. This option should be used when
the input AFNI dataset has different
float scale factors for different sub-bricks,
an option that NIfTI-1.1 does not support.
The following options affect the contents of the AFNI extension
field that is written by default into the NIfTI-1.1 header:
-pure = Do NOT write an AFNI extension field into
the output file. Only use this option if
needed. You can also use the 'nifti_tool'
program to strip extensions from a file.
-denote = When writing the AFNI extension field, remove
text notes that might contain subject
identifying information.
-oldid = Give the new dataset the input dataset's
AFNI ID code.
-newid = Give the new dataset a new AFNI ID code, to
distinguish it from the input dataset.
**** N.B.: -newid is now the default action.
This page auto-generated on Thu Aug 25 16:49:35 EDT 2005
|
| 3dAFNItoNIML |
Usage: 3dAFNItoNIML [options] dset
Dumps AFNI dataset header information to stdout in NIML format.
Mostly for debugging and testing purposes!
OPTIONS:
-data == Also put the data into the output (will be huge).
-tcp:host:port == Instead of stdout, send the dataset to a socket.
(implies '-data' as well)
-- RWCox - Mar 2005
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|
| 3dAFNItoRaw |
Usage: 3dAFNItoRaw [options] dataset
Convert an AFNI brik file with multiple sub-briks to a raw file with
each sub-brik voxel concatenated voxel-wise.
For example, a dataset with 3 sub-briks X,Y,Z with elements x1,x2,x3,...,xn,
y1,y2,y3,...,yn and z1,z2,z3,...,zn will be converted to a raw dataset with
elements x1,y1,z1, x2,y2,z2, x3,y3,z3, ..., xn,yn,zn
The dataset is kept in the original data format (float/short/int)
Options:
-output / -prefix = name of the output file (not an AFNI dataset prefix)
the default output name will be rawxyz.dat
-datum float = force floating point output. Floating point forced if any
sub-brik scale factors not equal to 1.
INPUT DATASET NAMES
-------------------
This program accepts datasets that are modified on input according to the
following schemes:
'r1+orig[3..5]' {sub-brick selector}
'r1+orig<100.200>' {sub-range selector}
'r1+orig[3..5]<100..200>' {both selectors}
'3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )' {calculation}
For the gruesome details, see the output of 'afni -help'.
This page auto-generated on Thu Aug 25 16:49:36 EDT 2005
|
| 3dANALYZEtoAFNI |
** DON'T USE THIS PROGRAM! REALLY!
USE 3dcopy OR to3d INSTEAD.
IF YOU CHOOSE TO USE IT ANYWAY, PERHAPS
BECAUSE IT WORKS BETTER ON YOUR 12th
CENTURY PLANTAGENET ANALYZE FILES,
ADD THE OPTION -OK TO YOUR COMMAND
LINE.
Usage: 3dANALYZEtoAFNI [options] file1.hdr file2.hdr ...
This program constructs a 'volumes' stored AFNI dataset
from the ANALYZE-75 files file1.img file2.img ....
In this type of dataset, there is only a .HEAD file; the
.BRIK file is replaced by the collection of .img files.
- Other AFNI programs can read (but not write) this type
of dataset.
- The advantage of using this type of dataset vs. one created
with to3d is that you don't have to duplicate the image data
into a .BRIK file, thus saving disk space.
- The disadvantage of using 'volumes' for a multi-brick dataset
is that all the .img files must be kept with the .HEAD file
if you move the dataset around.
- The .img files must be in the same directory as the .HEAD file.
- Note that you put the .hdr files on the command line, but it is
the .img files that will be named in the .HEAD file.
- After this program is run, you must keep the .img files with
the output .HEAD file. AFNI doesn't need the .hdr files, but
other programs (e.g., FSL, SPM) will want them as well.
Options:
-prefix ppp = Save the dataset with the prefix name 'ppp'.
[default='a2a']
-view vvv = Save the dataset in the 'vvv' view, where
'vvv' is one of 'orig', 'acpc', or 'tlrc'.
[default='orig']
-TR ttt = For multi-volume datasets, create it as a
3D+time dataset with TR set to 'ttt'.
-fbuc = For multi-volume datasets, create it as a
functional bucket dataset.
-abuc = For multi-volume datasets, create it as an
anatomical bucket dataset.
** If more than one ANALYZE file is input, and none of the
above options is given, the default is as if '-TR 1s'
was used.
** For single volume datasets (1 ANALYZE file input), the
default is '-abuc'.
-geomparent g = Use the .HEAD file from dataset 'g' to set
the geometry of this dataset.
** If you don't use -geomparent, then the following options
can be used to specify the geometry of this dataset:
-orient code = Tells the orientation of the 3D volumes. The code
must be 3 letters, one each from the pairs {R,L}
{A,P} {I,S}. The first letter gives the orientation
of the x-axis, the second the orientation of the
y-axis, the third the z-axis:
R = right-to-left L = left-to-right
A = anterior-to-posterior P = posterior-to-anterior
I = inferior-to-superior S = superior-to-inferior
-zorigin dz = Puts the center of the 1st slice off at the
given distance ('dz' in mm). This distance
is in the direction given by the corresponding
letter in the -orient code. For example,
-orient RAI -zorigin 30
would set the center of the first slice at
30 mm Inferior.
** If the above options are NOT used to specify the geometry
of the dataset, then the default is '-orient RAI', and the
z origin is set to center the slices about z=0.
It is likely that you will want to patch up the .HEAD file using
program 3drefit.
-- RWCox - June 2002.
** DON'T USE THIS PROGRAM! REALLY!
USE 3dcopy OR to3d INSTEAD.
IF YOU CHOOSE TO USE IT ANYWAY, PERHAPS
BECAUSE IT WORKS BETTER ON YOUR 12th
CENTURY PLANTAGENET ANALYZE FILES,
ADD THE OPTION -OK TO YOUR COMMAND
LINE.-- KRH - April 2005.
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|
| 3dAnatNudge |
Usage: 3dAnatNudge [options]
Moves the anat dataset around to best overlap the epi dataset.
OPTIONS:
-anat aaa = aaa is an 'scalped' (3dIntracranial) high-resolution
anatomical dataset [a mandatory option]
-epi eee = eee is an EPI dataset [a mandatory option]
The first [0] sub-brick from each dataset is used,
unless otherwise specified on the command line.
-prefix ppp = ppp is the prefix of the output dataset;
this dataset will differ from the input only
in its name and its xyz-axes origin
[default=don't write new dataset]
-step sss = set the step size to be sss times the voxel size
in the anat dataset [default=1.0]
-x nx = search plus and minus nx steps along the EPI
-y ny dataset's x-axis; similarly for ny and the
-z nz y-axis, and for nz and the z-axis
[default: nx=1 ny=5 nz=0]
-verb = print progress reports (this is a slow program)
NOTES
*Systematically moves the anat dataset around and find the shift
that maximizes overlap between the anat dataset and the EPI
dataset. No rotations are done.
*Note that if you use -prefix, a new dataset will be created that
is a copy of the anat, except that it's origin will be shifted
and it will have a different ID code than the anat. If you want
to use this new dataset as the anatomy parent for the EPI
datasets, you'll have to use
3drefit -apar ppp+orig eee1+orig eee2+orig ...
*If no new dataset is written (no -prefix option), then you
can use the 3drefit command emitted at the end to modify
the origin of the anat dataset. (Assuming you trust the
results - visual inspection is recommended!)
*The reason the default search grid is mostly along the EPI y-axis
is that axis is usually the phase-encoding direction, which is
most subject to displacement due to off-resonance effects.
*Note that the time this program takes will be proportional to
(2*nx+1)*(2*ny+1)*(2*nz+1), so using a very large search grid
will result in a very large usage of CPU time.
*Recommended usage:
+ Make a 1-brick function volume from a typical EPI dataset:
3dbucket -fbuc -prefix epi_fb epi+orig
+ Use 3dIntracranial to scalp a T1-weighted volume:
3dIntracranial -anat spgr+orig -prefix spgr_st
+ Use 3dAnatNudge to produce a shifted anat dataset
3dAnatNudge -anat spgr_st+orig -epi epi_fb+orig -prefix spgr_nudge
+ Start AFNI and look at epi_fb overlaid in color on the
anat datasets spgr_st+orig and spgr_nudge+orig, to see if the
nudged dataset seems like a better fit.
+ Delete the nudged dataset spgr_nudge.
+ If the nudged dataset DOES look better, then apply the
3drefit command output by 3dAnatNudge to spgr+orig.
*Note that the x-, y-, and z-axes for the epi and anat datasets
may point in different directions (e.g., axial SPGR and
coronal EPI). The 3drefit command applies to the anat
dataset, NOT to the EPI dataset.
*If the program runs successfully, the only thing set to stdout
will be the 3drefit command string; all other messages go to
stderr. This can be useful if you want to capture the command
to a shell variable and then execute it, as in the following
csh fragment:
set cvar = `3dAnatNudge ...`
if( $cvar[1] == "3drefit" ) $cvar
The test on the first sub-string in cvar allows for the
possibility that the program fails, or that the optimal
nudge is zero.
This page auto-generated on Thu Aug 25 16:49:36 EDT 2005
|
| 3dAnhist |
Usage: 3dAnhist [options] dataset
Input dataset is a T1-weighted high-res of the brain (shorts only).
Output is a list of peaks in the histogram, to stdout, in the form
( datasetname #peaks peak1 peak2 ... )
In the C-shell, for example, you could do
set anhist = `3dAnhist -q -w1 dset+orig`
Then the number of peaks found is in the shell variable $anhist[2].
Options:
-q = be quiet (don't print progress reports)
-h = dump histogram data to Anhist.1D and plot to Anhist.ps
-F = DON'T fit histogram with stupid curves.
-w = apply a Winsorizing filter prior to histogram scan
(or -w7 to Winsorize 7 times, etc.)
-2 = Analyze top 2 peaks only, for overlap etc.
-label xxx = Use 'xxx' for a label on the Anhist.ps plot file
instead of the input dataset filename.
-fname fff = Use 'fff' for the filename instead of 'Anhist'.
If the '-2' option is used, AND if 2 peaks are detected, AND if
the -h option is also given, then stdout will be of the form
( datasetname 2 peak1 peak2 thresh CER CJV count1 count2 count1/count2)
where 2 = number of peaks
thresh = threshold between peak1 and peak2 for decision-making
CER = classification error rate of thresh
CJV = coefficient of joint variation
count1 = area under fitted PDF for peak1
count2 = area under fitted PDF for peak2
count1/count2 = ratio of the above quantities
NOTA BENE
---------
* If the input is a T1-weighted MRI dataset (the usual case), then
peak 1 should be the gray matter (GM) peak and peak 2 the white
matter (WM) peak.
* For the definitions of CER and CJV, see the paper
Method for Bias Field Correction of Brain T1-Weighted Magnetic
Resonance Images Minimizing Segmentation Error
JD Gispert, S Reig, J Pascau, JJ Vaquero, P Garcia-Barreno,
and M Desco, Human Brain Mapping 22:133-144 (2004).
* Roughly speaking, CER is the ratio of the overlapping area of the
2 peak fitted PDFs to the total area of the fitted PDFS. CJV is
(sigma_GM+sigma_WM)/(mean_WM-mean_GM), and is a different, ad hoc,
measurement of how much the two PDF overlap.
* The fitted PDFs are NOT Gaussians. They are of the form
f(x) = b((x-p)/w,a), where p=location of peak, w=width, 'a' is
a skewness parameter between -1 and 1; the basic distribution
is defined by b(x)=(1-x^2)^2*(1+a*x*abs(x)) for -1 < x < 1.
-- RWCox - November 2004
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|
| 3dANOVA |
++ Program 3dANOVA: AFNI version=AFNI_2005_08_24_1751
This program performs single factor Analysis of Variance (ANOVA)
on 3D datasets
---------------------------------------------------------------
Usage:
-----
3dANOVA
-levels r : r = number of factor levels
-dset 1 filename : data set for factor level 1
. . . . . .
-dset 1 filename data set for factor level 1
. . . . . .
-dset r filename data set for factor level r
. . . . . .
-dset r filename data set for factor level r
[-voxel num] : screen output for voxel # num
[-diskspace] : print out disk space required for
program execution
The following commands generate individual AFNI 2-sub-brick datasets:
(In each case, output is written to the file with the specified
prefix file name.)
[-ftr prefix] : F-statistic for treatment effect
[-mean i prefix] : estimate of factor level i mean
[-diff i j prefix] : difference between factor levels
[-contr c1...cr prefix] : contrast in factor levels
The following command generates one AFNI 'bucket' type dataset:
[-bucket prefix] : create one AFNI 'bucket' dataset whose
sub-bricks are obtained by
concatenating the above output files;
the output 'bucket' is written to file
with prefix file name
N.B.: For this program, the user must specify 1 and only 1 sub-brick
with each -dset command. That is, if an input dataset contains
more than 1 sub-brick, a sub-brick selector must be used,
e.g., -dset 2 'fred+orig[3]'
Example of 3dANOVA:
------------------
Example is based on a study with one factor (independent variable)
called 'Pictures', with 3 levels:
(1) Faces, (2) Houses, and (3) Donuts
The ANOVA is being conducted on subject Fred's data:
3dANOVA -levels 3 \
-dset 1 fred_Faces+tlrc \
-dset 2 fred_Houses+tlrc \
-dset 3 fred_Donuts+tlrc \
-ftr Pictures \
-mean 1 Faces \
-mean 2 Houses \
-mean 3 Donuts \
-diff 1 2 FvsH \
-diff 2 3 HvsD \
-diff 1 3 FvsD \
-contr 1 1 -1 FHvsD \
-contr -1 1 1 FvsHD \
-contr 1 -1 1 FDvsH \
-bucket fred_ANOVA
INPUT DATASET NAMES
-------------------
This program accepts datasets that are modified on input according to the
following schemes:
'r1+orig[3..5]' {sub-brick selector}
'r1+orig<100.200>' {sub-range selector}
'r1+orig[3..5]<100..200>' {both selectors}
'3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )' {calculation}
For the gruesome details, see the output of 'afni -help'.
---------------------------------------------------
Also see HowTo#5 - Group Analysis on the AFNI website:
http://afni.nimh.nih.gov/pub/dist/HOWTO/howto/ht05_group/html/index.shtml
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|
| 3dANOVA2 |
Program: 3dANOVA2
Author: B. Douglas Ward
Initial Release: 09 Dec 1996
Latest Revision: 02 Aug 2005
This program performs two-factor ANOVA on 3D data sets
Usage:
3dANOVA2
-type k type of ANOVA model to be used:
k=1 fixed effects model (A and B fixed)
k=2 random effects model (A and B random)
k=3 mixed effects model (A fixed, B random)
-alevels a a = number of levels of factor A
-blevels b b = number of levels of factor B
-dset 1 1 filename data set for level 1 of factor A
and level 1 of factor B
. . . . . .
-dset i j filename data set for level i of factor A
and level j of factor B
. . . . . .
-dset a b filename data set for level a of factor A
and level b of factor B
[-voxel num] screen output for voxel # num
[-diskspace] print out disk space required for
program execution
The following commands generate individual AFNI 2 sub-brick datasets:
(In each case, output is written to the file with the specified
prefix file name.)
[-ftr prefix] F-statistic for treatment effect
[-fa prefix] F-statistic for factor A effect
[-fb prefix] F-statistic for factor B effect
[-fab prefix] F-statistic for interaction
[-amean i prefix] estimate mean of factor A level i
[-bmean j prefix] estimate mean of factor B level j
[-xmean i j prefix] estimate mean of cell at level i of
factor A, level j of factor B
[-adiff i j prefix] difference between levels i and j of
factor A
[-bdiff i j prefix] difference between levels i and j of
factor B
[-xdiff i j k l prefix] difference between cell mean at A=i,B=j
and cell mean at A=k,B=l
[-acontr c1 ... ca prefix] contrast in factor A levels
[-bcontr c1 ... cb prefix] contrast in factor B levels
[-xcontr c11 ... c1b c21 ... c2b ... ca1 ... cab prefix]
contrast in cell means
The following command generates one AFNI 'bucket' type dataset:
[-bucket prefix] create one AFNI 'bucket' dataset whose
sub-bricks are obtained by concatenating
the above output files; the output 'bucket'
is written to file with prefix file name
N.B.: For this program, the user must specify 1 and only 1 sub-brick
with each -dset command. That is, if an input dataset contains
more than 1 sub-brick, a sub-brick selector must be used, e.g.:
-dset 2 4 'fred+orig[3]'
INPUT DATASET NAMES
-------------------
This program accepts datasets that are modified on input according to the
following schemes:
'r1+orig[3..5]' {sub-brick selector}
'r1+orig<100.200>' {sub-range selector}
'r1+orig[3..5]<100..200>' {both selectors}
'3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )' {calculation}
For the gruesome details, see the output of 'afni -help'.
This page auto-generated on Thu Aug 25 16:49:36 EDT 2005
|
| 3dANOVA3 |
Program: 3dANOVA3
Author: B. Douglas Ward
Initial Release: 29 Jan 1997
Latest Revision: 19 Jul 2004
This program performs three-factor ANOVA on 3D data sets.
Usage:
3dANOVA3
-type k type of ANOVA model to be used:
k = 1 A,B,C fixed; AxBxC
k = 2 A,B,C random; AxBxC
k = 3 A fixed; B,C random; AxBxC
k = 4 A,B fixed; C random; AxBxC
k = 5 A,B fixed; C random; AxB,BxC,C(A)
-alevels a a = number of levels of factor A
-blevels b b = number of levels of factor B
-clevels c c = number of levels of factor C
-dset 1 1 1 filename data set for level 1 of factor A
and level 1 of factor B
and level 1 of factor C
. . . . . .
-dset i j k filename data set for level i of factor A
and level j of factor B
and level k of factor C
. . . . . .
-dset a b c filename data set for level a of factor A
and level b of factor B
and level c of factor C
[-voxel num] screen output for voxel # num
[-diskspace] print out disk space required for
program execution
The following commands generate individual AFNI 2 sub-brick datasets:
(In each case, output is written to the file with the specified
prefix file name.)
[-fa prefix] F-statistic for factor A effect
[-fb prefix] F-statistic for factor B effect
[-fc prefix] F-statistic for factor C effect
[-fab prefix] F-statistic for A*B interaction
[-fac prefix] F-statistic for A*C interaction
[-fbc prefix] F-statistic for B*C interaction
[-fabc prefix] F-statistic for A*B*C interaction
[-amean i prefix] estimate of factor A level i mean
[-bmean i prefix] estimate of factor B level i mean
[-cmean i prefix] estimate of factor C level i mean
[-xmean i j k prefix] estimate mean of cell at factor A level i,
factor B level j, factor C level k
[-adiff i j prefix] difference between factor A levels i and j
[-bdiff i j prefix] difference between factor B levels i and j
[-cdiff i j prefix] difference between factor C levels i and j
[-xdiff i j k l m n prefix] difference between cell mean at A=i,B=j,
C=k, and cell mean at A=l,B=m,C=n
[-acontr c1...ca prefix] contrast in factor A levels
[-bcontr c1...cb prefix] contrast in factor B levels
[-ccontr c1...cc prefix] contrast in factor C levels
The following command generates one AFNI 'bucket' type dataset:
[-bucket prefix] create one AFNI 'bucket' dataset whose
sub-bricks are obtained by concatenating
the above output files; the output 'bucket'
is written to file with prefix file name
N.B.: For this program, the user must specify 1 and only 1 sub-brick
with each -dset command. That is, if an input dataset contains
more than 1 sub-brick, a sub-brick selector must be used, e.g.:
-dset 2 4 5 'fred+orig[3]'
INPUT DATASET NAMES
-------------------
This program accepts datasets that are modified on input according to the
following schemes:
'r1+orig[3..5]' {sub-brick selector}
'r1+orig<100.200>' {sub-range selector}
'r1+orig[3..5]<100..200>' {both selectors}
'3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )' {calculation}
For the gruesome details, see the output of 'afni -help'.
This page auto-generated on Thu Aug 25 16:49:36 EDT 2005
|
| 3dAttribute |
Usage: 3dAttribute [options] aname dset
Prints (to stdout) the value of the attribute 'aname' from
the header of dataset 'dset'. If the attribute doesn't exist,
prints nothing and sets the exit status to 1.
Options:
-name = Include attribute name in printout
-all = Print all attributes [don't put aname on command line]
Also implies '-name'. Attributes print in whatever order
they are in the .HEAD file, one per line. You may want
to do '3dAttribute -all elvis+orig | sort' to get them
in alphabetical order.
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|
| 3dAutobox |
Usage: 3dAutobox dataset Computes size of a box that fits around the volume.This page auto-generated on Thu Aug 25 16:49:36 EDT 2005 |
| 3dAutomask |
Usage: 3dAutomask [options] dataset
Input dataset is EPI 3D+time.
Output dataset is a brain-only mask dataset.
Method:
+ Uses 3dClipLevel algorithm to find clipping level.
+ Keeps only the largest connected component of the
supra-threshold voxels, after an erosion/dilation step.
+ Writes result as a 'fim' type of functional dataset.
Options:
-prefix ppp = Write mask into dataset with prefix 'ppp'.
[default='automask']
-q = Don't write progress messages (i.e., be quiet).
-eclip = After creating the mask, remove exterior
voxels below the clip threshold.
-dilate nd = Dilate the mask outwards 'nd' times.
-SI hh = After creating the mask, find the most superior
voxel, then zero out everything more than 'hh'
millimeters inferior to that. hh=130 seems to
be decent (for human brains).
This page auto-generated on Thu Aug 25 16:49:36 EDT 2005
|
| 3dAutoTcorrelate |
Usage: 3dAutoTcorrelate [options] dset
Computes the correlation coefficient between each pair of
voxels in the input dataset, and stores the output into
a new anatomical bucket dataset.
Options:
-pearson = Correlation is the normal Pearson (product moment)
correlation coefficient [default].
-spearman = Correlation is the Spearman (rank) correlation
coefficient.
-quadrant = Correlation is the quadrant correlation coefficient.
-polort m = Remove polynomical trend of order 'm', for m=-1..3.
[default is m=1; removal is by least squares].
Using m=-1 means no detrending; this is only useful
for data/information that has been pre-processed.
-autoclip = Clip off low-intensity regions in the dataset,
-automask = so that the correlation is only computed between
high-intensity (presumably brain) voxels. The
intensity level is determined the same way that
3dClipLevel works.
-prefix p = Save output into dataset with prefix 'p'
[default prefix is 'ATcorr'].
-time = Save output as a 3D+time dataset instead
of a anat bucket.
Notes:
* The output dataset is anatomical bucket type of shorts.
* The output file might be gigantic and you might run out
of memory running this program. Use at your own risk!
* The program prints out an estimate of its memory usage
when it starts. It also prints out a progress 'meter'
of 1 dot per 10 output sub-bricks.
* This is a quick hack for Peter Bandettini. Now pay up.
-- RWCox - Jan 31 2002
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|
| 3daxialize |
Usage: 3daxialize [options] dataset
Purpose: Read in a dataset and write it out as a new dataset
with the data brick oriented as axial slices.
The input dataset must have a .BRIK file.
One application is to create a dataset that can
be used with the AFNI volume rendering plugin.
Options:
-prefix ppp = Use 'ppp' as the prefix for the new dataset.
[default = 'axialize']
-verb = Print out a progress report.
The following options determine the order/orientation
in which the slices will be written to the dataset:
-sagittal = Do sagittal slice order [-orient ASL]
-coronal = Do coronal slice order [-orient RSA]
-axial = Do axial slice order [-orient RAI]
This is the default AFNI axial order, and
is the one currently required by the
volume rendering plugin; this is also
the default orientation output by this
program (hence the program's name).
-orient code = Orientation code for output.
The code must be 3 letters, one each from the
pairs {R,L} {A,P} {I,S}. The first letter gives
the orientation of the x-axis, the second the
orientation of the y-axis, the third the z-axis:
R = Right-to-left L = Left-to-right
A = Anterior-to-posterior P = Posterior-to-anterior
I = Inferior-to-superior S = Superior-to-inferior
If you give an illegal code (e.g., 'LPR'), then
the program will print a message and stop.
N.B.: 'Neurological order' is -orient LPI
INPUT DATASET NAMES
-------------------
This program accepts datasets that are modified on input according to the
following schemes:
'r1+orig[3..5]' {sub-brick selector}
'r1+orig<100.200>' {sub-range selector}
'r1+orig[3..5]<100..200>' {both selectors}
'3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )' {calculation}
For the gruesome details, see the output of 'afni -help'.
This page auto-generated on Thu Aug 25 16:49:36 EDT 2005
|
| 3dBRAIN_VOYAGERtoAFNI |
Usage: 3dBRAIN_VOYAGERtoAFNI -input BV_VOLUME.vmr
Converts a BrainVoyager vmr dataset to AFNI's BRIK format
The conversion is based on information from BrainVoyager's
website: www.brainvoyager.com. Sample data and information
provided by Adam Greenberg and Nikolaus Kriegeskorte.
Common Debugging Options:
[-trace]: Turns on In/Out debug and Memory tracing.
For speeding up the tracing log, I recommend
you redirect stdout to a file when using this option.
For example, if you were running suma you would use:
suma -spec lh.spec -sv ... > TraceFile
This option replaces the old -iodbg and -memdbg.
[-TRACE]: Turns on extreme tracing.
[-nomall]: Turn off memory tracing.
[-yesmall]: Turn on memory tracing (default).
[-novolreg]: Ignore any Volreg or Tagalign transformations
present in the Surface Volume.
NOTE: For programs that output results to stdout
(that is to your shell/screen), the debugging info
might get mixed up with your results.
++ SUMA version 2004_12_29
CVS tag:
SUMA_2005_04_29_1733
Compile Date:
Aug 25 2005
Ziad S. Saad SSCC/NIMH/NIH ziad@nih.gov
This page auto-generated on Thu Aug 25 16:49:36 EDT 2005
|
| 3dbuc2fim |
Program: 3dbuc2fim
Author: B. D. Ward
Initial Release: 18 March 1998
Latest Revision: 15 August 2001
This program converts bucket sub-bricks to fim (fico, fitt, fift, ...)
type dataset.
Usage:
3dbuc2fim -prefix pname d1+orig[index]
This produces a fim dataset.
-or-
3dbuc2fim -prefix pname d1+orig[index1] d2+orig[index2]
This produces a fico (fitt, fift, ...) dataset,
depending on the statistic type of the 2nd subbrick,
with d1+orig[index1] -> intensity sub-brick of pname
d2+orig[index2] -> threshold sub-brick of pname
-or-
3dbuc2fim -prefix pname d1+orig[index1,index2]
This produces a fico (fitt, fift, ...) dataset,
depending on the statistic type of the 2nd subbrick,
with d1+orig[index1] -> intensity sub-brick of pname
d1+orig[index2] -> threshold sub-brick of pname
where the options are:
-prefix pname = Use 'pname' for the output dataset prefix name.
OR -output pname [default='buc2fim']
-session dir = Use 'dir' for the output dataset session directory.
[default='./'=current working directory]
-verb = Print out some verbose output as the program
proceeds
Command line arguments after the above are taken as input datasets.
A dataset is specified using one of these forms:
'prefix+view', 'prefix+view.HEAD', or 'prefix+view.BRIK'.
Sub-brick indexes start at 0.
N.B.: The sub-bricks are output in the order specified, which may
not be the order in the original datasets. For example, using
fred+orig[5,3]
will cause the sub-brick #5 in fred+orig to be output as the intensity
sub-brick, and sub-brick #3 to be output as the threshold sub-brick
in the new dataset.
N.B.: The '$', '(', ')', '[', and ']' characters are special to
the shell, so you will have to escape them. This is most easily
done by putting the entire dataset plus selection list inside
single quotes, as in 'fred+orig[5,9]'.
This page auto-generated on Thu Aug 25 16:49:36 EDT 2005
|
| 3dbucket |
Concatenate sub-bricks from input datasets into one big
'bucket' dataset.
Usage: 3dbucket options
where the options are:
-prefix pname = Use 'pname' for the output dataset prefix name.
OR -output pname [default='buck']
-session dir = Use 'dir' for the output dataset session directory.
[default='./'=current working directory]
-glueto fname = Append bricks to the end of the 'fname' dataset.
This command is an alternative to the -prefix
and -session commands.
-dry = Execute a 'dry run'; that is, only print out
what would be done. This is useful when
combining sub-bricks from multiple inputs.
-verb = Print out some verbose output as the program
proceeds (-dry implies -verb).
-fbuc = Create a functional bucket.
-abuc = Create an anatomical bucket. If neither of
these options is given, the output type is
determined from the first input type.
Command line arguments after the above are taken as input datasets.
A dataset is specified using one of these forms:
'prefix+view', 'prefix+view.HEAD', or 'prefix+view.BRIK'.
You can also add a sub-brick selection list after the end of the
dataset name. This allows only a subset of the sub-bricks to be
included into the output (by default, all of the input dataset
is copied into the output). A sub-brick selection list looks like
one of the following forms:
fred+orig[5] ==> use only sub-brick #5
fred+orig[5,9,17] ==> use #5, #9, and #12
fred+orig[5..8] or [5-8] ==> use #5, #6, #7, and #8
fred+orig[5..13(2)] or [5-13(2)] ==> use #5, #7, #9, #11, and #13
Sub-brick indexes start at 0. You can use the character '$'
to indicate the last sub-brick in a dataset; for example, you
can select every third sub-brick by using the selection list
fred+orig[0..$(3)]
N.B.: The sub-bricks are output in the order specified, which may
not be the order in the original datasets. For example, using
fred+orig[0..$(2),1..$(2)]
will cause the sub-bricks in fred+orig to be output into the
new dataset in an interleaved fashion. Using
fred+orig[$..0]
will reverse the order of the sub-bricks in the output.
N.B.: Bucket datasets have multiple sub-bricks, but do NOT have
a time dimension. You can input sub-bricks from a 3D+time dataset
into a bucket dataset. You can use the '3dinfo' program to see
how many sub-bricks a 3D+time or a bucket dataset contains.
N.B.: The '$', '(', ')', '[', and ']' characters are special to
the shell, so you will have to escape them. This is most easily
done by putting the entire dataset plus selection list inside
single quotes, as in 'fred+orig[5..7,9]'.
N.B.: In non-bucket functional datasets (like the 'fico' datasets
output by FIM, or the 'fitt' datasets output by 3dttest), sub-brick
[0] is the 'intensity' and sub-brick [1] is the statistical parameter
used as a threshold. Thus, to create a bucket dataset using the
intensity from dataset A and the threshold from dataset B, and
calling the output dataset C, you would type
3dbucket -prefix C -fbuc 'A+orig[0]' -fbuc 'B+orig[1]'
WARNING: using this program, it is possible to create a dataset that
has different basic datum types for different sub-bricks
(e.g., shorts for brick 0, floats for brick 1).
Do NOT do this! Very few AFNI programs will work correctly
with such datasets!
This page auto-generated on Thu Aug 25 16:49:36 EDT 2005
|
| 3dcalc |
Program: 3dcalc
Author: RW Cox et al
3dcalc - AFNI's calculator program
This program does voxel-by-voxel arithmetic on 3D datasets
(limited to inter-voxel computation).
The program assumes that the voxel-by-voxel computations are being
performed on datasets that occupy the same space and have the same
orientations.
------------------------------------------------------------------------
Usage:
-----
3dcalc -a dsetA [-b dsetB...] \
-expr EXPRESSION \
[options]
Examples:
--------
1. Average datasets together, on a voxel-by-voxel basis:
3dcalc -a fred+tlrc -b ethel+tlrc -c lucy+tlrc \
-expr '(a+b+c)/3' -prefix subjects_mean
2. Perform arithmetic calculations between the sub-bricks of a single
dataset by noting the sub-brick number on the command line:
3dcalc -a 'func+orig[2]' -b 'func+orig[4]' -expr 'sqrt(a*b)'
3. Create a simple mask that consists only of values in sub-brick #0
that are greater than 3.14159:
3dcalc -a 'func+orig[0]' -expr 'ispositive(a-3.14159)' \
-prefix mask
4. Normalize subjects' time series datasets to percent change values in
preparation for group analysis:
Voxel-by-voxel, the example below divides each intensity value in
the time series (epi_r1+orig) with the voxel's mean value (mean+orig)
to get a percent change value. The 'ispositive' command will ignore
voxels with mean values less than 167 (i.e., they are labeled as
'zero' in the output file 'percent_change+orig') and are most likely
background/noncortical voxels.
3dcalc -a epi_run1+orig -b mean+orig \
-expr '100 * a/b * ispositive(b-167)' -prefix percent_chng
5. Create a compound mask from a statistical dataset, where 3 stimuli
show activation.
NOTE: 'step' and 'ispositive' are identical expressions that can
be used interchangeably:
3dcalc -a 'func+orig[12]' -b 'func+orig[15]' -c 'func+orig[18]' \
-expr 'step(a-4.2)*step(b-2.9)*step(c-3.1)' \
-prefix compound_mask
6. Same as example #5, but this time create a mask of 8 different values
showing all combinations of activations (i.e., not only where
everything is active, but also each stimulus individually, and all
combinations). The output mask dataset labels voxel values as such:
0 = none active 1 = A only active 2 = B only active
3 = A and B only 4 = C only active 5 = A and C only
6 = B and C only 7 = all A, B, and C active
3dcalc -a 'func+orig[12]' -b 'func+orig[15]' -c 'func+orig[18]' \
-expr 'step(a-4.2)+2*step(b-2.9)+4*step(c-3.1)' \
-prefix mask_8
7. Create a region-of-interest mask comprised of a 3-dimensional sphere.
Values within the ROI sphere will be labeled as '1' while values
outside the mask will be labeled as '0'. Statistical analyses can
then be done on the voxels within the ROI sphere.
The example below puts a solid ball (sphere) of radius 3=sqrt(9)
about the point with coordinates (x,y,z)=(20,30,70):
3dcalc -a anat+tlrc \
-expr 'step((9-(x-20)*(x-20)-(y-30)*(y-30)-(z-70)*(z-70))'\
-prefix ball
8. Some datsets are 'short' (16 bit) integers with a scalar attached,
which allow them to be smaller than float datasets and to contain
fractional values.
Dataset 'a' is always used as a template for the output dataset. For
the examples below, assume that datasets d1+orig and d2+orig consist
of small integers.
a) When dividing 'a' by 'b', the result should be scaled, so that a
value of 2.4 is not truncated to '2'. To avoid this truncation,
force scaling with the -fscale option:
3dcalc -a d1+orig -b d2+orig -expr 'a/b' -prefix quot -fscale
b) If it is preferable that the result is of type 'float', then set
the output data type (datum) to float:
3dcalc -a d1+orig -b d2+orig -expr 'a/b' -prefix quot \
-datum float
c) Perhaps an integral division is desired, so that 9/4=2, not 2.24.
Force the results not to be scaled (opposite of example 8b) using
the -nscale option:
3dcalc -a d1+orig -b d2+orig -expr 'a/b' -prefix quot -nscale
------------------------------------------------------------------------
ARGUMENTS for 3dcalc (must be included on command line):
-------------------- ----
-a dname = Read dataset 'dname' and call the voxel values 'a' in the
expression (-expr) that is input below. Up to 24 dnames
(-a, -b, -c, ... -z) can be included in a single 3dcalc
calculation/expression.
** If some letter name is used in the expression, but
not present in one of the dataset options here, then
that variable is set to 0.
** If the letter is followed by a number, then that
number is used to select the sub-brick of the dataset
which will be used in the calculations.
E.g., '-b3 dname' specifies that the variable 'b'
refers to sub-brick '3' of that dataset
(indexes in AFNI start at 0).
-expr = Apply the expression - within quotes - to the input
datasets (dnames), one voxel at time, to produce the
output dataset.
------------------------------------------------------------------------
OPTIONS for 3dcalc:
-------
-verbose = Makes the program print out various information as it
progresses.
-datum type= Coerce the output data to be stored as the given type,
which may be byte, short, or float.
[default = datum of first input dataset]
-fscale = Force scaling of the output to the maximum integer
range. This only has effect if the output datum is byte
or short (either forced or defaulted). This option is
often necessary to eliminate unpleasant truncation
artifacts.
[The default is to scale only if the computed values
seem to need it -- are all <= 1.0 or there is at
least one value beyond the integer upper limit.]
** In earlier versions of 3dcalc, scaling (if used) was
applied to all sub-bricks equally -- a common scale
factor was used. This would cause trouble if the
values in different sub-bricks were in vastly
different scales. In this version, each sub-brick
gets its own scale factor. To override this behavior,
use the '-gscale' option.
-gscale = Same as '-fscale', but also forces each output sub-brick
to get the same scaling factor. This may be desirable
for 3D+time datasets, for example.
-nscale = Don't do any scaling on output to byte or short datasets.
This may be especially useful when operating on mask
datasets whose output values are only 0's and 1's.
** Another way to achieve the effect of '-b3' is described
below in the dataset 'INPUT' specification section.
-prefix pname = Use 'pname' for the output dataset prefix name.
[default='calc']
-session dir = Use 'dir' for the output dataset session directory.
[default='./'=current working directory]
-dt tstep = Use 'tstep' as the TR for manufactured 3D+time datasets.
-TR tstep = If not given, defaults to 1 second.
-taxis N = If only 3D datasets are input (no 3D+time or .1D files),
*OR* then normally only a 3D dataset is calculated. With
-taxis N:tstep: this option, you can force the creation of a time axis
of length 'N', optionally using time step 'tstep'. In
such a case, you will probably want to use the pre-
defined time variables 't' and/or 'k' in your
expression, or each resulting sub-brick will be
identical. For example:
'-taxis 121:0.1' will produce 121 points in time,
spaced with TR 0.1.
N.B.: You can also specify the TR using the -dt option.
N.B.: You can specify 1D input datasets using the
'1D:n@val,n@val' notation to get a similar effect.
For example:
-dt 0.1 -w '1D:121@0'
will have pretty much the same effect as
-taxis 121:0.1
N.B.: For both '-dt' and '-taxis', the 'tstep' value is in
seconds. You can suffix it with 'ms' to specify that
the value is in milliseconds instead; e.g., '-dt 2000ms'.
-rgbfac A B C = For RGB input datasets, the 3 channels (r,g,b) are
collapsed to one for the purposes of 3dcalc, using the
formula value = A*r + B*g + C*b
The default values are A=0.299 B=0.587 C=0.114, which
gives the grayscale intensity. To pick out the Green
channel only, use '-rgbfac 0 1 0', for example. Note
that each channel in an RGB dataset is a byte in the
range 0..255. Thus, '-rgbfac 0.001173 0.002302 0.000447'
will compute the intensity rescaled to the range 0..1.0
(i.e., 0.001173=0.299/255, etc.)
------------------------------------------------------------------------
DATASET TYPES:
-------------
The most common AFNI dataset types are 'byte', 'short', and 'float'.
A byte value is an 8-bit signed integer (0..255), a short value ia a
16-bit signed integer (-32768..32767), and a float value is a 32-bit
real number. A byte value has almost 3 decimals of accuracy, a short
has almost 5, and a float has approximately 7 (from a 23+1 bit
mantissa).
Datasets can also have a scalar attached to each sub-brick. The main
use of this is allowing a short type dataset to take on non-integral
values, while being half the size of a float dataset.
As an example, consider a short dataset with a scalar of 0.0001. This
could represent values between -32.768 and +32.767, at a resolution of
0.001. One could represnt the difference between 4.916 and 4.917, for
instance, but not 4.9165. Each number has 15 bits of accuracy, plus a
sign bit, which gives 4-5 decimal places of accuracy. If this is not
enough, then it makes sense to use the larger type, float.
------------------------------------------------------------------------
3D+TIME DATASETS:
----------------
This version of 3dcalc can operate on 3D+time datasets. Each input
dataset will be in one of these conditions:
(A) Is a regular 3D (no time) dataset; or
(B) Is a 3D+time dataset with a sub-brick index specified ('-b3'); or
(C) Is a 3D+time dataset with no sub-brick index specified ('-b').
If there is at least one case (C) dataset, then the output dataset will
also be 3D+time; otherwise it will be a 3D dataset with one sub-brick.
When producing a 3D+time dataset, datasets in case (A) or (B) will be
treated as if the particular brick being used has the same value at each
point in time.
Multi-brick 'bucket' datasets may also be used. Note that if multi-brick
(bucket or 3D+time) datasets are used, the lowest letter dataset will
serve as the template for the output; that is, '-b fred+tlrc' takes
precedence over '-c wilma+tlrc'. (The program 3drefit can be used to
alter the .HEAD parameters of the output dataset, if desired.)
------------------------------------------------------------------------
INPUT DATASET NAMES
-------------------
An input dataset is specified using one of these forms:
'prefix+view', 'prefix+view.HEAD', or 'prefix+view.BRIK'.
You can also add a sub-brick selection list after the end of the
dataset name. This allows only a subset of the sub-bricks to be
read in (by default, all of a dataset's sub-bricks are input).
A sub-brick selection list looks like one of the following forms:
fred+orig[5] ==> use only sub-brick #5
fred+orig[5,9,17] ==> use #5, #9, and #12
fred+orig[5..8] or [5-8] ==> use #5, #6, #7, and #8
fred+orig[5..13(2)] or [5-13(2)] ==> use #5, #7, #9, #11, and #13
Sub-brick indexes start at 0. You can use the character '$'
to indicate the last sub-brick in a dataset; for example, you
can select every third sub-brick by using the selection list
fred+orig[0..$(3)]
N.B.: The sub-bricks are read in the order specified, which may
not be the order in the original dataset. For example, using
fred+orig[0..$(2),1..$(2)]
will cause the sub-bricks in fred+orig to be input into memory
in an interleaved fashion. Using
fred+orig[$..0]
will reverse the order of the sub-bricks.
N.B.: You may also use the syntax <A..B> after the name of an input
dataset to restrict the range of values read in to the numerical
values in a..b, inclusive. For example,
fred+orig[5..7]<100..200>
creates a 3 sub-brick dataset with values less than 100 or
greater than 200 from the original set to zero.
If you use the <> sub-range selection without the [] sub-brick
selection, it is the same as if you had put [0..$] in front of
the sub-range selection.
N.B.: Datasets using sub-brick/sub-range selectors are treated as:
- 3D+time if the dataset is 3D+time and more than 1 brick is chosen
- otherwise, as bucket datasets (-abuc or -fbuc)
(in particular, fico, fitt, etc datasets are converted to fbuc!)
N.B.: The characters '$ ( ) [ ] < >' are special to the shell,
so you will have to escape them. This is most easily done by
putting the entire dataset plus selection list inside forward
single quotes, as in 'fred+orig[5..7,9]', or double quotes "x".
** WARNING: you cannot combine sub-brick selection of the form
-b3 bambam+orig (the old method)
with sub-brick selection of the form
-b 'bambam+orig[3]' (the new method)
If you try, the Doom of Mandos will fall upon you!
------------------------------------------------------------------------
1D TIME SERIES:
--------------
You can also input a '*.1D' time series file in place of a dataset.
In this case, the value at each spatial voxel at time index n will be
the same, and will be the n-th value from the time series file.
At least one true dataset must be input. If all the input datasets
are 3D (single sub-brick) or are single sub-bricks from multi-brick
datasets, then the output will be a 'manufactured' 3D+time dataset.
For example, suppose that 'a3D+orig' is a 3D dataset:
3dcalc -a a3D+orig -b b.1D -expr "a*b"
The output dataset will 3D+time with the value at (x,y,z,t) being
computed by a3D(x,y,z)*b(t). The TR for this dataset will be set
to 'tstep' seconds -- this could be altered later with program 3drefit.
Another method to set up the correct timing would be to input an
unused 3D+time dataset -- 3dcalc will then copy that dataset's time
information, but simply do not use that dataset's letter in -expr.
If the *.1D file has multiple columns, only the first read will be
used in this program. You can select a column to be the first by
using a sub-vector selection of the form 'b.1D[3]', which will
choose the 4th column (since counting starts at 0).
'{...}' row selectors can also be used - see the output of '1dcat -help'
for more details on these. Note that if multiple timeseries or 3D+time
or 3D bucket datasets are input, they must all have the same number of
points along the 'time' dimension.
------------------------------------------------------------------------
'1D:' INPUT:
-----------
You can input a 1D time series 'dataset' directly on the command line,
without an external file. The 'filename for such input takes the
general format
'1D:n_1@val_1,n_2@val_2,n_3@val_3,...'
where each 'n_i' is an integer and each 'val_i' is a float. For
example
-a '1D:5@0,10@1,5@0,10@1,5@0'
specifies that variable 'a' be assigned to a 1D time series of 35,
alternating in blocks between values 0 and value 1.
------------------------------------------------------------------------
'I:*.1D' and 'J:*.1D' and 'K:*.1D' INPUT:
----------------------------------------
You can input a 1D time series 'dataset' to be defined as spatially
dependent instead of time dependent using a syntax like:
-c I:fred.1D
This indicates that the n-th value from file fred.1D is to be associated
with the spatial voxel index i=n (respectively j=n and k=n for 'J: and
K: input dataset names). This technique can be useful if you want to
scale each slice by a fixed constant; for example:
-a dset+orig -b K:slicefactor.1D -expr 'a*b'
In this example, the '-b' value only varies in the k-index spatial
direction.
------------------------------------------------------------------------
COORDINATES and PREDEFINED VALUES:
---------------------------------
If you don't use '-x', '-y', or '-z' for a dataset, then the voxel
spatial coordinates will be loaded into those variables. For example,
the expression 'a*step(x*x+y*y+z*z-100)' will zero out all the voxels
inside a 10 mm radius of the origin x=y=z=0.
Similarly, the '-t' value, if not otherwise used by a dataset or *.1D
input, will be loaded with the voxel time coordinate, as determined
from the header file created for the OUTPUT. Please note that the units
of this are variable; they might be in milliseconds, seconds, or Hertz.
In addition, slices of the dataset might be offset in time from one
another, and this is allowed for in the computation of 't'. Use program
3dinfo to find out the structure of your datasets, if you are not sure.
If no input datasets are 3D+time, then the effective value of TR is
tstep in the output dataset, with t=0 at the first sub-brick.
Similarly, the '-i', '-j', and '-k' values, if not otherwise used,
will be loaded with the voxel spatial index coordinates. The '-l'
(letter 'ell') value will be loaded with the temporal index coordinate.
Otherwise undefined letters will be set to zero. In the future,
new default values for other letters may be added.
NOTE WELL: By default, the coordinate order of (x,y,z) is the order in
********* which the data array is stored on disk; this order is output
by 3dinfo. The options below control can change this order:
-dicom }= Sets the coordinates to appear in DICOM standard (RAI) order,
-RAI }= (the AFNI standard), so that -x=Right, -y=Anterior , -z=Inferior,
+x=Left , +y=Posterior, +z=Superior.
-SPM }= Sets the coordinates to appear in SPM (LPI) order,
-LPI }= so that -x=Left , -y=Posterior, -z=Inferior,
+x=Right, +y=Anterior , +z=Superior.
------------------------------------------------------------------------
DIFFERENTIAL SUBSCRIPTS [22 Nov 1999]:
-----------------------
Normal calculations with 3dcalc are strictly on a per-voxel basis:
there is no 'cross-talk' between spatial or temporal locations.
The differential subscript feature allows you to specify variables
that refer to different locations, relative to the base voxel.
For example,
-a fred+orig -b 'a[1,0,0,0]' -c 'a[0,-1,0,0]' -d 'a[0,0,2,0]'
means: symbol 'a' refers to a voxel in dataset fred+orig,
symbol 'b' refers to the following voxel in the x-direction,
symbol 'c' refers to the previous voxel in the y-direction
symbol 'd' refers to the 2nd following voxel in the z-direction
To use this feature, you must define the base dataset (e.g., 'a')
first. Then the differentially subscripted symbols are defined
using the base dataset symbol followed by 4 integer subscripts,
which are the shifts in the x-, y-, z-, and t- (or sub-brick index)
directions. For example,
-a fred+orig -b 'a[0,0,0,1]' -c 'a[0,0,0,-1]' -expr 'median(a,b,c)'
will produce a temporal median smoothing of a 3D+time dataset (this
can be done more efficiently with program 3dTsmooth).
Note that the physical directions of the x-, y-, and z-axes depend
on how the dataset was acquired or constructed. See the output of
program 3dinfo to determine what direction corresponds to what axis.
For convenience, the following abbreviations may be used in place of
some common subscript combinations:
[1,0,0,0] == +i [-1, 0, 0, 0] == -i
[0,1,0,0] == +j [ 0,-1, 0, 0] == -j
[0,0,1,0] == +k [ 0, 0,-1, 0] == -k
[0,0,0,1] == +l [ 0, 0, 0,-1] == -l
The median smoothing example can thus be abbreviated as
-a fred+orig -b a+l -c a-l -expr 'median(a,b,c)'
When a shift calls for a voxel that is outside of the dataset range,
one of three things can happen:
STOP => shifting stops at the edge of the dataset
WRAP => shifting wraps back to the opposite edge of the dataset
ZERO => the voxel value is returned as zero
Which one applies depends on the setting of the shifting mode at the
time the symbol using differential subscripting is defined. The mode
is set by one of the switches '-dsSTOP', '-dsWRAP', or '-dsZERO'. The
default mode is STOP. Suppose that a dataset has range 0..99 in the
x-direction. Then when voxel 101 is called for, the value returned is
STOP => value from voxel 99 [didn't shift past edge of dataset]
WRAP => value from voxel 1 [wrapped back through opposite edge]
ZERO => the number 0.0
You can set the shifting mode more than once - the most recent setting
on the command line applies when a differential subscript symbol is
encountered.
------------------------------------------------------------------------
PROBLEMS:
--------
* Complex-valued datasets cannot be processed.
* This program is not very efficient (but is faster than it once was).
* Differential subscripts slow the program down even more.
------------------------------------------------------------------------
EXPRESSIONS:
-----------
Arithmetic expressions are allowed, using + - * / ** and parentheses.
As noted above, datasets are referred to by single letter variable names.
At this time, C relational, boolean, and conditional expressions are
NOT implemented. Built in functions include:
sin , cos , tan , asin , acos , atan , atan2,
sinh , cosh , tanh , asinh , acosh , atanh , exp ,
log , log10, abs , int , sqrt , max , min ,
J0 , J1 , Y0 , Y1 , erf , erfc , qginv, qg ,
rect , step , astep, bool , and , or , mofn ,
sind , cosd , tand , median, lmode , hmode , mad ,
gran , uran , iran , eran , lran , orstat,
mean , stdev, sem , Pleg
where:
* qg(x) = reversed cdf of a standard normal distribution
* qginv(x) = inverse function to qg
* min, max, atan2 each take 2 arguments ONLY
* J0, J1, Y0, Y1 are Bessel functions (see Watson)
* Pleg(m,x) is the m'th Legendre polynomial evaluated at x
* erf, erfc are the error and complementary error functions
* sind, cosd, tand take arguments in degrees (vs. radians)
* median(a,b,c,...) computes the median of its arguments
* mad(a,b,c,...) computes the MAD of its arguments
* mean(a,b,c,...) computes the mean of its arguments
* stdev(a,b,c,...) computes the standard deviation of its arguments
* sem(a,b,c,...) computes the standard error of the mean of its arguments,
where sem(n arguments) = stdev(same)/sqrt(n)
* orstat(n,a,b,c,...) computes the n-th order statistic of
{a,b,c,...} - that is, the n-th value in size, starting
at the bottom (e.g., orstat(1,a,b,c) is the minimum)
* lmode(a,b,c,...) and hmode(a,b,c,...) compute the mode
of their arguments - lmode breaks ties by choosing the
smallest value with the maximal count, hmode breaks ties by
choosing the largest value with the maximal count
[median,lmode,hmode take a variable number of arguments]
* gran(m,s) returns a Gaussian deviate with mean=m, stdev=s
* uran(r) returns a uniform deviate in the range [0,r]
* iran(t) returns a random integer in the range [0..t]
* eran(s) returns an exponentially distributed deviate
* lran(t) returns a logistically distributed deviate
You may use the symbol 'PI' to refer to the constant of that name.
This is the only 2 letter symbol defined; all input files are
referred to by 1 letter symbols. The case of the expression is
ignored (in fact, it is converted to uppercase as the first step
in the parsing algorithm).
The following functions are designed to help implement logical
functions, such as masking of 3D volumes against some criterion:
step(x) = {1 if x>0 , 0 if x<=0},
astep(x,y) = {1 if abs(x) > y , 0 otherwise} = step(abs(x)-y)
rect(x) = {1 if abs(x)<=0.5, 0 if abs(x)>0.5},
bool(x) = {1 if x != 0.0 , 0 if x == 0.0},
notzero(x) = bool(x),
iszero(x) = 1-bool(x) = { 0 if x != 0.0, 1 if x == 0.0 },
equals(x,y) = 1-bool(x-y) = { 1 if x == y , 0 if x != y },
ispositive(x) = { 1 if x > 0; 0 if x <= 0 },
isnegative(x) = { 1 if x < 0; 0 if x >= 0 },
and(a,b,...,c) = {1 if all arguments are nonzero, 0 if any are zero}
or(a,b,...,c) = {1 if any arguments are nonzero, 0 if all are zero}
mofn(m,a,...,c) = {1 if at least 'm' arguments are nonzero, 0 otherwise}
argmax(a,b,...) = index of largest argument; = 0 if all args are 0
argnum(a,b,...) = number of nonzero arguments
[These last 5 functions take a variable number of arguments.]
The following 27 new [Mar 1999] functions are used for statistical
conversions, as in the program 'cdf':
fico_t2p(t,a,b,c), fico_p2t(p,a,b,c), fico_t2z(t,a,b,c),
fitt_t2p(t,a) , fitt_p2t(p,a) , fitt_t2z(t,a) ,
fift_t2p(t,a,b) , fift_p2t(p,a,b) , fift_t2z(t,a,b) ,
fizt_t2p(t) , fizt_p2t(p) , fizt_t2z(t) ,
fict_t2p(t,a) , fict_p2t(p,a) , fict_t2z(t,a) ,
fibt_t2p(t,a,b) , fibt_p2t(p,a,b) , fibt_t2z(t,a,b) ,
fibn_t2p(t,a,b) , fibn_p2t(p,a,b) , fibn_t2z(t,a,b) ,
figt_t2p(t,a,b) , figt_p2t(p,a,b) , figt_t2z(t,a,b) ,
fipt_t2p(t,a) , fipt_p2t(p,a) , fipt_t2z(t,a) .
See the output of 'cdf -help' for documentation on the meanings of
and arguments to these functions. (After using one of these, you
may wish to use program '3drefit' to modify the dataset statistical
auxiliary parameters.)
Computations are carried out in double precision before being
truncated to the final output 'datum'.
Note that the quotes around the expression are needed so the shell
doesn't try to expand * characters, or interpret parentheses.
(Try the 'ccalc' program to see how the expression evaluator works.
The arithmetic parser and evaluator is written in Fortran-77 and
is derived from a program written long ago by RW Cox to facilitate
compiling on an array processor hooked up to a VAX. It's a mess,
but it works - somewhat slowly.)
This page auto-generated on Thu Aug 25 16:49:36 EDT 2005
|
| 3dClipLevel |
Usage: 3dClipLevel [options] dataset
Estimates the value at which to clip the anatomical dataset so
that background regions are set to zero.
Method:
Find the median of all positive values >= clip value.
Set the clip value to 0.50 of this median.
Repeat until the clip value doesn't change.
Options:
-mfrac ff = Use the number ff instead of 0.50 in the algorithm.
-verb = The clip value is always printed to stdout. If
this option is used to select verbose output,
progress reports are printed to stderr as well.
N.B.: This program only works with byte- and short-valued
datasets, and prints a warning message if any input
voxels are negative. If the dataset has more than one
sub-brick, all sub-bricks are used to build the histogram.
N.B.: Use at your own risk! You might want to use the AFNI Histogram
plugin to see if the results are reasonable. This program is
likely to produce bad results on images gathered with local
RF coils, or with pulse sequences with unusual contrasts.
A csh command line for the truly adventurous:
afni -dset "v1:time+orig<`3dClipLevel 'v1:time+orig[4]'` .. 10000>"
(the dataset is from the 'sample96.tgz' data samples). Can you
figure out what this does?
(Hint: each type of quote "'` means something different to csh.)
This page auto-generated on Thu Aug 25 16:49:36 EDT 2005
|
| 3dclust |
Program: 3dclust
Author: RW Cox et al
Date: 21 Jul 2005
3dclust - performs simple-minded cluster detection in 3D datasets
This program can be used to find clusters of 'active' voxels and
print out a report about them.
* 'Active' refers to nonzero voxels that survive the threshold
that you (the user) have specified
* Clusters are defined by a connectivity radius parameter 'rmm'
Note: by default, this program clusters on the absolute values
of the voxels
-----------------------------------------------------------------------
Usage: 3dclust [editing options] [other options] rmm vmul dset ...
-----
Examples:
--------
3dclust -1clip 0.3 5 2000 func+orig'[1]'
3dclust -1noneg -1thresh 0.3 5 2000 func+orig'[1]'
3dclust -1noneg -1thresh 0.3 5 2000 func+orig'[1]' func+orig'[3]
3dclust -noabs -1clip 0.5 -dxyz=1 1 10 func+orig'[1]'
3dclust -noabs -1clip 0.5 5 700 func+orig'[1]'
3dclust -noabs -2clip 0 999 -dxyz=1 1 10 func+orig'[1]'
3dclust -1clip 0.3 5 3000 func+orig'[1]'
3dclust -quiet -1clip 0.3 5 3000 func+orig'[1]'
3dclust -summarize -quiet -1clip 0.3 5 3000 func+orig'[1]'
-----------------------------------------------------------------------
Arguments (must be included on command line):
---------
rmm : cluster connection radius (in millimeters).
All nonzero voxels closer than rmm millimeters
(center-to-center distance) to the given voxel are
included in the cluster.
* If rmm = 0, then clusters are defined by nearest-
neighbor connectivity
vmul : minimum cluster volume (micro-liters)
i.e., determines the size of the volume cluster.
* If vmul = 0, then all clusters are kept.
* If vmul < 0, then the absolute vmul is the minimum
number of voxels allowed in a cluster.
dset : input dataset (more than one allowed, but only the
first sub-brick of the dataset)
The results are sent to standard output (i.e., the screen)
-----------------------------------------------------------------------
Options:
-------
* Editing options are as in 3dmerge (see 3dmerge -help)
(including -1thresh, -1dindex, -1tindex, -dxyz=1 options)
* -noabs => Use the signed voxel intensities (not the absolute
value) for calculation of the mean and Standard
Error of the Mean (SEM)
* -summarize => Write out only the total nonzero voxel
count and volume for each dataset
* -nosum => Suppress printout of the totals
* -verb => Print out a progress report (to stderr)
as the computations proceed
* -quiet => Suppress all non-essential output
* -mni => If the input dataset is in +tlrc coordinates, this
option will stretch the output xyz-coordinates to the
MNI template brain.
N.B.1: The MNI template brain is about 5 mm higher (in S),
10 mm lower (in I), 5 mm longer (in PA), and tilted
about 3 degrees backwards, relative to the Talairach-
Tournoux Atlas brain. For more details, see
http://www.mrc-cbu.cam.ac.uk/Imaging/mnispace.html
N.B.2: If the input dataset is not in +tlrc coordinates,
then the only effect is to flip the output coordinates
to the 'LPI' (neuroscience) orientation, as if you
gave the '-orient LPI' option.)
* -isovalue => Clusters will be formed only from contiguous (in the
rmm sense) voxels that also have the same value.
N.B.: The normal method is to cluster all contiguous
nonzero voxels together.
* -isomerge => Clusters will be formed from each distinct value
in the dataset; spatial contiguity will not be
used (but you still have to supply rmm and vmul
on the command line).
N.B.: 'Clusters' formed this way may well have components
that are widely separated!
* -prefix ppp => Write a new dataset that is a copy of the
input, but with all voxels not in a cluster
set to zero; the new dataset's prefix is 'ppp'
N.B.: Use of the -prefix option only affects the
first input dataset
-----------------------------------------------------------------------
E.g., 3dclust -1clip 0.3 5 3000 func+orig'[1]'
The above command tells 3dclust to find potential cluster volumes for
dataset func+orig, sub-brick #1, where the threshold has been set
to 0.3 (i.e., ignore voxels with an activation threshold of >0.3 or
<-0.3. Voxels must be no more than 5 mm apart, and the cluster volume
must be at least 3000 micro-liters in size.
Explanation of 3dclust Output:
-----------------------------
Volume : Number of voxels that make up the volume cluster
CM RL : Center of mass (CM) for the cluster in the Right-Left
direction (i.e., the coordinates for the CM)
CM AP : Center of mass for the cluster in the
Anterior-Posterior direction
CM IS : Center of mass for the cluster in the
Inferior-Superior direction
minRL, maxRL : Bounding box for the cluster, min and max
coordinates in the Right-Left direction
minAP, maxAP : Min and max coordinates in the Anterior-Posterior
direction of the volume cluster
minIS, max IS: Min and max coordinates in the Inferior-Superior
direction of the volume cluster
Mean : Mean value for the volume cluster
SEM : Standard Error of the Mean for the volume cluster
Max Int : Maximum Intensity value for the volume cluster
MI RL : Maximum Intensity value in the Right-Left
direction of the volume cluster
MI AP : Maximum Intensity value in the Anterior-Posterior
direction of the volume cluster
MI IS : Maximum Intensity value in the Inferior-Superior
direction of the volume cluster
-----------------------------------------------------------------------
Nota Bene:
* The program does not work on complex- or rgb-valued datasets!
* Using the -1noneg option is strongly recommended!
* 3D+time datasets are allowed, but only if you use the
-1tindex and -1dindex options.
* Bucket datasets are allowed, but you will almost certainly
want to use the -1tindex and -1dindex options with these.
* SEM values are not realistic for interpolated data sets!
A ROUGH correction is to multiply the SEM of the interpolated
data set by the square root of the number of interpolated
voxels per original voxel.
* If you use -dxyz=1, then rmm should be given in terms of
voxel edges (not mm) and vmul should be given in terms of
voxel counts (not microliters). Thus, to connect to only
3D nearest neighbors and keep clusters of 10 voxels or more,
use something like '3dclust -dxyz=1 1.01 10 dset+orig'.
In the report, 'Volume' will be voxel count, but the rest of
the coordinate dependent information will be in actual xyz
millimeters.
* The default coordinate output order is DICOM. If you prefer
the SPM coordinate order, use the option '-orient LPI' or
set the environment variable AFNI_ORIENT to 'LPI'. For more
information, see file README.environment.
This page auto-generated on Thu Aug 25 16:49:36 EDT 2005
|
| 3dCM |
Usage: 3dCM [options] dset
Output = center of mass of dataset, to stdout.
-mask mset Means to use the dataset 'mset' as a mask:
Only voxels with nonzero values in 'mset'
will be averaged from 'dataset'. Note
that the mask dataset and the input dataset
must have the same number of voxels.
-automask Generate the mask automatically.
-set x y z After computing the CM of the dataset, set the
origin fields in the header so that the CM
will be at (x,y,z) in DICOM coords.
This page auto-generated on Thu Aug 25 16:49:36 EDT 2005
|
| 3dConvolve |
Program: 3dConvolve
Author: B. Douglas Ward
Initial Release: 28 June 2001
Latest Revision: 28 Feb 2002
Program to calculate the voxelwise convolution of given impulse response
function (IRF) time series contained in a 3d+time dataset with a specified
input stimulus function time series. This program will also calculate
convolutions involving multiple IRF's and multiple stimulus functions.
Input options include addition of system noise to the estimated output.
Output consists of an AFNI 3d+time dataset which contains the estimated
system response. Alternatively, if all inputs are .1D time series files,
then the output will be a single .1D time series file.
Usage:
3dConvolve
-input fname fname = filename of 3d+time template dataset
[-input1D] flag to indicate all inputs are .1D time series
[-mask mname] mname = filename of 3d mask dataset
[-censor cname] cname = filename of censor .1D time series
[-concat rname] rname = filename for list of concatenated runs
[-nfirst fnum] fnum = number of first time point to calculate by
convolution procedure. (default = max maxlag)
[-nlast lnum] lnum = number of last time point to calculate by
convolution procedure. (default = last point)
[-polort pnum] pnum = degree of polynomial corresponding to the
baseline model (default: pnum = 1)
[-base_file bname] bname = file containing baseline parameters
-num_stimts num num = number of input stimulus time series
(default: num = 0)
-stim_file k sname sname = filename of kth time series input stimulus
[-stim_minlag k m] m = minimum time lag for kth input stimulus
(default: m = 0)
[-stim_maxlag k n] n = maximum time lag for kth input stimulus
(default: n = 0)
[-stim_nptr k p] p = number of stimulus function points per TR
Note: This option requires 0 slice offset times
(default: p = 1)
[-iresp k iprefix] iprefix = prefix of 3d+time input dataset which
contains the kth impulse response function
[-errts eprefix] eprefix = prefix of 3d+time input dataset which
contains the residual error time series
(i.e., noise which will be added to the output)
[-sigma s] s = std. dev. of additive Gaussian noise
(default: s = 0)
[-seed d] d = seed for random number generator
(default: d = 1234567)
[-xout] flag to write X matrix to screen
[-output tprefix] tprefix = prefix of 3d+time output dataset which
will contain the convolved time series data
(or tprefix = prefix of .1D output time series
if the -input1D option is used)
This page auto-generated on Thu Aug 25 16:49:36 EDT 2005
|
| 3dcopy |
Usage 1: 3dcopy [-verb] [-denote] old_prefix new_prefix
Will copy all datasets using the old_prefix to use the new_prefix;
3dcopy fred ethel
will copy fred+orig.HEAD to ethel+orig.HEAD
fred+orig.BRIK to ethel+orig.BRIK
fred+tlrc.HEAD to ethel+tlrc.HEAD
fred+tlrc.BRIK.gz to ethel+tlrc.BRIK.gz
Usage 2: 3dcopy old_prefix+view new_prefix
Will copy only the dataset with the given view (orig, acpc, tlrc).
Usage 3: 3dcopy old_dataset new_prefix
Will copy the non-AFNI formatted dataset (e.g., MINC, ANALYZE, CTF)
to the AFNI formatted dataset with the given new prefix.
Notes:
* The new datasets have new ID codes. If you are renaming
multiple datasets (as in Usage 1), then if the old +orig
dataset is the warp parent of the old +acpc and/or +tlrc
datasets, then the new +orig dataset will be the warp
parent of the new +acpc and +tlrc datasets. If any other
datasets point to the old datasets as anat or warp parents,
they will still point to the old datasets, not these new ones.
* The BRIK files are copied if they exist, keeping the compression
suffix unchanged (if any).
* The old_prefix may have a directory name attached in front,
as in 'gerard/manley/hopkins'.
* If the new_prefix does not have a directory name attached
(i.e., does NOT look like 'homer/simpson'), then the new
datasets will be written in the current directory ('./').
* The new_prefix cannot JUST be a directory (unlike the Unix
utility 'cp'); you must supply a filename prefix, even if
is identical to the filename prefix in old_prefix.
* The '-verb' option will print progress reports; otherwise, the
program operates silently (unless an error is detected).
* The '-denote' option will remove any Notes from the file.
This page auto-generated on Thu Aug 25 16:49:36 EDT 2005
|
| 3dCRUISEtoAFNI |
Usage: 3dCRUISEtoAFNI -input CRUISE_HEADER.dx
Converts a CRUISE dataset defined by a heder in OpenDX format
The conversion is based on sample data and information
provided by Aaron Carass from JHU's IACL iacl.ece.jhu.edu
Common Debugging Options:
[-trace]: Turns on In/Out debug and Memory tracing.
For speeding up the tracing log, I recommend
you redirect stdout to a file when using this option.
For example, if you were running suma you would use:
suma -spec lh.spec -sv ... > TraceFile
This option replaces the old -iodbg and -memdbg.
[-TRACE]: Turns on extreme tracing.
[-nomall]: Turn off memory tracing.
[-yesmall]: Turn on memory tracing (default).
[-novolreg]: Ignore any Volreg or Tagalign transformations
present in the Surface Volume.
NOTE: For programs that output results to stdout
(that is to your shell/screen), the debugging info
might get mixed up with your results.
++ SUMA version 2004_12_29
CVS tag:
SUMA_2005_04_29_1733
Compile Date:
Aug 25 2005
Ziad S. Saad SSCC/NIMH/NIH ziad@nih.gov
This page auto-generated on Thu Aug 25 16:49:36 EDT 2005
|
| 3dDeconvolve |
++ Program 3dDeconvolve: AFNI version=AFNI_2005_08_24_1751
Program to calculate the deconvolution of a measurement 3d+time dataset
with a specified input stimulus time series. This program will also
perform multiple linear regression using multiple input stimulus time
series. Output consists of an AFNI 'bucket' type dataset containing the
least squares estimates of the linear regression coefficients, t-statistics
for significance of the coefficients, partial F-statistics for significance
of the individual input stimuli, and the F-statistic for significance of
the overall regression. Additional output consists of a 3d+time dataset
containing the estimated system impulse response function.
Usage:
3dDeconvolve
**** Input data and control options:
-input fname fname = filename of 3d+time input dataset
(more than one filename can be given)
(here, and these datasets will be)
(catenated in time; if you do this, )
('-concat' is not needed and is ignored)
[-input1D dname] dname = filename of single (fMRI) .1D time series
[-nodata [NT [TR]] Evaluate experimental design only (no input data)
[-mask mname] mname = filename of 3d mask dataset
[-automask] build a mask automatically from input data
(will be slow for long time series datasets)
[-censor cname] cname = filename of censor .1D time series
[-concat rname] rname = filename for list of concatenated runs
[-nfirst fnum] fnum = number of first dataset image to use in the
deconvolution procedure. (default = max maxlag)
[-nlast lnum] lnum = number of last dataset image to use in the
deconvolution procedure. (default = last point)
[-polort pnum] pnum = degree of polynomial corresponding to the
null hypothesis (default: pnum = 1)
[-legendre] use Legendre polynomials for null hypothesis
[-nolegendre] use power polynomials for null hypotheses
(default is -legendre)
[-nodmbase] don't de-mean baseline time series
(i.e., polort>1 and -stim_base inputs)
[-dmbase] de-mean baseline time series (default if polort>0)
[-nocond] don't calculate matrix condition number
[-svd] Use SVD instead of Gaussian elimination (default)
[-nosvd] Use Gaussian elimination instead of SVD
[-rmsmin r] r = minimum rms error to reject reduced model
**** Input stimulus options:
-num_stimts num num = number of input stimulus time series
(0 <= num) (default: num = 0)
-stim_file k sname sname = filename of kth time series input stimulus
[-stim_label k slabel] slabel = label for kth input stimulus
[-stim_base k] kth input stimulus is part of the baseline model
[-stim_minlag k m] m = minimum time lag for kth input stimulus
(default: m = 0)
[-stim_maxlag k n] n = maximum time lag for kth input stimulus
(default: n = 0)
[-stim_nptr k p] p = number of stimulus function points per TR
Note: This option requires 0 slice offset times
(default: p = 1)
[-stim_times k tname Rmodel]
Generate the k-th response model from a set of stimulus times
given in file 'tname'. The response model is specified by the
'Rmodel' argument, which can be one of
'GAM(p,q)' = 1 parameter gamma variate
'SPMG' = 2 parameter SPM gamma variate + derivative
'POLY(b,c,n)' = n parameter polynomial expansion
'SIN(b,c,n)' = n parameter sine series expansion
'TENT(b,c,n)' = n parameter tent function expansion
'BLOCK(d,p)' = 1 parameter block stimulus of duration 'd'
(can also be called 'IGFUN' which stands)
(for 'incomplete gamma function' )
'EXPR(b,c) exp1 ... expn' = n parameter; arbitrary expressions
[-basis_normall a]
Normalize all basis functions for '-stim_times' to have
amplitude 'a' (must have a > 0). The peak absolute value
of each basis function will be scaled to be 'a'.
NOTE: -basis_normall only affect -stim_times options that
appear LATER on the command line
[-slice_base k sname]
Inputs the k'th stimulus time series from file sname,
AND specifies that this regressor belongs to the baseline,
AND specifies that the regressor is different for each slice in
the input 3D+time dataset. The sname file should have exactly
nz columns of input, where nz=number of slices, OR it should
have exactly 1 column, in which case this input is the same
as using '-stim_file k sname' and '-stim_base k'.
N.B.: * You can't use -stim_minlag or -stim_maxlag or -stim_nptr
with this value of k.
* You can't use this option with -input1D or -nodata.
* The intended use of this option is to provide slice-
dependent physiological noise regressors, e.g., from program
1dCRphase.
**** General linear test (GLT) options:
-num_glt num num = number of general linear tests (GLTs)
(0 <= num) (default: num = 0)
[-glt s gltname] Perform s simultaneous linear tests, as specified
by the matrix contained in file gltname
[-glt_label k glabel] glabel = label for kth general linear test
[-gltsym gltname] Read the GLT with symbolic names from the file
[-TR_irc dt]
Use 'dt' as the stepsize for computation of integrals in -IRC_times
options. Default is to use value given in '-TR_times'.
**** Options for output 3d+time datasets:
[-iresp k iprefix] iprefix = prefix of 3d+time output dataset which
will contain the kth estimated impulse response
[-tshift] Use cubic spline interpolation to time shift the
estimated impulse response function, in order to
correct for differences in slice acquisition
times. Note that this effects only the 3d+time
output dataset generated by the -iresp option.
[-sresp k sprefix] sprefix = prefix of 3d+time output dataset which
will contain the standard deviations of the
kth impulse response function parameters
[-fitts fprefix] fprefix = prefix of 3d+time output dataset which
will contain the (full model) time series fit
to the input data
[-errts eprefix] eprefix = prefix of 3d+time output dataset which
will contain the residual error time series
from the full model fit to the input data
[-TR_times dt]
Use 'dt' as the stepsize for output of -iresp and -sresp file
for response models generated by '-stim_times' options.
Default is same as time spacing in the '-input' 3D+time dataset.
The units here are in seconds!
**** Options to control the contents of the output bucket dataset:
[-fout] Flag to output the F-statistics
[-rout] Flag to output the R^2 statistics
[-tout] Flag to output the t-statistics
[-vout] Flag to output the sample variance (MSE) map
[-nobout] Flag to suppress output of baseline coefficients
(and associated statistics)
[-nocout] Flag to suppress output of regression coefficients
(and associated statistics)
[-full_first] Flag to specify that the full model statistics will
appear first in the bucket dataset output
[-bucket bprefix] Create one AFNI 'bucket' dataset containing various
parameters of interest, such as the estimated IRF
coefficients, and full model fit statistics.
Output 'bucket' dataset is written to bprefix.
[-xsave] Flag to save X matrix into file bprefix.xsave
(only works if -bucket option is also given)
[-noxsave] Don't save X matrix (this is the default)
[-cbucket cprefix] Save the regression coefficients (no statistics)
into a dataset named 'cprefix'. This dataset
will be used in a -xrestore run instead of the
bucket dataset, if possible.
[-xrestore f.xsave] Restore the X matrix, etc. from a previous run
that was saved into file 'f.xsave'. You can
then carry out new -glt tests. When -xrestore
is used, most other command line options are
ignored.
**** The following options control the screen output only:
[-quiet] Flag to suppress most screen output
[-xout] Flag to write X and inv(X'X) matrices to screen
[-xjpeg filename] Write a JPEG file graphing the X matrix
[-progress n] Write statistical results for every nth voxel
[-fdisp fval] Write statistical results for those voxels
whose full model F-statistic is > fval
-jobs J Run the program with 'J' jobs (sub-processes).
On a multi-CPU machine, this can speed the
program up considerably. On a single CPU
machine, using this option is silly.
J should be a number from 1 up to the
number of CPU sharing memory on the system.
J=1 is normal (single process) operation.
The maximum allowed value of J is 32.
* For more information on parallelizing, see
http://afni.nimh.nih.gov/afni/doc/misc/afni_parallelize
* Use -mask to get more speed; cf. 3dAutomask.
** NOTE **
This version of the program has been compiled to use
double precision arithmetic for most internal calculations.
This page auto-generated on Thu Aug 25 16:49:36 EDT 2005
|
| 3dDeconvolve_f |
** ** 3dDeconvolve_f is now disabled by default. ** It is dangerous, due to roundoff problems. ** Please use 3dDeconvolve from now on! ** ** HOWEVER, if you insist on using 3dDeconvolve_f, then: ** + Use '-OK' as the first command line option. ** + Check the matrix condition number; ** if it is greater than 100, BEWARE! ** ** RWCox - July 2004 **This page auto-generated on Thu Aug 25 16:49:36 EDT 2005 |
| 3ddelay |
Program: 3ddelay
Author: Ziad Saad (using B. Douglas Ward's 3dfim+ to read and write bricks)
Date: Jul 22 2005
The program estimates the time delay between each voxel time series
in a 3D+time dataset and a reference time series[1][2].
The estimated delays are relative to the reference time series.
For example, a delay of 4 seconds means that the voxel time series
is delayed by 4 seconds with respectto the reference time series.
Usage:
3ddelay
-input fname fname = filename of input 3d+time dataset
-ideal_file rname rname = input ideal time series file name
The length of the reference time series should be equal to
that of the 3d+time data set.
The reference time series vector is stored in an ascii file.
The programs assumes that there is one value per line and that all
values in the file are part of the reference vector.
PS: Unlike with 3dfim, and FIM in AFNI, values over 33333 are treated
as part of the time series.
-fs fs Sampling frequency in Hz. of data time series (1/TR).
-T Tstim Stimulus period in seconds.
If the stimulus is not periodic, you can set Tstim to 0.
[-prefix bucket] The prefix for the results Brick.
The first subbrick is for Delay.
The second subbrick is for Covariance, which is an estimate
of the power in voxel time series at the frequencies present
in the reference time series.
The third subbrick is for the Cross Correlation Coefficients between
FMRI time series and reference time series.
The fourth subbrick contains estimates of the Variance of voxel time series.
The default prefix is the prefix of the input 3D+time brick
with a '.DEL' extension appended to it.
[-uS/-uD/-uR] Units for delay estimates. (Seconds/Degrees/Radians)
You can't use Degrees or Radians as units unless
you specify a value for Tstim > 0.
[-phzwrp] Delay (or phase) wrap.
This switch maps delays from:
(Seconds) 0->T/2 to 0->T/2 and T/2->T to -T/2->0
(Degrees) 0->180 to 0->180 and 180->360 to -180->0
(Radians) 0->pi to 0->pi and pi->2pi to -pi->0
You can't use this option unless you specify a
value for Tstim > 0.
[-bias] Do not correct for the bias in the estimates [1][2]
[-mask mname] mname = filename of 3d mask dataset
only voxels with non-zero values in the mask would be
considered.
[-nfirst fnum] fnum = number of first dataset image to use in
the delay estimate. (default = 0)
[-nlast lnum] lnum = number of last dataset image to use in
the delay estimate. (default = last)
[-nodsamp ] Do not correct a voxel's estimated delay by the time
at which the slice containing that voxel was acquired.
[-co CCT] Cross Correlation Coefficient threshold value.
This is only used to limit the ascii output (see below).
[-nodtrnd] Do not remove the linear trend from the data time series.
Only the mean is removed. Regardless of this option,
No detrending is done to the reference time series.
[-asc [out]] Write the results to an ascii file for voxels with
[-ascts [out]] cross correlation coefficients larger than CCT.
If 'out' is not specified, a default name similar
to the default output prefix is used.
-asc, only files 'out' and 'out.log' are written to disk (see ahead)
-ascts, an additional file, 'out.ts', is written to disk (see ahead)
There a 9 columns in 'out' which hold the following values:
1- Voxel Index (VI) : Each voxel in an AFNI brick has a unique index.
Indices map directly to XYZ coordinates.
See AFNI plugin documentations for more info.
2..4- Voxel coordinates (X Y Z): Those are the voxel slice coordinates.
You can see these coordinates in the upper left side of the
AFNI window.To do so, you must first switch the voxel
coordinate units from mm to slice coordinates.
Define Datamode -> Misc -> Voxel Coords ?
PS: The coords that show up in the graph window
could be different from those in the upper left side
of AFNI's main window.
5- Duff : A value of no interest to you. It is preserved for backward
compatibility.
6- Delay (Del) : The estimated voxel delay.
7- Covariance (Cov) : Covariance estimate.
8- Cross Correlation Coefficient (xCorCoef) : Cross Correlation Coefficient.
9- Variance (VTS) : Variance of voxel's time series.
The file 'out' can be used as an input to two plugins:
'4Ddump' and '3D+t Extract'
The log file 'out.log' contains all parameter settings used for generating
the output brick. It also holds any warnings generated by the plugin.
Some warnings, such as 'null time series ...' , or
'Could not find zero crossing ...' are harmless. '
I might remove them in future versions.
A line (L) in the file 'out.ts' contains the time series of the voxel whose
results are written on line (L) in the file 'out'.
The time series written to 'out.ts' do not contain the ignored samples,
they are detrended and have zero mean.
Random Comments/Advice:
The longer you time series, the better. It is generally recomended that
the largest delay be less than N/10, N being the length of the time series.
The algorithm does go all the way to N/2.
If you have/find questions/comments/bugs about the plugin,
send me an E-mail: ziad@nih.gov
Ziad Saad Dec 8 00.
[1] : Bendat, J. S. (1985). The Hilbert transform and applications to correlation measurements,
Bruel and Kjaer Instruments Inc.
[2] : Bendat, J. S. and G. A. Piersol (1986). Random Data analysis and measurement procedures,
John Wiley & Sons.
Author's publications on delay estimation using the Hilbert Transform:
[3] : Saad, Z.S., et al., Analysis and use of FMRI response delays.
Hum Brain Mapp, 2001. 13(2): p. 74-93.
[4] : Saad, Z.S., E.A. DeYoe, and K.M. Ropella, Estimation of FMRI Response Delays.
Neuroimage, 2003. 18(2): p. 494-504.
This page auto-generated on Thu Aug 25 16:49:36 EDT 2005
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| 3dDespike |
Usage: 3dDespike [options] dataset
Removes 'spikes' from the 3D+time input dataset and writes
a new dataset with the spike values replaced by something
more pleasing.
Method:
* L1 fit a smooth-ish curve to each voxel time series
[see -corder option for description of the curve].
* Compute the MAD of the difference between the curve and
the data time series (the residuals).
* Estimate the standard deviation 'sigma' of the residuals
as sqrt(PI/2)*MAD.
* For each voxel value, define s = (value-curve)/sigma.
* Values with s > c1 are replaced with a value that yields
a modified s' = c1+(c2-c1)*tanh((s-c1)/(c2-c1)).
* c1 is the threshold value of s for a 'spike' [default c1=2.5].
* c2 is the upper range of the allowed deviation from the curve:
s=[c1..infinity) is mapped to s'=[c1..c2) [default c2=4].
Options:
-ignore I = Ignore the first I points in the time series:
these values will just be copied to the
output dataset [default I=0].
-corder L = Set the curve fit order to L:
the curve that is fit to voxel data v(t) is
k=L [ (2*PI*k*t) (2*PI*k*t) ]
f(t) = a+b*t+c*t*t + SUM [ d * sin(--------) + e * cos(--------) ]
k=1 [ k ( T ) k ( T ) ]
where T = duration of time series;
the a,b,c,d,e parameters are chosen to minimize
the sum over t of |v(t)-f(t)| (L1 regression);
this type of fitting is is insensitive to large
spikes in the data. The default value of L is
NT/30, where NT = number of time points.
-cut c1 c2 = Alter default values for the spike cut values
[default c1=2.5, c2=4.0].
-prefix pp = Save de-spiked dataset with prefix 'pp'
[default pp='despike']
-ssave ttt = Save 'spikiness' measure s for each voxel into a
3D+time dataset with prefix 'ttt' [default=no save]
-nomask = Process all voxels
[default=use a mask of high-intensity voxels, ]
[as created via '3dAutomask -dilate 4 dataset'].
Caveats:
* Despiking may interfere with image registration, since head
movement may produce 'spikes' at the edge of the brain, and
this information would be used in the registration process.
This possibility has not been explored.
* Check your data visually before and after despiking and
registration!
[Hint: open 2 AFNI controllers, and turn Time Lock on.]
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| 3dDetrend |
Usage: 3dDetrend [options] dataset
This program removes components from voxel time series using
linear least squares. Each voxel is treated independently.
The input dataset may have a sub-brick selector string; otherwise,
all sub-bricks will be used.
General Options:
-prefix pname = Use 'pname' for the output dataset prefix name.
[default='detrend']
-session dir = Use 'dir' for the output dataset session directory.
[default='./'=current working directory]
-verb = Print out some verbose output as the program runs.
-replace = Instead of subtracting the fit from each voxel,
replace the voxel data with the time series fit.
-normalize = Normalize each output voxel time series; that is,
make the sum-of-squares equal to 1.
N.B.: This option is only valid if the input dataset is
stored as floats!
-byslice = Treat each input vector (infra) as describing a set of
time series interlaced across slices. If NZ is the
number of slices and NT is the number of time points,
then each input vector should have NZ*NT values when
this option is used (usually, they only need NT values).
The values must be arranged in slice order, then time
order, in each vector column, as shown here:
f(z=0,t=0) // first slice, first time
f(z=1,t=0) // second slice, first time
...
f(z=NZ-1,t=0) // last slice, first time
f(z=0,t=1) // first slice, second time
f(z=1,t=1) // second slice, second time
...
f(z=NZ-1,t=NT-1) // last slice, last time
Component Options:
These options determine the components that will be removed from
each dataset voxel time series. They may be repeated to specify
multiple regression. At least one component must be specified.
-vector vvv = Remove components proportional to the columns vectors
of the ASCII *.1D file 'vvv'. You may use a
sub-vector selector string to specify which columns
to use; otherwise, all columns will be used.
For example:
-vector 'xyzzy.1D[3,5]'
will remove the 4th and 6th columns of file xyzzy.1D
from the dataset (sub-vector indexes start at 0).
-expr eee = Remove components proportional to the function
specified in the expression string 'eee'.
Any single letter from a-z may be used as the
independent variable in 'eee'. For example:
-expr 'cos(2*PI*t/40)' -expr 'sin(2*PI*t/40)'
will remove sine and cosine waves of period 40
from the dataset. Another example:
-expr '1' -expr 't' -expr 't*t'
will remove a quadratic trend from the data.
-del ddd = Use the numerical value 'ddd' for the stepsize
in subsequent -expr options. If no -del option
is ever given, then the TR given in the dataset
header is used for 'ddd'; if that isn't available,
then 'ddd'=1.0 is assumed. The j-th time point
will have independent variable = j * ddd, starting
at j=0. For example:
-expr 'sin(x)' -del 2.0 -expr 'z**3'
means that the stepsize in 'sin(x)' is delta-x=TR,
but the stepsize in 'z**3' is delta-z = 2.
N.B.: expressions are NOT calculated on a per-slice basis when the
-byslice option is used. If you want to do this, you could
compute vectors with the required time series using 1devel.
INPUT DATASET NAMES
-------------------
This program accepts datasets that are modified on input according to the
following schemes:
'r1+orig[3..5]' {sub-brick selector}
'r1+orig<100.200>' {sub-range selector}
'r1+orig[3..5]<100..200>' {both selectors}
'3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )' {calculation}
For the gruesome details, see the output of 'afni -help'.
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| 3ddot |
Usage: 3ddot [options] dset1 dset2
Output = correlation coefficient between 2 dataset bricks
- you can use sub-brick selectors on the dsets
- the result is a number printed to stdoutOptions:
-mask mset Means to use the dataset 'mset' as a mask:
Only voxels with nonzero values in 'mset'
will be averaged from 'dataset'. Note
that the mask dataset and the input dataset
must have the same number of voxels.
-mrange a b Means to further restrict the voxels from
'mset' so that only those mask values
between 'a' and 'b' (inclusive) will
be used. If this option is not given,
all nonzero values from 'mset' are used.
Note that if a voxel is zero in 'mset', then
it won't be included, even if a < 0 < b.
-demean Means to remove the mean from each volume
prior to computing the correlation.
INPUT DATASET NAMES
-------------------
This program accepts datasets that are modified on input according to the
following schemes:
'r1+orig[3..5]' {sub-brick selector}
'r1+orig<100.200>' {sub-range selector}
'r1+orig[3..5]<100..200>' {both selectors}
'3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )' {calculation}
For the gruesome details, see the output of 'afni -help'.
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| 3dDTeig |
Usage: 3dDTeig [options] dataset
Computes eigenvalues and eigenvectors for an input dataset of
6 sub-bricks Dxx,Dxy,Dxz,Dyy,Dyz,Dzz.
The results are stored in a 14-subbrick bucket dataset.
The resulting 14-subbricks are
lambda_1,lambda_2,lambda_3,
eigvec_1[1-3],eigvec_2[1-3],eigvec_3[1-3],
FA,MD.
The output is a bucket dataset. The input dataset
may use a sub-brick selection list, as in program 3dcalc.
Mean diffusivity (MD) calculated as simple average of eigenvalues.
Fractional Anisotropy (FA) calculated according to Pierpaoli C, Basser PJ.
Microstructural and physiological features of tissues elucidated by
quantitative-diffusion tensor MRI, J Magn Reson B 1996; 111:209-19
INPUT DATASET NAMES
-------------------
This program accepts datasets that are modified on input according to the
following schemes:
'r1+orig[3..5]' {sub-brick selector}
'r1+orig<100.200>' {sub-range selector}
'r1+orig[3..5]<100..200>' {both selectors}
'3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )' {calculation}
For the gruesome details, see the output of 'afni -help'.
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| 3ddup |
Usage: 3ddup [options] dataset
'Duplicates' a 3D dataset by making a warp-on-demand copy.
Applications:
- allows AFNI to resample a dataset to a new grid without
destroying an existing data .BRIK
- change a functional dataset to anatomical, or vice-versa
OPTIONS:
-'type' = Convert to the given 'type', which must be
chosen from the same list as in to3d
-session dirname = Write output into given directory (default=./)
-prefix pname = Use 'pname' for the output directory prefix
(default=dup)
N.B.: Even if the new dataset is anatomical, it will not contain
any markers, duplicated from the original, or otherwise.
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|
| 3dDWItoDT |
Usage: 3dDWItoDT [options] gradient-file dataset
Computes 6 principle direction tensors from multiple gradient vectors
and corresponding DTI image volumes.
The program takes two parameters as input :
a 1D file of the gradient vectors with lines of ASCII floats Gxi,Gyi,Gzi.
Only the non-zero gradient vectors are included in this file (no G0 line).
a 3D bucket dataset with Np+1 sub-briks where the first sub-brik is the
volume acquired with no diffusion weighting.
Options:
-prefix pname = Use 'pname' for the output dataset prefix name.
[default='DT']
-automask = mask dataset so that the tensors are computed only for
high-intensity (presumably brain) voxels. The intensity level is
determined the same way that 3dClipLevel works.
-mask dset = use dset as mask to include/exclude voxels
-nonlinear = compute iterative solution to avoid negative eigenvalues.
This is the default method.
-linear = compute simple linear solution.
-reweight = recompute weight factors at end of iterations and restart
-max_iter n = maximum number of iterations for convergence (Default=10).
Values can range from -1 to any positive integer less than 101.
A value of -1 is equivalent to the linear solution.
A value of 0 results in only the initial estimate of the diffusion tensor
solution adjusted to avoid negative eigenvalues.
-max_iter_rw n = max number of iterations after reweighting (Default=5)
values can range from 1 to any positive integer less than 101.
-eigs = compute eigenvalues, eigenvectors, fractional anisotropy and mean
diffusivity in sub-briks 6-19. Computed as in 3dDTeig
-debug_briks = add sub-briks with Ed (error functional), Ed0 (orig. error),
number of steps to convergence and I0 (modeled B0 volume)
-cumulative_wts = show overall weight factors for each gradient level
May be useful as a quality control
-verbose nnnnn = print convergence steps every nnnnn voxels that survive to
convergence loops (can be quite lengthy).
-drive_afni nnnnn = show convergence graphs every nnnnn voxels that survive
to convergence loops. AFNI must have NIML communications on (afni -niml).
Example:
3dDWItoDT -prefix rw01 -automask -reweight -max_iter 10 \
-max_iter_rw 10 tensor25.1D grad02+orig.
The output is a 6 sub-brick bucket dataset containing Dxx,Dxy,Dxz,Dyy,Dyz,Dzz.
Additional sub-briks may be appended with the -eigs and -debug_briks options.
These results are appropriate as the input to the 3dDTeig program.
INPUT DATASET NAMES
-------------------
This program accepts datasets that are modified on input according to the
following schemes:
'r1+orig[3..5]' {sub-brick selector}
'r1+orig<100.200>' {sub-range selector}
'r1+orig[3..5]<100..200>' {both selectors}
'3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )' {calculation}
For the gruesome details, see the output of 'afni -help'.
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|
| 3dEntropy |
Usage: 3dEntropy dataset ...This page auto-generated on Thu Aug 25 16:49:36 EDT 2005 |
| 3dExtrema |
++ Program 3dExtrema: AFNI version=AFNI_2005_08_24_1751
This program finds local extrema (minima or maxima) of the input
dataset values for each sub-brick of the input dataset. The extrema
may be determined either for each volume, or for each individual slice.
Only those voxels whose corresponding intensity value is greater than
the user specified data threshold will be considered.
Usage: 3dExtrema options datasets
where the options are:
-prefix pname = Use 'pname' for the output dataset prefix name.
OR [default = NONE; only screen output]
-output pname
-session dir = Use 'dir' for the output dataset session directory.
[default='./'=current working directory]
-quiet = Flag to suppress screen output
-mask_file mname = Use mask statistic from file mname.
Note: If file mname contains more than 1 sub-brick,
the mask sub-brick must be specified!
-mask_thr m Only voxels whose mask statistic is greater
than m in abolute value will be considered.
-data_thr d Only voxels whose value (intensity) is greater
than d in abolute value will be considered.
-sep_dist d Min. separation distance [mm] for distinct extrema
Choose type of extrema (one and only one choice):
-minima Find local minima.
-maxima Find local maxima.
Choose form of binary relation (one and only one choice):
-strict > for maxima, < for minima
-partial >= for maxima, <= for minima
Choose boundary criteria (one and only one choice):
-interior Extrema must be interior points (not on boundary)
-closure Extrema may be boudary points
Choose domain for finding extrema (one and only one choice):
-slice Each slice is considered separately
-volume The volume is considered as a whole
Choose option for merging of extrema (one and only one choice):
-remove Remove all but strongest of neighboring extrema
-average Replace neighboring extrema by average
-weight Replace neighboring extrema by weighted average
Command line arguments after the above are taken to be input datasets.
INPUT DATASET NAMES
-------------------
This program accepts datasets that are modified on input according to the
following schemes:
'r1+orig[3..5]' {sub-brick selector}
'r1+orig<100.200>' {sub-range selector}
'r1+orig[3..5]<100..200>' {both selectors}
'3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )' {calculation}
For the gruesome details, see the output of 'afni -help'.
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|
| 3dFDR |
Program: 3dFDR
Author: B. Douglas Ward
Initial Release: 31 January 2002
Latest Revision: 31 January 2002
This program implements the False Discovery Rate (FDR) algorithm for
thresholding of voxelwise statistics.
Program input consists of a functional dataset containing one (or more)
statistical sub-bricks. Output consists of a bucket dataset with one
sub-brick for each input sub-brick. For non-statistical input sub-bricks,
the output is a copy of the input. However, statistical input sub-bricks
are replaced by their corresponding FDR values, as follows:
For each voxel, the minimum value of q is determined such that
E(FDR) <= q
leads to rejection of the null hypothesis in that voxel. Only voxels inside
the user specified mask will be considered. These q-values are then mapped
to z-scores for compatibility with the AFNI statistical threshold display:
stat ==> p-value ==> FDR q-value ==> FDR z-score
Usage:
3dFDR
-input fname fname = filename of input 3d functional dataset
OR
-input1D dname dname = .1D file containing column of p-values
-mask_file mname Use mask values from file mname.
Note: If file mname contains more than 1 sub-brick,
the mask sub-brick must be specified!
Default: No mask
-mask_thr m Only voxels whose corresponding mask value is
greater than or equal to m in absolute value will
be considered. Default: m=1
Constant c(N) depends on assumption about p-values:
-cind c(N) = 1 p-values are independent across N voxels
-cdep c(N) = sum(1/i), i=1,...,N any joint distribution
Default: c(N) = 1
-quiet Flag to suppress screen output
-list Write sorted list of voxel q-values to screen
-prefix pname Use 'pname' for the output dataset prefix name.
OR
-output pname
INPUT DATASET NAMES
-------------------
This program accepts datasets that are modified on input according to the
following schemes:
'r1+orig[3..5]' {sub-brick selector}
'r1+orig<100.200>' {sub-range selector}
'r1+orig[3..5]<100..200>' {both selectors}
'3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )' {calculation}
For the gruesome details, see the output of 'afni -help'.
This page auto-generated on Thu Aug 25 16:49:36 EDT 2005
|
| 3dfim |
Program: 3dfim
Author: R. W. Cox and B. D. Ward
Initial Release: 06 Sept 1996
Latest Revision: 15 August 2001
Program: 3dfim
Purpose: Calculate functional image from 3d+time data file.
Usage: 3dfim [-im1 num] -input fname -prefix name
-ideal fname [-ideal fname] [-ort fname]
options are:
-im1 num num = index of first image to be used in time series
correlation; default is 1
-input fname fname = filename of 3d + time data file for input
-prefix name name = prefix of filename for saving functional data
-ideal fname fname = filename of a time series to which the image data
is to be correlated.
-percent p Calculate percentage change due to the ideal time series
p = maximum allowed percentage change from baseline
Note: values greater than p are set equal to p.
-ort fname fname = filename of a time series to which the image data
is to be orthogonalized
N.B.: It is possible to specify more than
one ideal time series file. Each one is separately correlated
with the image time series and the one most highly correlated
is selected for each pixel. Multiple ideals are specified
using more than one '-ideal fname' option, or by using the
form '-ideal [ fname1 fname2 ... ]' -- this latter method
allows the use of wildcarded ideal filenames.
The '[' character that indicates the start of a group of
ideals can actually be any ONE of these: [{/%
and the ']' that ends the group can be: ]}/%
[Format of ideal time series files:
ASCII; one number per line;
Same number of lines as images in the time series;
Value over 33333 --> don't use this image in the analysis]
N.B.: It is also possible to specify more than
one ort time series file. The image time series is
orthogonalized to each ort time series. Multiple orts are
specified by using more than one '-ort fname' option,
or by using the form '-ort [ fname1 fname2 ... ]'. This
latter method allows the use of wildcarded ort filenames.
The '[' character that indicates the start of a group of
ideals can actually be any ONE of these: [{/%
and the ']' that ends the group can be: ]}/%
[Format of ort time series files:
ASCII; one number per line;
At least same number of lines as images in the time series]
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|
| 3dfim+ |
Program: 3dfim+
Author: B. Douglas Ward
Initial Release: 28 April 2000
Latest Revision: 29 October 2004
Program to calculate the cross-correlation of an ideal reference waveform
with the measured FMRI time series for each voxel.
Usage:
3dfim+
-input fname fname = filename of input 3d+time dataset
[-input1D dname] dname = filename of single (fMRI) .1D time series
[-mask mname] mname = filename of 3d mask dataset
[-nfirst fnum] fnum = number of first dataset image to use in
the cross-correlation procedure. (default = 0)
[-nlast lnum] lnum = number of last dataset image to use in
the cross-correlation procedure. (default = last)
[-polort pnum] pnum = degree of polynomial corresponding to the
baseline model (pnum = 0, 1, etc.)
(default: pnum = 1)
[-fim_thr p] p = fim internal mask threshold value (0 <= p <= 1)
(default: p = 0.0999)
[-cdisp cval] Write (to screen) results for those voxels
whose correlation stat. > cval (0 <= cval <= 1)
(default: disabled)
[-ort_file sname] sname = input ort time series file name
-ideal_file rname rname = input ideal time series file name
Note: The -ort_file and -ideal_file commands may be used
more than once.
Note: If files sname or rname contain multiple columns,
then ALL columns will be used as ort or ideal
time series. However, individual columns or
a subset of columns may be selected using a file
name specification like 'fred.1D[0,3,5]', which
indicates that only columns #0, #3, and #5 will
be used for input.
[-out param] Flag to output the specified parameter, where
the string 'param' may be any one of the following:
Fit Coef L.S. fit coefficient for Best Ideal
Best Index Index number for Best Ideal
% Change P-P amplitude of signal response / Baseline
Baseline Average of baseline model response
Correlation Best Ideal product-moment correlation coefficient
% From Ave P-P amplitude of signal response / Average
Average Baseline + average of signal response
% From Top P-P amplitude of signal response / Topline
Topline Baseline + P-P amplitude of signal response
Sigma Resid Std. Dev. of residuals from best fit
All This specifies all of the above parameters
Spearman CC Spearman correlation coefficient
Quadrant CC Quadrant correlation coefficient
Note: Multiple '-out' commands may be used.
Note: If a parameter name contains imbedded spaces, the
entire parameter name must be enclosed by quotes,
e.g., -out 'Fit Coef'
[-bucket bprefix] Create one AFNI 'bucket' dataset containing the
parameters of interest, as specified by the above
'-out' commands.
The output 'bucket' dataset is written to a file
with the prefix name bprefix.
This page auto-generated on Thu Aug 25 16:49:36 EDT 2005
|
| 3dFourier |
3dFourier
(c) 1999 Medical College of Wisconsin
by T. Ross and K. Heimerl
Version 0.8 last modified 8-17-99
Usage: 3dFourier [options] dataset
The paramters and options are:
dataset an afni compatible 3d+time dataset to be operated upon
-prefix name output name for new 3d+time dataset [default = fourier]
-lowpass f low pass filter with a cutoff of f Hz
-highpass f high pass filter with a cutoff of f Hz
-ignore n ignore the first n images [default = 1]
-retrend Any mean and linear trend are removed before filtering.
This will restore the trend after filtering.
Note that by combining the lowpass and highpass options, one can construct
bandpass and notch filters
INPUT DATASET NAMES
-------------------
This program accepts datasets that are modified on input according to the
following schemes:
'r1+orig[3..5]' {sub-brick selector}
'r1+orig<100.200>' {sub-range selector}
'r1+orig[3..5]<100..200>' {both selectors}
'3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )' {calculation}
For the gruesome details, see the output of 'afni -help'.
This page auto-generated on Thu Aug 25 16:49:36 EDT 2005
|
| 3dfractionize |
Usage: 3dfractionize [options]
* For each voxel in the output dataset, computes the fraction
of it that is occupied by nonzero voxels from the input.
* The fraction is stored as a short in the range 0..10000,
indicating fractions running from 0..1.
* The template dataset is used only to define the output grid;
its brick(s) will not be read into memory. (The same is
true of the warp dataset, if it is used.)
* The actual values stored in the input dataset are irrelevant,
except in that they are zero or nonzero (UNLESS the -preserve
option is used).
The purpose of this program is to allow the resampling of a mask
dataset (the input) from a fine grid to a coarse grid (defined by
the template). When you are using the output, you will probably
want to threshold the mask so that voxels with a tiny occupancy
fraction aren't used. This can be done in 3dmaskave, by using
3calc, or with the '-clip' option below.
Options are [the first 2 are 'mandatory options']:
-template tset = Use dataset 'tset' as a template for the output.
The output dataset will be on the same grid as
this dataset.
-input iset = Use dataset 'iset' for the input.
Only the sub-brick #0 of the input is used.
You can use the sub-brick selection technique
described in '3dcalc -help' to choose the
desired sub-brick from a multi-brick dataset.
-prefix ppp = Use 'ppp' for the prefix of the output.
[default prefix = 'fractionize']
-clip fff = Clip off voxels that are less than 'fff' occupied.
'fff' can be a number between 0.0 and 1.0, meaning
the fraction occupied, can be a number between 1.0
and 100.0, meaning the percent occupied, or can be
a number between 100.0 and 10000.0, meaning the
direct output value to use as a clip level.
** Some sort of clipping is desirable; otherwise,
an output voxel that is barely overlapped by a
single nonzero input voxel will enter the mask.
[default clip = 0.0]
-warp wset = If this option is used, 'wset' is a dataset that
provides a transformation (warp) from +orig
coordinates to the coordinates of 'iset'.
In this case, the output dataset will be in
+orig coordinates rather than the coordinates
of 'iset'. With this option:
** 'tset' must be in +orig coordinates
** 'iset' must be in +acpc or +tlrc coordinates
** 'wset' must be in the same coordinates as 'iset'
-preserve = When this option is used, the program will copy
or the nonzero values of input voxels to the output
-vote dataset, rather than create a fractional mask.
Since each output voxel might be overlapped
by more than one input voxel, the program 'votes'
for which input value to preserve. For example,
if input voxels with value=1 occupy 10% of an
output voxel, and inputs with value=2 occupy 20%
of the same voxel, then the output value in that
voxel will be set to 2 (provided that 20% is >=
to the clip fraction).
** Voting can only be done on short-valued datasets,
or on byte-valued datasets.
** Voting is a relatively time-consuming option,
since a separate loop is made through the
input dataset for each distinct value found.
** Combining this with the -warp option does NOT
make a general +trlc to +orig transformer!
This is because for any value to survive the
vote, its fraction in the output voxel must be
>= clip fraction, regardless of other values
present in the output voxel.
Example usage:
3dfractionize -template a+orig -input b+tlrc -warp anat+tlrc -clip 0.2
This program will also work in going from a coarse grid to a fine grid,
but it isn't clear that this capability has any purpose.
-- RWCox - February 1999
- October 1999: added -warp and -preserve options
This page auto-generated on Thu Aug 25 16:49:36 EDT 2005
|
| 3dFriedman |
Program: 3dFriedman
Author: B. Douglas Ward
Initial Release: 23 July 1997
Latest Revision: 02 December 2002
This program performs nonparametric Friedman test for
randomized complete block design experiments.
Usage:
3dFriedman
-levels s s = number of treatments
-dset 1 filename data set for treatment #1
. . . . . .
-dset 1 filename data set for treatment #1
. . . . . .
-dset s filename data set for treatment #s
. . . . . .
-dset s filename data set for treatment #s
[-workmem mega] number of megabytes of RAM to use
for statistical workspace
[-voxel num] screen output for voxel # num
-out prefixname Friedman statistics are written
to file prefixname
N.B.: For this program, the user must specify 1 and only 1 sub-brick
with each -dset command. That is, if an input dataset contains
more than 1 sub-brick, a sub-brick selector must be used, e.g.:
-dset 2 'fred+orig[3]'
INPUT DATASET NAMES
-------------------
This program accepts datasets that are modified on input according to the
following schemes:
'r1+orig[3..5]' {sub-brick selector}
'r1+orig<100.200>' {sub-range selector}
'r1+orig[3..5]<100..200>' {both selectors}
'3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )' {calculation}
For the gruesome details, see the output of 'afni -help'.
This page auto-generated on Thu Aug 25 16:49:36 EDT 2005
|
| 3dFWHM |
Program: 3dFWHM
Author: B. Douglas Ward
Initial Release: 20 February 1997
Latest Revision: 08 March 2004
This program estimates the Filter Width Half Maximum (FWHM).
Usage:
3dFWHM
-dset file file = name of input AFNI 3d dataset
[-mask mname] mname = filename of 3d mask dataset
[-quiet] suppress screen output
[-out file] file = name of output file
INPUT DATASET NAMES
-------------------
This program accepts datasets that are modified on input according to the
following schemes:
'r1+orig[3..5]' {sub-brick selector}
'r1+orig<100.200>' {sub-range selector}
'r1+orig[3..5]<100..200>' {both selectors}
'3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )' {calculation}
For the gruesome details, see the output of 'afni -help'.
This page auto-generated on Thu Aug 25 16:49:36 EDT 2005
|
| 3dhistog |
Compute histogram of 3D Dataset
Usage: 3dhistog [editing options] [histogram options] dataset
The editing options are the same as in 3dmerge
(i.e., the options starting with '-1').
The histogram options are:
-nbin # Means to use '#' bins [default=100]
Special Case: for short or byte dataset bricks,
set '#' to zero to have the number
of bins set by the brick range.
-dind i Means to take data from sub-brick #i, rather than #0
-omit x Means to omit the value 'x' from the count;
-omit can be used more than once to skip multiple values.
-mask m Means to use dataset 'm' to determine which voxels to use
-doall Means to include all sub-bricks in the calculation;
otherwise, only sub-brick #0 (or that from -dind) is used.
-notit Means to leave the title line off the output.
-log10 Output log10() of the counts, instead of the count values.
-min x Means specify minimum of histogram.
-max x Means specify maximum of histogram.
The histogram is written to stdout. Use redirection '>' if you
want to save it to a file. The format is a title line, then
three numbers printed per line:
bottom-of-interval count-in-interval cumulative-count
-- by RW Cox (V Roopchansingh added the -mask option)
INPUT DATASET NAMES
-------------------
This program accepts datasets that are modified on input according to the
following schemes:
'r1+orig[3..5]' {sub-brick selector}
'r1+orig<100.200>' {sub-range selector}
'r1+orig[3..5]<100..200>' {both selectors}
'3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )' {calculation}
For the gruesome details, see the output of 'afni -help'.
This page auto-generated on Thu Aug 25 16:49:36 EDT 2005
|
| 3dinfo |
Prints out sort-of-useful information from a 3D dataset's header Usage: 3dinfo [-verb OR -short] dataset [dataset ...] -verb means to print out lots of stuff -short means to print out less stuffThis page auto-generated on Thu Aug 25 16:49:36 EDT 2005 |
| 3dIntracranial |
Program: 3dIntracranial
Author: B. D. Ward
Initial Release: 04 June 1999
Latest Revision: 21 July 2005
3dIntracranial - performs automatic segmentation of intracranial region.
This program will strip the scalp and other non-brain tissue from a
high-resolution T1 weighted anatomical dataset.
-----------------------------------------------------------------------
Usage:
-----
3dIntracranial
-anat filename => Filename of anat dataset to be segmented
[-min_val a] => Minimum voxel intensity limit
Default: Internal PDF estimate for lower bound
[-max_val b] => Maximum voxel intensity limit
Default: Internal PDF estimate for upper bound
[-min_conn m] => Minimum voxel connectivity to enter
Default: m=4
[-max_conn n] => Maximum voxel connectivity to leave
Default: n=2
[-nosmooth] => Suppress spatial smoothing of segmentation mask
[-mask] => Generate functional image mask (complement)
Default: Generate anatomical image
[-quiet] => Suppress output to screen
-prefix pname => Prefix name for file to contain segmented image
** NOTE **: The newer program 3dSkullStrip will probably give
better segmentation results than 3dIntracranial!
-----------------------------------------------------------------------
Examples:
--------
3dIntracranial -anat elvis+orig -prefix elvis_strip
3dIntracranial -min_val 30 -max_val 350 -anat elvis+orig -prefix strip
3dIntracranial -nosmooth -quiet -anat elvis+orig -prefix elvis_strip
-----------------------------------------------------------------------
This page auto-generated on Thu Aug 25 16:49:36 EDT 2005
|
| 3dKruskalWallis |
Program: 3dKruskalWallis
Author: B. Douglas Ward
Initial Release: 23 July 1997
Latest Revision: 02 Dec 2002
This program performs nonparametric Kruskal-Wallis test for
comparison of multiple treatments.
Usage:
3dKruskalWallis
-levels s s = number of treatments
-dset 1 filename data set for treatment #1
. . . . . .
-dset 1 filename data set for treatment #1
. . . . . .
-dset s filename data set for treatment #s
. . . . . .
-dset s filename data set for treatment #s
[-workmem mega] number of megabytes of RAM to use
for statistical workspace
[-voxel num] screen output for voxel # num
-out prefixnamename Kruskal-Wallis statistics are written
to file prefixname
N.B.: For this program, the user must specify 1 and only 1 sub-brick
with each -dset command. That is, if an input dataset contains
more than 1 sub-brick, a sub-brick selector must be used, e.g.:
-dset 2 'fred+orig[3]'
INPUT DATASET NAMES
-------------------
This program accepts datasets that are modified on input according to the
following schemes:
'r1+orig[3..5]' {sub-brick selector}
'r1+orig<100.200>' {sub-range selector}
'r1+orig[3..5]<100..200>' {both selectors}
'3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )' {calculation}
For the gruesome details, see the output of 'afni -help'.
This page auto-generated on Thu Aug 25 16:49:36 EDT 2005
|
| 3dLocalstat |
Usage: 3dLocalstat [options] dataset
This program computes statistics at each voxel, based on a
local neighborhood of that voxel.
- The neighborhood is defined by the '-nbhd' option.
- Statistics to be calculated are defined by the '-stat' option(s).
OPTIONS
-------
-nbhd 'nnn' = The string 'nnn' defines the region around each
voxel that will be extracted for the statistics
calculation. The format of the 'nnn' string are:
* 'SPHERE(r)' where 'r' is the radius in mm;
the neighborhood is all voxels whose center-to-
center distance is less than or equal to 'r'.
** A negative value for 'r' means that the region
is calculated using voxel indexes rather than
voxel dimensions; that is, the neighborhood
region is a "sphere" in voxel indexes of
"radius" abs(r).
* 'RECT(a,b,c)' is a rectangular block which
proceeds plus-or-minus 'a' mm in the x-direction,
'b' mm in the y-direction, and 'c' mm in the
z-direction. The correspondence between the
dataset xyz axes and the actual spatial orientation
can be determined by using program 3dinfo.
** A negative value for 'a' means that the region
extends plus-and-minus abs(a) voxels in the
x-direction, rather than plus-and-minus a mm.
Mutatis mutandum for negative 'b' and/or 'c'.
* If no '-nbhd' option is given, the region extracted
will just be the voxel and its 6 nearest neighbors.
-stat sss = Compute the statistic named 'sss' on the values
extracted from the region around each voxel:
* mean = average of the values
* stdev = standard deviation
* var = variance (stdev*stdev)
* cvar = coefficient of variation = stdev/fabs(mean)
* median = median of the values
* MAD = median absolute deviation
* min = minimum
* max = maximum
* absmax = maximum of the absolute values
* num = number of the values in the region:
with the use of -mask or -automask,
the size of the region around any given
voxel will vary; this option lets you
map that size. It may be useful if you
plan to compute a t-statistic (say) from
the mean and stdev outputs.
* ALL = all of the above, in that order
More than one '-stat' option can be used.
-mask mset = Read in dataset 'mset' and use the nonzero voxels
therein as a mask. Voxels NOT in the mask will
not be used in the neighborhood of any voxel. Also,
a voxel NOT in the mask will have its statistic(s)
computed as zero (0).
-automask = Compute the mask as in program 3dAutomask.
-mask and -automask are mutually exclusive: that is,
you can only specify one mask.
-prefix ppp = Use string 'ppp' as the prefix for the output dataset.
The output dataset is always stored as floats.
Author: RWCox - August 2005. Instigator: ZSSaad.
This page auto-generated on Thu Aug 25 16:49:36 EDT 2005
|
| 3dLRflip |
Usage: 3dLRflip [-prefix ppp] dataset Flips the Left-to-Right rows of a dataset.This page auto-generated on Thu Aug 25 16:49:36 EDT 2005 |
| 3dMannWhitney |
Program: 3dMannWhitney
Author: B. Douglas Ward
Initial Release: 23 July 1997
Latest Revision: 02 Dec 2002
This program performs nonparametric Mann-Whitney two-sample test.
Usage:
3dMannWhitney
-dset 1 filename data set for X observations
. . . . . .
-dset 1 filename data set for X observations
-dset 2 filename data set for Y observations
. . . . . .
-dset 2 filename data set for Y observations
[-workmem mega] number of megabytes of RAM to use
for statistical workspace
[-voxel num] screen output for voxel # num
-out prefixname estimated population delta and
Wilcoxon-Mann-Whitney statistics
written to file prefixname
N.B.: For this program, the user must specify 1 and only 1 sub-brick
with each -dset command. That is, if an input dataset contains
more than 1 sub-brick, a sub-brick selector must be used, e.g.:
-dset 2 'fred+orig[3]'
INPUT DATASET NAMES
-------------------
This program accepts datasets that are modified on input according to the
following schemes:
'r1+orig[3..5]' {sub-brick selector}
'r1+orig<100.200>' {sub-range selector}
'r1+orig[3..5]<100..200>' {both selectors}
'3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )' {calculation}
For the gruesome details, see the output of 'afni -help'.
This page auto-generated on Thu Aug 25 16:49:36 EDT 2005
|
| 3dmaskave |
Usage: 3dmaskave [options] dataset
Computes average of all voxels in the input dataset
which satisfy the criterion in the options list.
If no options are given, then all voxels are included.
Options:
-mask mset Means to use the dataset 'mset' as a mask:
Only voxels with nonzero values in 'mset'
will be averaged from 'dataset'. Note
that the mask dataset and the input dataset
must have the same number of voxels.
SPECIAL CASE: If 'mset' is the string 'SELF',
then the input dataset will be
used to mask itself. That is,
only nonzero voxels from the
#miv sub-brick will be used.
-mindex miv Means to use sub-brick #'miv' from the mask
dataset. If not given, miv=0.
-mrange a b Means to further restrict the voxels from
'mset' so that only those mask values
between 'a' and 'b' (inclusive) will
be used. If this option is not given,
all nonzero values from 'mset' are used.
Note that if a voxel is zero in 'mset', then
it won't be included, even if a < 0 < b.
-dindex div Means to use sub-brick #'div' from the dataset.
If not given, all sub-bricks will be processed.
-drange a b Means to only include voxels from the dataset whose
values fall in the range 'a' to 'b' (inclusive).
Otherwise, all voxel values are included.
-slices p q Means to only included voxels from the dataset
whose slice numbers are in the range 'p' to 'q'
(inclusive). Slice numbers range from 0 to
NZ-1, where NZ can be determined from the output
of program 3dinfo. The default is to include
data from all slices.
[There is no provision for geometrical voxel]
[selection except in the slice (z) direction]
-sigma Means to compute the standard deviation as well
as the mean.
-median Means to compute the median instead of the mean.
-max Means to compute the max instead of the mean.
-min Means to compute the min instead of the mean.
(-sigma is ignored with -median, -max, or -min)
-dump Means to print out all the voxel values that
go into the average.
-udump Means to print out all the voxel values that
go into the average, UNSCALED by any internal
factors.
N.B.: the scale factors for a sub-brick
can be found using program 3dinfo.
-indump Means to print out the voxel indexes (i,j,k) for
each dumped voxel. Has no effect if -dump
or -udump is not also used.
N.B.: if nx,ny,nz are the number of voxels in
each direction, then the array offset
in the brick corresponding to (i,j,k)
is i+j*nx+k*nx*ny.
-q or
-quiet Means to print only the minimal results.
This is useful if you want to create a *.1D file.
The output is printed to stdout (the terminal), and can be
saved to a file using the usual redirection operation '>'.
INPUT DATASET NAMES
-------------------
This program accepts datasets that are modified on input according to the
following schemes:
'r1+orig[3..5]' {sub-brick selector}
'r1+orig<100.200>' {sub-range selector}
'r1+orig[3..5]<100..200>' {both selectors}
'3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )' {calculation}
For the gruesome details, see the output of 'afni -help'.
This page auto-generated on Thu Aug 25 16:49:36 EDT 2005
|
| 3dmaskdump |
Usage: 3dmaskdump [options] dataset dataset ...
Writes to an ASCII file values from the input datasets
which satisfy the mask criteria given in the options.
If no options are given, then all voxels are included.
This might result in a GIGANTIC output file.
Options:
-mask mset Means to use the dataset 'mset' as a mask:
Only voxels with nonzero values in 'mset'
will be printed from 'dataset'. Note
that the mask dataset and the input dataset
must have the same number of voxels.
-mrange a b Means to further restrict the voxels from
'mset' so that only those mask values
between 'a' and 'b' (inclusive) will
be used. If this option is not given,
all nonzero values from 'mset' are used.
Note that if a voxel is zero in 'mset', then
it won't be included, even if a < 0 < b.
-index Means to write out the dataset index values.
-noijk Means not to write out the i,j,k values.
-xyz Means to write the x,y,z coordinates from
the 1st input dataset at the start of each
output line. These coordinates are in
the 'RAI' order.
-o fname Means to write output to file 'fname'.
[default = stdout, which you won't like]
-cmask 'opts' Means to execute the options enclosed in single
quotes as a 3dcalc-like program, and produce
produce a mask from the resulting 3D brick.
Examples:
-cmask '-a fred+orig[7] -b zork+orig[3] -expr step(a-b)'
produces a mask that is nonzero only where
the 7th sub-brick of fred+orig is larger than
the 3rd sub-brick of zork+orig.
-cmask '-a fred+orig -expr 1-bool(k-7)'
produces a mask that is nonzero only in the
7th slice (k=7); combined with -mask, you
could use this to extract just selected voxels
from particular slice(s).
Notes: * You can use both -mask and -cmask in the same
run - in this case, only voxels present in
both masks will be dumped.
* Only single sub-brick calculations can be
used in the 3dcalc-like calculations -
if you input a multi-brick dataset here,
without using a sub-brick index, then only
its 0th sub-brick will be used.
* Do not use quotes inside the 'opts' string!
-xbox x y z Means to put a 'mask' down at the dataset (not DICOM)
coordinates of 'x y z' mm. By default, this box is
1 voxel wide in each direction. You can specify
instead a range of coordinates using a colon ':'
after the coordinates; for example:
-xbox 22:27 31:33 44
means a box from (x,y,z)=(22,31,44) to (27,33,44).
-dbox x y z Means the same as -xbox, but the coordinates are in
DICOM order (+x=Left, +y=Posterior, +z=Superior).
These coordinates correspond to those you'd enter
into the 'Jump to (xyz)' control in AFNI, and to
those output by default from 3dclust.
-nbox x y z Means the same as -xbot, but the coordinates are in
'neuroscience' order (+x=Right, +y=Anterior, +z=Superior)
-ibox i j k Means to put a 'mask' down at the voxel indexes
given by 'i j k'. By default, this picks out
just 1 voxel. Again, you can use a ':' to specify
a range (now in voxels) of locations.
Notes: * Boxes are cumulative; that is, if you specify more
than 1 box, you'll get more than one region.
* If a -mask and/or -cmask option is used, then
the intersection of the boxes with these masks
determines which voxels are output; that is,
a voxel must be inside some box AND inside the
mask in order to be selected for output.
* If boxes select more than 1 voxel, the output lines
are NOT necessarily in the order of the options on
the command line.
* Coordinates (for -xbox, -dbox, and -nbox) are relative
to the first dataset on the command line.
-quiet Means not to print progress messages to stderr.
Inputs after the last option are datasets whose values you
want to be dumped out. These datasets (and the mask) can
use the sub-brick selection mechanism (described in the
output of '3dcalc -help') to choose which values you get.
Each selected voxel gets one line of output:
i j k val val val ....
where (i,j,k) = 3D index of voxel in the dataset arrays,
and val = the actual voxel value. Note that if you want
the mask value to be output, you have to include that
dataset in the dataset input list again, after you use
it in the '-mask' option.
N.B.: This program doesn't work with complex-valued datasets!
INPUT DATASET NAMES
-------------------
This program accepts datasets that are modified on input according to the
following schemes:
'r1+orig[3..5]' {sub-brick selector}
'r1+orig<100.200>' {sub-range selector}
'r1+orig[3..5]<100..200>' {both selectors}
'3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )' {calculation}
For the gruesome details, see the output of 'afni -help'.
This page auto-generated on Thu Aug 25 16:49:36 EDT 2005
|
| 3dMax |
Usage: 3dMax [options] dataset
Compute maximum and/or minimum voxel values of an input dataset
The output is a number to the console. The input dataset
may use a sub-brick selection list, as in program 3dcalc.
Options :
-quick = get the information from the header only (default)
-slow = read the whole dataset to find the min and max values
-min = print the minimum value in dataset
-max = print the minimum value in dataset (default)
-mean = print the mean value in dataset (implies slow)
-count = print the number of voxels included (implies slow)
-positive = include only positive voxel values (implies slow)
-negative = include only negative voxel values (implies slow)
-zero = include only zero voxel values (implies slow)
-non-positive = include only voxel values 0 or negative (implies slow)
-non-negative = include only voxel values 0 or greater (implies slow)
-non-zero = include only voxel values not equal to 0 (implies slow)
-mask dset = use dset as mask to include/exclude voxels
-automask = automatically compute mask for dataset
Can not be combined with -mask
-help = print this help screen
INPUT DATASET NAMES
-------------------
This program accepts datasets that are modified on input according to the
following schemes:
'r1+orig[3..5]' {sub-brick selector}
'r1+orig<100.200>' {sub-range selector}
'r1+orig[3..5]<100..200>' {both selectors}
'3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )' {calculation}
For the gruesome details, see the output of 'afni -help'.
This page auto-generated on Thu Aug 25 16:49:36 EDT 2005
|
| 3dMean |
Usage: 3dMean [options] dset dset ...
Takes the voxel-by-voxel mean of all input datasets;
the main reason is to be faster than 3dcalc.
Options [see 3dcalc -help for more details on these]:
-verbose = Print out some information along the way.
-prefix ppp = Sets the prefix of the output dataset.
-datum ddd = Sets the datum of the output dataset.
-fscale = Force scaling of the output to the maximum integer range.
-gscale = Same as '-fscale', but also forces each output sub-brick to
to get the same scaling factor.
-nscale = Don't do any scaling on output to byte or short datasets.
-sd *OR* = Calculate the standard deviation (variance/n-1) instead
-stdev of the mean (cannot be used with -sqr or -sum).
-sqr = Average the squares, instead of the values.
-sum = Just take the sum (don't divide by number of datasets).
N.B.: All input datasets must have the same number of voxels along
each axis (x,y,z,t).
* At least 2 input datasets are required.
* Dataset sub-brick selectors [] are allowed.
* The output dataset origin, time steps, etc., are taken from the
first input dataset.
This page auto-generated on Thu Aug 25 16:49:36 EDT 2005
|
| 3dMedianFilter |
Usage: 3dMedianFilter [options] dataset Computes the median in a spherical nbhd around each point in the input to produce the output. Options: -irad x = Radius in voxels of spherical regions -verb = Be verbose during run -prefix pp = Use 'pp' for prefix of output dataset -automask = Create a mask (a la 3dAutomask) Output dataset is always stored in float format. If the input dataset has more than 1 sub-brick, only sub-brick #0 is processed. -- Feb 2005 - RWCoxThis page auto-generated on Thu Aug 25 16:49:36 EDT 2005 |
| 3dmerge |
Program 3dmerge
Last revision: 02 Nov 2001
Edit and/or merge 3D datasets
Usage: 3dmerge [options] datasets ...
where the options are:
EDITING OPTIONS APPLIED TO EACH INPUT DATASET:
-1thtoin = Copy threshold data over intensity data.
This is only valid for datasets with some
thresholding statistic attached. All
subsequent operations apply to this
substituted data.
-2thtoin = The same as -1thtoin, but do NOT scale the
threshold values from shorts to floats when
processing. This option is only provided
for compatibility with the earlier versions
of the AFNI package '3d*' programs.
-1noneg = Zero out voxels with negative intensities
-1abs = Take absolute values of intensities
-1clip val = Clip intensities in range (-val,val) to zero
-2clip v1 v2 = Clip intensities in range (v1,v2) to zero
-1uclip val = These options are like the above, but do not apply
-2uclip v1 v2 any automatic scaling factor that may be attached
to the data. These are for use only in special
circumstances. (The 'u' means 'unscaled'. Program
'3dinfo' can be used to find the scaling factors.)
N.B.: Only one of these 'clip' options can be used; you cannot
combine them to have multiple clipping executed.
-1thresh thr = Use the threshold data to censor the intensities
(only valid for 'fith', 'fico', or 'fitt' datasets).
N.B.: The value 'thr' is floating point, in the range
0.0 < thr < 1.0 for 'fith' and 'fico' datasets,
and 0.0 < thr < 32.7 for 'fitt' datasets.
-1blur_sigma bmm = Gaussian blur with sigma = bmm (in mm)
-1blur_rms bmm = Gaussian blur with rms deviation = bmm
-1blur_fwhm bmm = Gaussian blur with FWHM = bmm
-t1blur_sigma bmm= Gaussian blur of threshold with sigma = bmm(in mm)
-t1blur_rms bmm = Gaussian blur of threshold with rms deviation = bmm
-t1blur_fwhm bmm = Gaussian blur of threshold with FWHM = bmm
-1zvol x1 x2 y1 y2 z1 z2
= Zero out entries inside the 3D volume defined
by x1 <= x <= x2, y1 <= y <= y2, z1 <= z <= z2 ;
N.B.: The ranges of x,y,z in a dataset can be found
using the '3dinfo' program. Dimensions are in mm.
N.B.: This option may not work correctly at this time, but
I've not figured out why!
CLUSTERING
-dxyz=1 = In the cluster editing options, the spatial clusters
are defined by connectivity in true 3D distance, using
the voxel dimensions recorded in the dataset header.
This option forces the cluster editing to behave as if
all 3 voxel dimensions were set to 1 mm. In this case,
'rmm' is then the max number of grid cells apart voxels
can be to be considered directly connected, and 'vmul'
is the min number of voxels to keep in the cluster.
N.B.: The '=1' is part of the option string, and can't be
replaced by some other value. If you MUST have some
other value for voxel dimensions, use program 3drefit.
The following cluster options are mutually exclusive:
-1clust rmm vmul = Form clusters with connection distance rmm
and clip off data not in clusters of
volume at least vmul microliters
-1clust_mean rmm vmul = Same as -1clust, but all voxel intensities
within a cluster are replaced by the average
intensity of the cluster.
-1clust_max rmm vmul = Same as -1clust, but all voxel intensities
within a cluster are replaced by the maximum
intensity of the cluster.
-1clust_amax rmm vmul = Same as -1clust, but all voxel intensities
within a cluster are replaced by the maximum
absolute intensity of the cluster.
-1clust_smax rmm vmul = Same as -1clust, but all voxel intensities
within a cluster are replaced by the maximum
signed intensity of the cluster.
-1clust_size rmm vmul = Same as -1clust, but all voxel intensities
within a cluster are replaced by the size
of the cluster (in multiples of vmul).
-1clust_order rmm vmul= Same as -1clust, but all voxel intensities
within a cluster are replaced by the cluster
size index (largest cluster=1, next=2, ...).
* If rmm is given as 0, this means to use the 6 nearest neighbors to
form clusters of nonzero voxels.
* If vmul is given as zero, then all cluster sizes will be accepted
(probably not very useful!).
* If vmul is given as negative, then abs(vmul) is the minimum number
of voxels to keep.
The following commands produce erosion and dilation of 3D clusters.
These commands assume that one of the -1clust commands has been used.
The purpose is to avoid forming strange clusters with 2 (or more)
main bodies connected by thin 'necks'. Erosion can cut off the neck.
Dilation will minimize erosion of the main bodies.
Note: Manipulation of values inside a cluster (-1clust commands)
occurs AFTER the following two commands have been executed.
-1erode pv For each voxel, set the intensity to zero unless pv %
of the voxels within radius rmm are nonzero.
-1dilate Restore voxels that were removed by the previous
command if there remains a nonzero voxel within rmm.
The following filter options are mutually exclusive:
-1filter_mean rmm = Set each voxel to the average intensity of the
voxels within a radius of rmm.
-1filter_nzmean rmm = Set each voxel to the average intensity of the
non-zero voxels within a radius of rmm.
-1filter_max rmm = Set each voxel to the maximum intensity of the
voxels within a radius of rmm.
-1filter_amax rmm = Set each voxel to the maximum absolute intensity
of the voxels within a radius of rmm.
-1filter_smax rmm = Set each voxel to the maximum signed intensity
of the voxels within a radius of rmm.
-1filter_aver rmm = Same idea as '_mean', but implemented using a
new code that should be faster.
The following threshold filter options are mutually exclusive:
-t1filter_mean rmm = Set each correlation or threshold voxel to the
average of the voxels within a radius of rmm.
-t1filter_nzmean rmm = Set each correlation or threshold voxel to the
average of the non-zero voxels within
a radius of rmm.
-t1filter_max rmm = Set each correlation or threshold voxel to the
maximum of the voxels within a radius of rmm.
-t1filter_amax rmm = Set each correlation or threshold voxel to the
maximum absolute intensity of the voxels
within a radius of rmm.
-t1filter_smax rmm = Set each correlation or threshold voxel to the
maximum signed intensity of the voxels
within a radius of rmm.
-t1filter_aver rmm = Same idea as '_mean', but implemented using a
new code that should be faster.
-1mult factor = Multiply intensities by the given factor
-1zscore = If the sub-brick is labeled as a statistic from
a known distribution, it will be converted to
an equivalent N(0,1) deviate (or 'z score').
If the sub-brick is not so labeled, nothing will
be done.
The above '-1' options are carried out in the order given above,
regardless of the order in which they are entered on the command line.
N.B.: The 3 '-1blur' options just provide different ways of
specifying the radius used for the blurring function.
The relationships among these specifications are
sigma = 0.57735027 * rms = 0.42466090 * fwhm
The requisite convolutions are done using FFTs; this is by
far the slowest operation among the editing options.
OTHER OPTIONS:
-datum type = Coerce the output data to be stored as the given type,
which may be byte, short, or float.
N.B.: Byte data cannot be negative. If this datum type is chosen,
any negative values in the edited and/or merged dataset
will be set to zero.
-keepthr = When using 3dmerge to edit exactly one dataset of a
functional type with a threshold statistic attached,
normally the resulting dataset is of the 'fim'
(intensity only) type. This option tells 3dmerge to
copy the threshold data (unedited in any way) into
the output dataset.
N.B.: This option is ignored if 3dmerge is being used to
combine 2 or more datasets.
N.B.: The -datum option has no effect on the storage of the
threshold data. Instead use '-thdatum type'.
-doall = Apply editing and merging options to ALL sub-bricks
uniformly in a dataset.
N.B.: All input datasets must have the same number of sub-bricks
when using the -doall option.
N.B.: The threshold specific options (such as -1thresh,
-keepthr, -tgfisher, etc.) are not compatible with
the -doall command. Neither are the -1dindex or
the -1tindex options.
N.B.: All labels and statistical parameters for individual
sub-bricks are copied from the first dataset. It is
the responsibility of the user to verify that these
are appropriate. Note that sub-brick auxiliary data
can be modified using program 3drefit.
-1dindex j = Uses sub-brick #j as the data source , and uses sub-brick
-1tindex k = #k as the threshold source. With these, you can operate
on any given sub-brick of the inputs dataset(s) to produce
as output a 1 brick dataset. If desired, a collection
of 1 brick datasets can later be assembled into a
multi-brick bucket dataset using program '3dbucket'
or into a 3D+time dataset using program '3dTcat'.
N.B.: If these options aren't used, j=0 and k=1 are the defaults
The following option allows you to specify a mask dataset that
limits the action of the 'filter' options to voxels that are
nonzero in the mask:
-1fmask mset = Read dataset 'mset' (which can include a
sub-brick specifier) and use the nonzero
voxels as a mask for the filter options.
Filtering calculations will not use voxels
that are outside the mask. If an output
voxel does not have ANY masked voxels inside
the rmm radius, then that output voxel will
be set to 0.
N.B.: * Only the -1filter_* and -t1filter_* options are
affected by -1fmask.
* In the linear averaging filters (_mean, _nzmean,
and _expr), voxels not in the mask will not be used
or counted in either the numerator or denominator.
This can give unexpected results. If the mask is
designed to exclude the volume outside the brain,
then voxels exterior to the brain, but within 'rmm',
will have a few voxels inside the brain included
in the filtering. Since the sum of weights (the
denominator) is only over those few intra-brain
voxels, the effect will be to extend the significant
part of the result outward by rmm from the surface
of the brain. In contrast, without the mask, the
many small-valued voxels outside the brain would
be included in the numerator and denominator sums,
which would barely change the numerator (since the
voxel values are small outside the brain), but would
increase the denominator greatly (by including many
more weights). The effect in this case (no -1fmask)
is to make the filtering taper off gradually in the
rmm-thickness shell around the brain.
* Thus, if the -1fmask is intended to clip off non-brain
data from the filtering, its use should be followed by
masking operation using 3dcalc:
3dmerge -1filter_aver 12 -1fmask mask+orig -prefix x input+orig
3dcalc -a x -b mask+orig -prefix y -expr 'a*step(b)'
rm -f x+orig.*
The desired result is y+orig - filtered using only
brain voxels (as defined by mask+orig), and with
the output confined to the brain voxels as well.
The following option allows you to specify an almost arbitrary
weighting function for 3D linear filtering:
-1filter_expr rmm expr
Defines a linear filter about each voxel of radius 'rmm' mm.
The filter weights are proportional to the expression evaluated
at each voxel offset in the rmm neighborhood. You can use only
these symbols in the expression:
r = radius from center
x = dataset x-axis offset from center
y = dataset y-axis offset from center
z = dataset z-axis offset from center
i = x-axis index offset from center
j = y-axis index offset from center
k = z-axis index offset from center
Example:
-1filter_expr 12.0 'exp(-r*r/36.067)'
This does a Gaussian filter over a radius of 12 mm. In this
example, the FWHM of the filter is 10 mm. [in general, the
denominator in the exponent would be 0.36067 * FWHM * FWHM.
This is the only way to get a Gaussian blur combined with the
-1fmask option. The radius rmm=12 is chosen where the weights
get smallish.] Another example:
-1filter_expr 20.0 'exp(-(x*x+16*y*y+z*z)/36.067)'
which is a non-spherical Gaussian filter.
The following option lets you apply a 'Winsor' filter to the data:
-1filter_winsor rmm nw
The data values within the radius rmm of each voxel are sorted.
Suppose there are 'N' voxels in this group. We index the
sorted voxels as s[0] <= s[1] <= ... <= s[N-1], and we call the
value of the central voxel 'v' (which is also in array s[]).
If v < s[nw] , then v is replaced by s[nw]
otherwise If v > s[N-1-nw], then v is replace by s[N-1-nw]
otherwise v is unchanged
The effect is to increase 'too small' values up to some
middling range, and to decrease 'too large' values.
If N is odd, and nw=(N-1)/2, this would be a median filter.
In practice, I recommend that nw be about N/4; for example,
-dxyz=1 -1filter_winsor 2.5 19
is a filter with N=81 that gives nice results.
N.B.: This option is NOT affected by -1fmask
N.B.: This option is slow!
MERGING OPTIONS APPLIED TO FORM THE OUTPUT DATASET:
[That is, different ways to combine results. The]
[following '-g' options are mutually exclusive! ]
-gmean = Combine datasets by averaging intensities
(including zeros) -- this is the default
-gnzmean = Combine datasets by averaging intensities
(not counting zeros)
-gmax = Combine datasets by taking max intensity
(e.g., -7 and 2 combine to 2)
-gamax = Combine datasets by taking max absolute intensity
(e.g., -7 and 2 combine to 7)
-gsmax = Combine datasets by taking max signed intensity
(e.g., -7 and 2 combine to -7)
-gcount = Combine datasets by counting number of 'hits' in
each voxel (see below for defintion of 'hit')
-gorder = Combine datasets in order of input:
* If a voxel is nonzero in dataset #1, then
that value goes into the voxel.
* If a voxel is zero in dataset #1 but nonzero
in dataset #2, then the value from #2 is used.
* And so forth: the first dataset with a nonzero
entry in a given voxel 'wins'
-gfisher = Takes the arctanh of each input, averages these,
and outputs the tanh of the average. If the input
datum is 'short', then input values are scaled by
0.0001 and output values by 10000. This option
is for merging bricks of correlation coefficients.
-nscale = If the output datum is shorts, don't do the scaling
to the max range [similar to 3dcalc's -nscale option]
MERGING OPERATIONS APPLIED TO THE THRESHOLD DATA:
[That is, different ways to combine the thresholds. If none of these ]
[are given, the thresholds will not be merged and the output dataset ]
[will not have threshold data attached. Note that the following '-tg']
[command line options are mutually exclusive, but are independent of ]
[the '-g' options given above for merging the intensity data values. ]
-tgfisher = This option is only applicable if each input dataset
is of the 'fico' or 'fith' types -- functional
intensity plus correlation or plus threshold.
(In the latter case, the threshold values are
interpreted as correlation coefficients.)
The correlation coefficients are averaged as
described by -gfisher above, and the output
dataset will be of the fico type if all inputs
are fico type; otherwise, the output datasets
will be of the fith type.
N.B.: The difference between the -tgfisher and -gfisher
methods is that -tgfisher applies to the threshold
data stored with a dataset, while -gfisher
applies to the intensity data. Thus, -gfisher
would normally be applied to a dataset created
from correlation coefficients directly, or from
the application of the -1thtoin option to a fico
or fith dataset.
OPTIONAL WAYS TO POSTPROCESS THE COMBINED RESULTS:
[May be combined with the above methods.]
[Any combination of these options may be used.]
-ghits count = Delete voxels that aren't !=0 in at least
count datasets (!=0 is a 'hit')
-gclust rmm vmul = Form clusters with connection distance rmm
and clip off data not in clusters of
volume at least vmul microliters
The '-g' and '-tg' options apply to the entire group of input datasets.
OPTIONS THAT CONTROL THE NAMES OF THE OUTPUT DATASET:
-session dirname = write output into given directory (default=./)
-prefix pname = use 'pname' for the output directory prefix
(default=mrg)
NOTES:
** If only one dataset is read into this program, then the '-g'
options do not apply, and the output dataset is simply the
'-1' options applied to the input dataset (i.e., edited).
** A merged output dataset is ALWAYS of the intensity-only variety.
** You can combine the outputs of 3dmerge with other sub-bricks
using the program 3dbucket.
** Complex-valued datasets cannot be merged.
** This program cannot handle time-dependent datasets without -doall.
** Note that the input datasets are specified by their .HEAD files,
but that their .BRIK files must exist also!
INPUT DATASET NAMES
-------------------
This program accepts datasets that are modified on input according to the
following schemes:
'r1+orig[3..5]' {sub-brick selector}
'r1+orig<100.200>' {sub-range selector}
'r1+orig[3..5]<100..200>' {both selectors}
'3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )' {calculation}
For the gruesome details, see the output of 'afni -help'.
** Input datasets using sub-brick selectors are treated as follows:
- 3D+time if the dataset is 3D+time and more than 1 brick is chosen
- otherwise, as bucket datasets (-abuc or -fbuc)
(in particular, fico, fitt, etc. datasets are converted to fbuc)
** If you are NOT using -doall, and choose more than one sub-brick
with the selector, then you may need to use -1dindex to further
pick out the sub-brick on which to operate (why you would do this
I cannot fathom). If you are also using a thresholding operation
(e.g., -1thresh), then you also MUST use -1tindex to choose which
sub-brick counts as the 'threshold' value. When used with sub-brick
selection, 'index' refers the dataset AFTER it has been read in:
-1dindex 1 -1tindex 3 'dset+orig[4..7]'
means to use the #5 sub-brick of dset+orig as the data for merging
and the #7 sub-brick of dset+orig as the threshold values.
** The above example would better be done with
-1tindex 1 'dset+orig[5,7]'
since the default data index is 0. (You would only use -1tindex if
you are actually using a thresholding operation.)
** -1dindex and -1tindex apply to all input datasets.
This page auto-generated on Thu Aug 25 16:49:37 EDT 2005
|
| 3dMINCtoAFNI |
Usage: 3dMINCtoAFNI [-prefix ppp] dataset.mnc Reads in a MINC formatted file and writes it out as an AFNI dataset file pair with the given prefix. If the prefix option isn't used, the input filename will be used, after the '.mnc' is chopped off. NOTES: * Setting environment variable AFNI_MINC_FLOATIZE to Yes will cause MINC datasets to be converted to floats on input. Otherwise, they will be kept in their 'native' data type if possible, which may cause problems with scaling on occasion. * The TR recorded in MINC files is often incorrect. You may need to fix this (or other parameters) using 3drefit.This page auto-generated on Thu Aug 25 16:49:37 EDT 2005 |
| 3dnewid |
Assigns a new ID code to a dataset; this is useful when making
a copy of a dataset, so that the internal ID codes remain unique.
Usage: 3dnewid dataset [dataset ...]
or
3dnewid -fun [n]
to see what n randomly generated ID codes look like.
(If the integer n is not present, 1 ID code is printed.)
How ID codes are created (here and in other AFNI programs):
----------------------------------------------------------
The AFNI ID code generator attempts to create a globally unique
string identifier, using the following steps.
1) A long string is created from the system identifier
information ('uname -a'), the current epoch time in seconds
and microseconds, the process ID, and the number of times
the current process has called the ID code function.
2) This string is then hashed into a 128 bit code using the
MD5 algorithm. (cf. file thd_md5.c)
3) This bit code is then converted to a 22 character string
using Base64 encoding, replacing '/' with '-' and '+' with '_'.
With these changes, the ID code can be used as a Unix filename
or an XML name string. (cf. file thd_base64.c)
4) A 4 character prefix is attached at the beginning to produce
the final ID code. If you set the environment variable
IDCODE_PREFIX to something, then its first 3 characters and an
underscore will be used for the prefix of the new ID code,
provided that the first character is alphabetic and the other
2 alphanumeric; otherwise, the default prefix 'NIH_' will be
used.
The source code is function UNIQ_idcode() in file niml.c.
This page auto-generated on Thu Aug 25 16:49:37 EDT 2005
|
| 3dNLfim |
Program: 3dNLfim
Author: B. Douglas Ward
Initial Release: 19 June 1997
Latest Revision: 07 May 2003
This program calculates a nonlinear regression for each voxel of the
input AFNI 3d+time data set. The nonlinear regression is calculated
by means of a least squares fit to the signal plus noise models which
are specified by the user.
Usage:
3dNLfim
-input fname fname = filename of 3d + time data file for input
[-mask mset] Use the 0 sub-brick of dataset 'mset' as a mask
to indicate which voxels to analyze (a sub-brick
selector is allowed) [default = use all voxels]
[-ignore num] num = skip this number of initial images in the
time series for regresion analysis; default = 3
[-inTR] set delt = TR of the input 3d+time dataset
[The default is to compute with delt = 1.0 ]
[The model functions are calculated using a
time grid of: 0, delt, 2*delt, 3*delt, ... ]
[-time fname] fname = ASCII file containing each time point
in the time series. Defaults to even spacing
given by TR (this option overrides -inTR).
-signal slabel slabel = name of (non-linear) signal model
-noise nlabel nlabel = name of (linear) noise model
-sconstr k c d constraints for kth signal parameter:
c <= gs[k] <= d
-nconstr k c d constraints for kth noise parameter:
c+b[k] <= gn[k] <= d+b[k]
[-nabs] use absolute constraints for noise parameters:
c <= gn[k] <= d
[-nrand n] n = number of random test points
[-nbest b] b = find opt. soln. for b best test points
[-rmsmin r] r = minimum rms error to reject reduced model
[-fdisp fval] display (to screen) results for those voxels
whose f-statistic is > fval
The following commands generate individual AFNI 2 sub-brick datasets:
[-freg fname] perform f-test for significance of the regression;
output 'fift' is written to prefix filename fname
[-frsqr fname] calculate R^2 (coef. of multiple determination);
store along with f-test for regression;
output 'fift' is written to prefix filename fname
[-fsmax fname] estimate signed maximum of signal; store along
with f-test for regression; output 'fift' is
written to prefix filename fname
[-ftmax fname] estimate time of signed maximum; store along
with f-test for regression; output 'fift' is
written to prefix filename fname
[-fpsmax fname] calculate (signed) maximum percentage change of
signal from baseline; output 'fift' is
written to prefix filename fname
[-farea fname] calculate area between signal and baseline; store
with f-test for regression; output 'fift' is
written to prefix filename fname
[-fparea fname] percentage area of signal relative to baseline;
store with f-test for regression; output 'fift'
is written to prefix filename fname
[-fscoef k fname] estimate kth signal parameter gs[k]; store along
with f-test for regression; output 'fift' is
written to prefix filename fname
[-fncoef k fname] estimate kth noise parameter gn[k]; store along
with f-test for regression; output 'fift' is
written to prefix filename fname
[-tscoef k fname] perform t-test for significance of the kth signal
parameter gs[k]; output 'fitt' is written
to prefix filename fname
[-tncoef k fname] perform t-test for significance of the kth noise
parameter gn[k]; output 'fitt' is written
to prefix filename fname
The following commands generate one AFNI 'bucket' type dataset:
[-bucket n prefixname] create one AFNI 'bucket' dataset containing
n sub-bricks; n=0 creates default output;
output 'bucket' is written to prefixname
The mth sub-brick will contain:
[-brick m scoef k label] kth signal parameter regression coefficient
[-brick m ncoef k label] kth noise parameter regression coefficient
[-brick m tmax label] time at max. abs. value of signal
[-brick m smax label] signed max. value of signal
[-brick m psmax label] signed max. value of signal as percent
above baseline level
[-brick m area label] area between signal and baseline
[-brick m parea label] signed area between signal and baseline
as percent of baseline area
[-brick m tscoef k label] t-stat for kth signal parameter coefficient
[-brick m tncoef k label] t-stat for kth noise parameter coefficient
[-brick m resid label] std. dev. of the full model fit residuals
[-brick m rsqr label] R^2 (coefficient of multiple determination)
[-brick m fstat label] F-stat for significance of the regression
The following commands write the time series fit for each voxel
to an AFNI 3d+time dataset:
[-sfit fname] fname = prefix for output 3d+time signal model fit
[-snfit fname] fname = prefix for output 3d+time signal+noise fit
-jobs J Run the program with 'J' jobs (sub-processes).
On a multi-CPU machine, this can speed the
program up considerably. On a single CPU
machine, using this option is silly.
J should be a number from 1 up to the
number of CPU sharing memory on the system.
J=1 is normal (single process) operation.
The maximum allowed value of J is 32.
* For more information on parallelizing, see
http://afni.nimh.nih.gov/afni/doc/misc/parallize.html
* Use -mask to get more speed; cf. 3dAutomask.
This page auto-generated on Thu Aug 25 16:49:37 EDT 2005
|
| 3dnoise |
Usage: 3dnoise [-blast] [-snr fac] [-nl x ] datasets ...
Estimates noise level in 3D datasets, and optionally
set voxels below the noise threshold to zero.
This only works on datasets that are stored as shorts,
and whose elements are all nonnegative.
-blast = Set values at or below the cutoff to zero.
In 3D+time datasets, a spatial location
is set to zero only if a majority of time
points fall below the cutoff; in that case
all the values at that location are zeroed.
-snr fac = Set cutoff to 'fac' times the estimated
noise level. Default fac = 2.5. What to
use for this depends strongly on your MRI
system -- I often use 5, but our true SNR
is about 100 for EPI.
-nl x = Set the noise level to 'x', skipping the
estimation procedure. Also sets fac=1.0.
You can use program 3dClipLevel to get an
estimate of a value for 'x'.
Author -- RW Cox
This page auto-generated on Thu Aug 25 16:49:37 EDT 2005
|
| 3dNotes |
Program: 3dNotes
Author: T. Ross
(c)1999 Medical College of Wisconsin
3dNotes - a program to add, delete and show notes for AFNI datasets.
-----------------------------------------------------------------------
Usage: 3dNotes [-a "string"] [-h "string"][-d num] [-help] dataset
Examples:
3dNotes -a "Subject sneezed in scanner, Aug 13 2004" elvis+orig
3dNotes -h "Subject likes fried PB & banana sandwiches" elvis+orig
3dNotes -HH "Subject has left the building" elvis +orig
3dNotes -d 2 -h "Subject sick of PB'n'banana sandwiches" elvis+orig
-----------------------------------------------------------------------
Explanation of Options:
----------------------
dataset : AFNI compatible dataset [required].
-a "str" : Add the string "str" to the list of notes.
Note that you can use the standard C escape codes,
\n for newline \t for tab, etc.
-h "str" : Append the string "str" to the dataset's history. This
can only appear once on the command line. As this is
added to the history, it cannot easily be deleted. But,
history is propagated to the children of this dataset.
-HH "str" : Replace any existing history note with "str". This
line cannot be used with '-h'.
-d num : deletes note number num.
-help : Displays this screen.
The default action, with no options, is to display the notes for the
dataset. If there are options, all deletions occur first and esentially
simutaneously. Then, notes are added in the order listed on the command
line. If you do something like -d 10 -d 10, it will delete both notes 10
and 11. Don't do that.
This page auto-generated on Thu Aug 25 16:49:37 EDT 2005
|
| 3dnvals |
Prints out the number of sub-bricks in a 3D dataset Usage: 3dnvals [-verb] datasetThis page auto-generated on Thu Aug 25 16:49:37 EDT 2005 |
| 3dOverlap |
Usage: 3dOverlap [options] dset1 dset2 ...
Output = count of number of voxels that are nonzero in ALL
of the input dataset sub-bricks
The result is simply a number printed to stdout. (If a single
brick was input, this is just the count of the number of nonzero
voxels in that brick.)
Options:
-save ppp = Save the count of overlaps at each voxel into a
dataset with prefix 'ppp' (properly thresholded,
this could be used as a mask dataset).
Example:
3dOverlap -save abcnum a+orig b+orig c+orig
3dmaskave -mask 'abcnum+orig<3..3>' a+orig
This page auto-generated on Thu Aug 25 16:49:37 EDT 2005
|
| 3dpc |
Principal Component Analysis of 3D Datasets
Usage: 3dpc [options] dataset dataset ...
Each input dataset may have a sub-brick selector list.
Otherwise, all sub-bricks from a dataset will be used.
OPTIONS:
-dmean = remove the mean from each input brick (across space)
-vmean = remove the mean from each input voxel (across bricks)
[N.B.: -dmean and -vmean are mutually exclusive]
[default: don't remove either mean]
-vnorm = L2 normalize each input voxel time series
[occurs after the de-mean operations above,]
[and before the brick normalization below. ]
-normalize = L2 normalize each input brick (after mean subtraction)
[default: don't normalize]
-pcsave sss = 'sss' is the number of components to save in the output;
it can't be more than the number of input bricks
[default = all of them = number of input bricks]
-prefix pname = Name for output dataset (will be a bucket type);
also, the eigen-timeseries will be in 'pname'.1D
(all of them) and in 'pnameNN.1D' for eigenvalue
#NN individually (NN=00 .. 'sss'-1, corresponding
to the brick index in the output dataset)
[default value of pname = 'pc']
-1ddum ddd = Add 'ddd' dummy lines to the top of each *.1D file.
These lines will have the value 999999, and can
be used to align the files appropriately.
[default value of ddd = 0]
-verbose = Print progress reports during the computations
-float = Save eigen-bricks as floats
[default = shorts, scaled so that |max|=10000]
-mask mset = Use the 0 sub-brick of dataset 'mset' as a mask
to indicate which voxels to analyze (a sub-brick
selector is allowed) [default = use all voxels]
INPUT DATASET NAMES
-------------------
This program accepts datasets that are modified on input according to the
following schemes:
'r1+orig[3..5]' {sub-brick selector}
'r1+orig<100.200>' {sub-range selector}
'r1+orig[3..5]<100..200>' {both selectors}
'3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )' {calculation}
For the gruesome details, see the output of 'afni -help'.
This page auto-generated on Thu Aug 25 16:49:37 EDT 2005
|
| 3dproject |
Projection along cardinal axes from a 3D dataset
Usage: 3dproject [editing options]
[-sum|-max|-amax|-smax] [-output root] [-nsize] [-mirror]
[-RL {all | x1 x2}] [-AP {all | y1 y2}] [-IS {all | z1 z2}]
[-ALL] dataset
Program to produce orthogonal projections from a 3D dataset.
-sum ==> Add the dataset voxels along the projection direction
-max ==> Take the maximum of the voxels [the default is -sum]
-amax ==> Take the absolute maximum of the voxels
-smax ==> Take the signed maximum of the voxels; for example,
-max ==> -7 and 2 go to 2 as the projected value
-amax ==> -7 and 2 go to 7 as the projected value
-smax ==> -7 and 2 go to -7 as the projected value
-first x ==> Take the first value greater than x
-nsize ==> Scale the output images up to 'normal' sizes
(e.g., 64x64, 128x128, or 256x256)
This option only applies to byte or short datasets.
-mirror ==> The radiologists' and AFNI convention is to display
axial and coronal images with the subject's left on
the right of the image; the use of this option will
mirror the axial and coronal projections so that
left is left and right is right.
-output root ==> Output projections will named
root.sag, root.cor, and root.axi
[the default root is 'proj']
-RL all ==> Project in the Right-to-Left direction along
all the data (produces root.sag)
-RL x1 x2 ==> Project in the Right-to-Left direction from
x-coordinate x1 to x2 (mm)
[negative x is Right, positive x is Left]
[OR, you may use something like -RL 10R 20L
to project from x=-10 mm to x=+20 mm ]
-AP all ==> Project in the Anterior-to-Posterior direction along
all the data (produces root.cor)
-AP y1 y2 ==> Project in the Anterior-to-Posterior direction from
y-coordinate y1 to y2 (mm)
[negative y is Anterior, positive y is Posterior]
[OR, you may use something like -AP 10A 20P
to project from y=-10 mm to y=+20 mm ]
-IS all ==> Project in the Inferior-to-Superior direction along
all the data (produces root.axi)
-IS y1 y2 ==> Project in the Inferior-to-Superior direction from
z-coordinate z1 to z2 (mm)
[negative z is Inferior, positive z is Superior]
[OR, you may use something like -IS 10I 20S
to project from z=-10 mm to z=+20 mm ]
-ALL ==> Equivalent to '-RL all -AP all -IS all'
* NOTE that a projection direction will not be used if the bounds aren't
given for that direction; thus, at least one of -RL, -AP, or -IS must
be used, or nothing will be computed!
* NOTE that in the directions transverse to the projection direction,
all the data is used; that is, '-RL -5 5' will produce a full sagittal
image summed over a 10 mm slice, irrespective of the -IS or -AP extents.
* NOTE that the [editing options] are the same as in 3dmerge.
In particular, the '-1thtoin' option can be used to project the
threshold data (if available).
INPUT DATASET NAMES
-------------------
This program accepts datasets that are modified on input according to the
following schemes:
'r1+orig[3..5]' {sub-brick selector}
'r1+orig<100.200>' {sub-range selector}
'r1+orig[3..5]<100..200>' {both selectors}
'3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )' {calculation}
For the gruesome details, see the output of 'afni -help'.
This page auto-generated on Thu Aug 25 16:49:37 EDT 2005
|
| 3drefit |
Changes some of the information inside a 3D dataset's header.
Note that this program does NOT change the .BRIK file at all;
the main purpose of 3drefit is to fix up errors made when
using to3d.
To see the current values stored in a .HEAD file, use the command
'3dinfo dataset'. Using 3dinfo both before and after 3drefit is
a good idea to make sure the changes have been made correctly!
Usage: 3drefit [options] dataset ...
where the options are
-orient code Sets the orientation of the 3D volume(s) in the .BRIK.
The code must be 3 letters, one each from the
pairs {R,L} {A,P} {I,S}. The first letter gives
the orientation of the x-axis, the second the
orientation of the y-axis, the third the z-axis:
R = right-to-left L = left-to-right
A = anterior-to-posterior P = posterior-to-anterior
I = inferior-to-superior S = superior-to-inferior
** WARNING: when changing the orientation, you must be sure
to check the origins as well, to make sure that the volume
is positioned correctly in space.
-xorigin distx Puts the center of the edge voxel off at the given
-yorigin disty distance, for the given axis (x,y,z); distances in mm.
-zorigin distz (x=first axis, y=second axis, z=third axis).
Usually, only -zorigin makes sense. Note that this
distance is in the direction given by the corresponding
letter in the -orient code. For example, '-orient RAI'
would mean that '-zorigin 30' sets the center of the
first slice at 30 mm Inferior. See the to3d manual
for more explanations of axes origins.
** SPECIAL CASE: you can use the string 'cen' in place of
a distance to force that axis to be re-centered.
-xorigin_raw xx Puts the center of the edge voxel at the given COORDINATE
-yorigin_raw yy rather than the given DISTANCE. That is, these values
-zorigin_raw zz directly replace the offsets in the dataset header,
without any possible sign changes.
-duporigin cset Copies the xorigin, yorigin, and zorigin values from
the header of dataset 'cset'.
-dxorigin dx Adds distance 'dx' (or 'dy', or 'dz') to the center
-dyorigin dy coordinate of the edge voxel. Can be used with the
-dzorigin dz values input to the 'Nudge xyz' plugin.
** WARNING: you can't use these options at the same
time you use -orient.
-xdel dimx Makes the size of the voxel the given dimension,
-ydel dimy for the given axis (x,y,z); dimensions in mm.
-zdel dimz ** WARNING: if you change a voxel dimension, you will
probably have to change the origin as well.
-TR time Changes the TR time to a new value (see 'to3d -help').
-notoff Removes the slice-dependent time-offsets.
-Torg ttt Set the time origin of the dataset to value 'ttt'.
(Time origins are set to 0 in to3d.)
** WARNING: these 3 options apply only to 3D+time datasets.
-newid Changes the ID code of this dataset as well.
-nowarp Removes all warping information from dataset.
-apar aset Set the dataset's anatomy parent dataset to 'aset'
** N.B.: The anatomy parent is the dataset from which the
transformation from +orig to +acpc and +tlrc coordinates
is taken. It is appropriate to use -apar when there is
more than 1 anatomical dataset in a directory that has
been transformed. In this way, you can be sure that
AFNI will choose the correct transformation. You would
use this option on all the +orig dataset that are
aligned with 'aset' (i.e., that were acquired in the
same scanning session).
** N.B.: Special cases of 'aset'
aset = NULL --> remove the anat parent info from the dataset
aset = SELF --> set the anat parent to be the dataset itself
-clear_bstat Clears the statistics (min and max) stored for each sub-brick
in the dataset. This is useful if you have done something to
modify the contents of the .BRIK file associated with this
dataset.
-redo_bstat Re-computes the statistics for each sub-brick. Requires
reading the .BRIK file, of course. Also does -clear_bstat
before recomputing statistics, so that if the .BRIK read
fails for some reason, then you'll be left without stats.
-statpar v ... Changes the statistical parameters stored in this
dataset. See 'to3d -help' for more details.
-markers Adds an empty set of AC-PC markers to the dataset,
if it can handle them (is anatomical, is in the +orig
view, and isn't 3D+time).
** WARNING: this will erase any markers that already exist!
-view code Changes the 'view' to be 'code', where the string 'code'
is one of 'orig', 'acpc', or 'tlrc'.
** WARNING: The program will also change the .HEAD and .BRIK
filenames to match. If the dataset filenames already
exist in the '+code' view, then this option will fail.
You will have to rename the dataset files before trying
to use '-view'. If you COPY the files and then use
'-view', don't forget to use '-newid' as well!
-label2 llll Set the 'label2' field in a dataset .HEAD file to the
string 'llll'. (Can be used as in AFNI window titlebars.)
-denote Means to remove all possibly-identifying notes from
the header. This includes the History Note, other text
Notes, keywords, and labels.
-byteorder bbb Sets the byte order string in the header.
Allowable values for 'bbb' are:
LSB_FIRST MSB_FIRST NATIVE_ORDER
Note that this does not change the .BRIK file!
This is done by programs 2swap and 4swap.
-appkey ll Appends the string 'll' to the keyword list for the
whole dataset.
-repkey ll Replaces the keyword list for the dataset with the
string 'll'.
-empkey Destroys the keyword list for the dataset.
-atrcopy dd nn Copy AFNI header attribute named 'nn' from dataset 'dd'
into the header of the dataset(s) being modified.
For more information on AFNI header attributes, see
documentation file README.attributes. More than one
'-atrcopy' option can be used.
**N.B.: This option is for those who know what they are doing!
It can only be used to alter attributes that are NOT
directly mapped into dataset internal structures, since
those structures are mapped back into attribute values
as the dataset is being written to disk. If you want
to change such an attribute, you have to use the
corresponding 3drefit option directly.
-atrstring n 'x' Copy the string 'x' into the dataset(s) being
modified, giving it the attribute name 'n'.
To be safe, the 'x' string should be in quotes.
**N.B.: You can store attributes with almost any name in
the .HEAD file. AFNI will ignore those it doesn't
know anything about. This technique can be a way of
communicating information between programs. However,
when most AFNI programs write a new dataset, they will
not preserve any such non-standard attributes.
-'type' Changes the type of data that is declared for this
dataset, where 'type' is chosen from the following:
ANATOMICAL TYPES
spgr == Spoiled GRASS fse == Fast Spin Echo
epan == Echo Planar anat == MRI Anatomy
ct == CT Scan spct == SPECT Anatomy
pet == PET Anatomy mra == MR Angiography
bmap == B-field Map diff == Diffusion Map
omri == Other MRI abuc == Anat Bucket
FUNCTIONAL TYPES
fim == Intensity fith == Inten+Thr
fico == Inten+Cor fitt == Inten+Ttest
fift == Inten+Ftest fizt == Inten+Ztest
fict == Inten+ChiSq fibt == Inten+Beta
fibn == Inten+Binom figt == Inten+Gamma
fipt == Inten+Poisson fbuc == Func-Bucket
-copyaux auxset Copies the 'auxiliary' data from dataset 'auxset'
over the auxiliary data for the dataset being
modified. Auxiliary data comprises sub-brick labels,
keywords, and statistics codes.
'-copyaux' occurs BEFORE the '-sub' operations below,
so you can use those to alter the auxiliary data
that is copied from auxset.
The options below allow you to attach auxiliary data to sub-bricks
in the dataset. Each option may be used more than once so that
multiple sub-bricks can be modified in a single run of 3drefit.
-sublabel n ll Attach to sub-brick #n the label string 'll'.
-subappkey n ll Add to sub-brick #n the keyword string 'll'.
-subrepkey n ll Replace sub-brick #n's keyword string with 'll'.
-subempkey n Empty out sub-brick #n' keyword string
-substatpar n type v ...
Attach to sub-brick #n the statistical type and
the auxiliary parameters given by values 'v ...',
where 'type' is one of the following:
type Description PARAMETERS
---- ----------- ----------------------------------------
fico Cor SAMPLES FIT-PARAMETERS ORT-PARAMETERS
fitt Ttest DEGREES-of-FREEDOM
fift Ftest NUMERATOR and DENOMINATOR DEGREES-of-FREEDOM
fizt Ztest N/A
fict ChiSq DEGREES-of-FREEDOM
fibt Beta A (numerator) and B (denominator)
fibn Binom NUMBER-of-TRIALS and PROBABILITY-per-TRIAL
figt Gamma SHAPE and SCALE
fipt Poisson MEAN
The following options allow you to modify VOLREG fields:
-vr_mat <VAL1> ... <VAL12> Use these twelve values for VOLREG_MATVEC_index.
[-vr_mat_ind <INDEX>] Index of VOLREG_MATVEC_index field to be modified. Optional, default index is 0.
Note: You can only modify one VOLREG_MATVEC_index at a time.
-vr_center_old <X> <Y> <Z> Use these 3 values for VOLREG_CENTER_OLD.
-vr_center_base <X> <Y> <Z> Use these 3 values for VOLREG_CENTER_BASE.
++ Last program update: 08 Jul 2005
This page auto-generated on Thu Aug 25 16:49:37 EDT 2005
|
| 3dRegAna |
Program: 3dRegAna
Author: B. Douglas Ward
Initial Release: 10 Oct 1997
Latest Revision: 24 Aug 2005
This program performs multiple linear regression analysis.
Usage:
3dRegAna
-rows n number of input datasets
-cols m number of X variables
-xydata X11 X12 ... X1m filename X variables and Y observations
. .
. .
. .
-xydata Xn1 Xn2 ... Xnm filename X variables and Y observations
-model i1 ... iq : j1 ... jr definition of linear regression model;
reduced model:
Y = f(Xj1,...,Xjr)
full model:
Y = f(Xj1,...,Xjr,Xi1,...,Xiq)
[-diskspace] print out disk space required for program execution
[-workmem mega] number of megabytes of RAM to use for statistical
workspace (default = 12)
[-rmsmin r] r = minimum rms error to reject constant model
[-fdisp fval] display (to screen) results for those voxels
whose F-statistic is > fval
[-flof alpha] alpha = minimum p value for F due to lack of fit
The following commands generate individual AFNI 2 sub-brick datasets:
[-fcoef k prefixname] estimate of kth regression coefficient
along with F-test for the regression
is written to AFNI `fift' dataset
[-rcoef k prefixname] estimate of kth regression coefficient
along with coef. of mult. deter. R^2
is written to AFNI `fith' dataset
[-tcoef k prefixname] estimate of kth regression coefficient
along with t-test for the coefficient
is written to AFNI `fitt' dataset
The following commands generate one AFNI 'bucket' type dataset:
[-bucket n prefixname] create one AFNI 'bucket' dataset having
n sub-bricks; n=0 creates default output;
output 'bucket' is written to prefixname
The mth sub-brick will contain:
[-brick m coef k label] kth parameter regression coefficient
[-brick m fstat label] F-stat for significance of regression
[-brick m rstat label] coefficient of multiple determination R^2
[-brick m tstat k label] t-stat for kth regression coefficient
N.B.: For this program, the user must specify 1 and only 1 sub-brick
with each -xydata command. That is, if an input dataset contains
more than 1 sub-brick, a sub-brick selector must be used, e.g.:
-xydata 2.17 4.59 7.18 'fred+orig[3]'
INPUT DATASET NAMES
-------------------
This program accepts datasets that are modified on input according to the
following schemes:
'r1+orig[3..5]' {sub-brick selector}
'r1+orig<100.200>' {sub-range selector}
'r1+orig[3..5]<100..200>' {both selectors}
'3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )' {calculation}
For the gruesome details, see the output of 'afni -help'.
This page auto-generated on Thu Aug 25 16:49:37 EDT 2005
|
| 3drename |
Usage 1: 3drename old_prefix new_prefix
Will rename all datasets using the old_prefix to use the new_prefix;
3drename fred ethel
will change fred+orig.HEAD to ethel+orig.HEAD
fred+orig.BRIK to ethel+orig.BRIK
fred+tlrc.HEAD to ethel+tlrc.HEAD
fred+tlrc.BRIK.gz to ethel+tlrc.BRIK.gz
Usage 2: 3drename old_prefix+view new_prefix
Will rename only the dataset with the given view (orig, acpc, tlrc).
This page auto-generated on Thu Aug 25 16:49:37 EDT 2005
|
| 3dresample |
/var/www/html/pub/dist/bin/linux_gcc32/3dresample - reorient and/or resample a dataset
This program can be used to change the orientation of a
dataset (via the -orient option), or the dx,dy,dz
grid spacing (via the -dxyz option), or change them
both to match that of a master dataset (via the -master
option).
Note: if both -master and -dxyz are used, the dxyz values
will override those from the master dataset.
** Warning: this program is not meant to transform datasets
between view types (such as '+orig' and '+tlrc').
For that purpose, please see '3dfractionize -help'.
------------------------------------------------------------
usage: /var/www/html/pub/dist/bin/linux_gcc32/3dresample [options] -prefix OUT_DSET -inset IN_DSET
examples:
/var/www/html/pub/dist/bin/linux_gcc32/3dresample -orient asl -rmode NN -prefix asl.dset -inset in+orig
/var/www/html/pub/dist/bin/linux_gcc32/3dresample -dxyz 1.0 1.0 0.9 -prefix 119.dset -inset in+tlrc
/var/www/html/pub/dist/bin/linux_gcc32/3dresample -master master+orig -prefix new.dset -inset old+orig
note:
Information about a dataset's voxel size and orientation
can be found in the output of program 3dinfo
------------------------------------------------------------
options:
-help : show this help information
-hist : output the history of program changes
-debug LEVEL : print debug info along the way
e.g. -debug 1
default level is 0, max is 2
-version : show version information
-dxyz DX DY DZ : resample to new dx, dy and dz
e.g. -dxyz 1.0 1.0 0.9
default is to leave unchanged
Each of DX,DY,DZ must be a positive real number,
and will be used for a voxel delta in the new
dataset (according to any new orientation).
-orient OR_CODE : reorient to new axis order.
e.g. -orient asl
default is to leave unchanged
The orientation code is a 3 character string,
where the characters come from the respective
sets {A,P}, {I,S}, {L,R}.
For example OR_CODE = LPI is the standard
'neuroscience' orientation, where the x-axis is
Left-to-Right, the y-axis is Posterior-to-Anterior,
and the z-axis is Inferior-to-Superior.
-rmode RESAM : use this resampling method
e.g. -rmode Linear
default is NN (nearest neighbor)
The resampling method string RESAM should come
from the set {'NN', 'Li', 'Cu', 'Bk'}. These
are for 'Nearest Neighbor', 'Linear', 'Cubic'
and 'Blocky' interpolation, respectively.
See 'Anat resam mode' under the 'Define Markers'
window in afni.
-master MAST_DSET: align dataset grid to that of MAST_DSET
e.g. -master master.dset+orig
Get dxyz and orient from a master dataset. The
resulting grid will match that of the master. This
option can be used with -dxyz, but not with -orient.
-prefix OUT_DSET : required prefix for output dataset
e.g. -prefix reori.asl.pickle
-inset IN_DSET : required input dataset to reorient
e.g. -inset old.dset+orig
------------------------------------------------------------
Author: R. Reynolds - Version 1.8 <AUGUST 2005 3,>
This page auto-generated on Thu Aug 25 16:49:37 EDT 2005
|
| 3dretroicor |
Usage: 3dretroicor [options] dataset
Performs Retrospective Image Correction for physiological
motion effects, using a slightly modified version of the
RETROICOR algorithm described in:
Glover, G. H., Li, T., & Ress, D. (2000). Image-based method
for retrospective correction of physiological motion effects in
fMRI: RETROICOR. Magnetic Resonance in Medicine, 44, 162-167.
Options (defaults in []'s):
-ignore = The number of initial timepoints to ignore in the
input (These points will be passed through
uncorrected) [0]
-prefix = Prefix for new, corrected dataset [retroicor]
-card = 1D cardiac data file for cardiac correction
-cardphase = Filename for 1D cardiac phase output
-threshold = Threshold for detection of R-wave peaks in input
(Make sure it's above the background noise level;
Try 3/4 or 4/5 times range plus minimum) [1]
-resp = 1D respiratory waveform data for correction
-respphase = Filename for 1D resp phase output
-order = The order of the correction (2 is typical;
higher-order terms yield little improvement
according to Glover et al.) [2]
-help = Display this message and stop (must be first arg)
Dataset: 3D+time dataset to process
** The input dataset and at least one of -card and -resp are
required.
NOTES
-----
The durations of the physiological inputs are assumed to equal
the duration of the dataset. Any constant sampling rate may be
used, but 40 Hz seems to be acceptable. This program's cardiac
peak detection algorithm is rather simplistic, so you might try
using the scanner's cardiac gating output (transform it to a
spike wave if necessary).
This program uses slice timing information embedded in the
dataset to estimate the proper cardiac/respiratory phase for
each slice. It makes sense to run this program before any
program that may destroy the slice timings (e.g. 3dvolreg for
motion correction).
Author -- Fred Tam, August 2002
INPUT DATASET NAMES
-------------------
This program accepts datasets that are modified on input according to the
following schemes:
'r1+orig[3..5]' {sub-brick selector}
'r1+orig<100.200>' {sub-range selector}
'r1+orig[3..5]<100..200>' {both selectors}
'3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )' {calculation}
For the gruesome details, see the output of 'afni -help'.
This page auto-generated on Thu Aug 25 16:49:37 EDT 2005
|
| 3dROIstats |
Usage: 3dROIstats -mask[n] mset [options] datasets
Options:
-mask[n] mset Means to use the dataset 'mset' as a mask:
If n is present, it specifies which sub-brick
in mset to use a la 3dcalc. Note: do not include
the brackets if specifing a sub-brick, they are
there to indicate that they are optional. If not
present, 0 is assumed
Voxels with the same nonzero values in 'mset'
will be statisticized from 'dataset'. This will
be repeated for all the different values in mset.
I.e. all of the 1s in mset are one ROI, as are all
of the 2s, etc.
Note that the mask dataset and the input dataset
must have the same number of voxels and that mset
must be BYTE or SHORT (i.e., float masks won't work
without the -mask_f2short option).
-mask_f2short Tells the program to convert a float mask to short
integers, by simple rounding. This option is needed
when the mask dataset is a 1D file, for instance
(since 1D files are read as floats).
Be careful with this, it may not be appropriate to do!
-numROI n Forces the assumption that the mask dataset's ROIs are
denoted by 1 to n inclusive. Normally, the program
figures out the ROIs on its own. This option is
useful if a) you are certain that the mask dataset
has no values outside the range [0 n], b) there may
be some ROIs missing between [1 n] in the mask data-
set and c) you want those columns in the output any-
way so the output lines up with the output from other
invocations of 3dROIstats. Confused? Then don't use
this option!
-debug Print out debugging information
-quiet Do not print out labels for columns or rows
The following options specify what stats are computed. By default
the mean is always computed.
-nzmean Compute the mean using only non_zero voxels. Implies
the oppisite for the normal mean computed
-nzvoxels Compute the number of non_zero voxels
-minmax Compute the min/max of all voxels
-nzminmax Compute the min/max of non_zero voxels
-sigma Means to compute the standard deviation as well
as the mean.
-summary Only output a summary line with the grand mean across all briks
in the input dataset.
The output is printed to stdout (the terminal), and can be
saved to a file using the usual redirection operation '>'.
N.B.: The input datasets and the mask dataset can use sub-brick
selectors, as detailed in the output of 3dcalc -help.
INPUT DATASET NAMES
-------------------
This program accepts datasets that are modified on input according to the
following schemes:
'r1+orig[3..5]' {sub-brick selector}
'r1+orig<100.200>' {sub-range selector}
'r1+orig[3..5]<100..200>' {both selectors}
'3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )' {calculation}
For the gruesome details, see the output of 'afni -help'.
This page auto-generated on Thu Aug 25 16:49:37 EDT 2005
|
| 3drotate |
Usage: 3drotate [options] dataset
Rotates and/or translates all bricks from an AFNI dataset.
'dataset' may contain a sub-brick selector list.
GENERIC OPTIONS:
-prefix fname = Sets the output dataset prefix name to be 'fname'
-verbose = Prints out progress reports (to stderr)
OPTIONS TO SPECIFY THE ROTATION/TRANSLATION:
-------------------------------------------
*** METHOD 1 = direct specification:
At most one of these shift options can be used:
-ashift dx dy dz = Shifts the dataset 'dx' mm in the x-direction, etc.,
AFTER rotation.
-bshift dx dy dz = Shifts the dataset 'dx' mm in the x-direction, etc.,
BEFORE rotation.
The shift distances by default are along the (x,y,z) axes of the dataset
storage directions (see the output of '3dinfo dataset'). To specify them
anatomically, you can suffix a distance with one of the symbols
'R', 'L', 'A', 'P', 'I', and 'S', meaning 'Right', 'Left', 'Anterior',
'Posterior', 'Inferior', and 'Superior', respectively.
-rotate th1 th2 th3
Specifies the 3D rotation to be composed of 3 planar rotations:
1) 'th1' degrees about the 1st axis, followed by
2) 'th2' degrees about the (rotated) 2nd axis, followed by
3) 'th3' degrees about the (doubly rotated) 3rd axis.
Which axes are used for these rotations is specified by placing
one of the symbols 'R', 'L', 'A', 'P', 'I', and 'S' at the end
of each angle (e.g., '10.7A'). These symbols denote rotation
about the 'Right-to-Left', 'Left-to-Right', 'Anterior-to-Posterior',
'Posterior-to-Anterior', 'Inferior-to-Superior', and
'Superior-to-Inferior' axes, respectively. A positive rotation is
defined by the right-hand rule.
*** METHOD 2 = copy from output of 3dvolreg:
-rotparent rset
Specifies that the rotation and translation should be taken from the
first 3dvolreg transformation found in the header of dataset 'rset'.
-gridparent gset
Specifies that the output dataset of 3drotate should be shifted to
match the grid of dataset 'gset'. Can only be used with -rotparent.
This dataset should be one this is properly aligned with 'rset' when
overlaid in AFNI.
* If -rotparent is used, then don't use -matvec, -rotate, or -[ab]shift.
* If 'gset' has a different number of slices than the input dataset,
then the output dataset will be zero-padded in the slice direction
to match 'gset'.
* These options are intended to be used to align datasets between sessions:
S1 = SPGR from session 1 E1 = EPI from session 1
S2 = SPGR from session 2 E2 = EPI from session 2
3dvolreg -twopass -twodup -base S1+orig -prefix S2reg S2+orig
3drotate -rotparent S2reg+orig -gridparent E1+orig -prefix E2reg E2+orig
The result will have E2reg rotated from E2 in the same way that S2reg
was from S2, and also shifted/padded (as needed) to overlap with E1.
*** METHOD 3 = give the transformation matrix/vector directly:
-matvec_dicom mfile
-matvec_order mfile
Specifies that the rotation and translation should be read from file
'mfile', which should be in the format
u11 u12 u13 v1
u21 u22 u23 v2
u31 u32 u33 u3
where each 'uij' and 'vi' is a number. The 3x3 matrix [uij] is the
orthogonal matrix of the rotation, and the 3-vector [vi] is the -ashift
vector of the translation.
*** METHOD 4 = copy the transformation from 3dTagalign:
-matvec_dset mset
Specifies that the rotation and translation should be read from
the .HEAD file of dataset 'mset', which was created by program
3dTagalign.
* If -matvec_dicom is used, the matrix and vector are given in Dicom
coordinate order (+x=L, +y=P, +z=S). This is the option to use
if mfile is generated using 3dTagalign -matvec mfile.
* If -matvec_order is used, the the matrix and vector are given in the
coordinate order of the dataset axes, whatever they may be.
* You can't mix -matvec_* options with -rotate and -*shift.
*** METHOD 5 = input rotation+shift parameters from an ASCII file:
-dfile dname *OR* -1Dfile dname
With these methods, the movement parameters for each sub-brick
of the input dataset are read from the file 'dname'. This file
should consist of columns of numbers in ASCII format. Six (6)
numbers are read from each line of the input file. If the
'-dfile' option is used, each line of the input should be at
least 7 numbers, and be of the form
ignored roll pitch yaw dS dL dP
If the '-1Dfile' option is used, then each line of the input
should be at least 6 numbers, and be of the form
roll pitch yaw dS dL dP
(These are the forms output by the '-dfile' and
'-1Dfile' options of program 3dvolreg; see that
program's -help output for the hideous details.)
The n-th sub-brick of the input dataset will be transformed
using the parameters from the n-th line of the dname file.
If the dname file doesn't contain as many lines as the
input dataset has sub-bricks, then the last dname line will
be used for all subsequent sub-bricks. Excess columns or
rows will be ignored.
N.B.: Rotation is always about the center of the volume.
If the parameters are derived from a 3dvolreg run
on a dataset with a different center in xyz-space,
the results may not be what you want!
N.B.: You can't use -dfile/-1Dfile with -points (infra).
POINTS OPTIONS (instead of datasets):
------------------------------------
-points
-origin xo yo zo
These options specify that instead of rotating a dataset, you will
be rotating a set of (x,y,z) points. The points are read from stdin.
* If -origin is given, the point (xo,yo,zo) is used as the center for
the rotation.
* If -origin is NOT given, and a dataset is given at the end of the
command line, then the center of the dataset brick is used as
(xo,yo,zo). The dataset will NOT be rotated if -points is given.
* If -origin is NOT given, and NO dataset is given at the end of the
command line, then xo=yo=zo=0 is assumed. You probably don't
want this.
* (x,y,z) points are read from stdin as 3 ASCII-formatted numbers per
line, as in 3dUndump. Any succeeding numbers on input lines will
be copied to the output, which will be written to stdout.
* The input (x,y,z) coordinates are taken in the same order as the
axes of the input dataset. If there is no input dataset, then
negative x = R positive x = L }
negative y = A positive y = P } e.g., the DICOM order
negative z = I positive z = S }
One way to dump some (x,y,z) coordinates from a dataset is:
3dmaskdump -mask something+tlrc -o xyzfilename -noijk
'3dcalc( -a dset+tlrc -expr x -datum float )'
'3dcalc( -a dset+tlrc -expr y -datum float )'
'3dcalc( -a dset+tlrc -expr z -datum float )'
(All of this should be on one command line.)
============================================================================
Example: 3drotate -prefix Elvis -bshift 10S 0 0 -rotate 30R 0 0 Sinatra+orig
This will shift the input 10 mm in the superior direction, followed by a 30
degree rotation about the Right-to-Left axis (i.e., nod the head forward).
============================================================================
Algorithm: The rotation+shift is decomposed into 4 1D shearing operations
(a 3D generalization of Paeth's algorithm). The interpolation
(i.e., resampling) method used for these shears can be controlled
by the following options:
-Fourier = Use a Fourier method (the default: most accurate; slowest).
-NN = Use the nearest neighbor method.
-linear = Use linear (1st order polynomial) interpolation (least accurate).
-cubic = Use the cubic (3rd order) Lagrange polynomial method.
-quintic = Use the quintic (5th order) Lagrange polynomial method.
-heptic = Use the heptic (7th order) Lagrange polynomial method.
-Fourier_nopad = Use the Fourier method WITHOUT padding
* If you don't mind - or even want - the wraparound effect
* Works best if dataset grid size is a power of 2, possibly
times powers of 3 and 5, in all directions being altered.
* The main use would seem to be to un-wraparound poorly
reconstructed images, by using a shift; for example:
3drotate -ashift 30A 0 0 -Fourier_nopad -prefix Anew A+orig
* This option is also available in the Nudge Dataset plugin.
-clipit = Clip results to input brick range [now the default].
-noclip = Don't clip results to input brick range.
-zpad n = Zeropad around the edges by 'n' voxels during rotations
(these edge values will be stripped off in the output)
N.B.: Unlike to3d, in this program '-zpad' adds zeros in
all directions.
N.B.: The environment variable AFNI_ROTA_ZPAD can be used
to set a nonzero default value for this parameter.
INPUT DATASET NAMES
-------------------
This program accepts datasets that are modified on input according to the
following schemes:
'r1+orig[3..5]' {sub-brick selector}
'r1+orig<100.200>' {sub-range selector}
'r1+orig[3..5]<100..200>' {both selectors}
'3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )' {calculation}
For the gruesome details, see the output of 'afni -help'.
This page auto-generated on Thu Aug 25 16:49:37 EDT 2005
|
| 3dRowFillin |
Usage: 3dRowFillin [options] dataset
Extracts 1D rows in the given direction from a 3D dataset,
searches for blank (zero) regions, and fills them in if
the blank region isn't too large and it is flanked by
the same value on either edge. For example:
input row = 0 1 2 0 0 2 3 0 3 0 0 4 0
output row = 0 1 2 2 2 2 3 3 3 0 0 4 0
OPTIONS:
-maxgap N = set the maximum length of a blank region that
will be filled in to 'N' [default=9].
-dir D = set the direction of fill to 'D', which can
be one of the following:
A-P, P-A, I-S, S-I, L-R, R-L, x, y, z
The first 6 are anatomical directions;
the last 3 are reference to the dataset
internal axes [no default value].
-prefix P = set the prefix to 'P' for the output dataset.
N.B.: If the input dataset has more than one sub-brick,
only the first one will be processed.
The intention of this program is to let you fill in slice gaps
made when drawing ROIs with the 'Draw Dataset' plugin. If you
draw every 5th coronal slice, say, then you could fill in using
3dRowFillin -maxgap 4 -dir A-P -prefix fredfill fred+orig
This page auto-generated on Thu Aug 25 16:49:37 EDT 2005
|
| 3dSkullStrip |
Usage: A program to extract the brain from surrounding.
tissue from MRI T1-weighted images. The largely automated
process consists of three steps:
1- Preprocessing of volume to remove gross spatial image
non-uniformity artifacts and reposition the brain in
a reasonable manner for convenience.
2- Expand a spherical surface iteratively until it envelopes
the brain. This is a modified version of the BET algorithm:
Fast robust automated brain extraction,
by Stephen M. Smith, HBM 2002 v 17:3 pp 143-155
Modifications include the use of:
. outer brain surface
. expansion driven by data inside and outside the surface
. avoidance of eyes and ventricles
. a set of operations to avoid the clipping of certain brain
areas and reduce leakage into the skull in heavily shaded
data
. two additional processing stages to ensure convergence and
reduction of clipped areas.
3- The creation of various masks and surfaces modeling brain
and portions of the skull
3dSkullStrip < -input VOL >
[< -o_TYPE PREFIX >] [< -prefix Vol_Prefix >]
[< -spatnorm >] [< -no_spatnorm >] [< -write_spatnorm >]
[< -niter N_ITER >] [< -ld LD >]
[< -shrink_fac SF >] [< -var_shrink_fac >]
[< -no_var_shrink_fac >] [< shrink_fac_bot_lim SFBL >]
[< -pushout >] [< -no_pushout >] [< -exp_frac FRAC]
[< -touchup >] [< -no_touchup >]
[< -fill_hole R >] [< -NN_smooth NN_SM >]
[< -smooth_final SM >] [< -avoid_vent >] [< -no_avoid_vent >]
[< -use_skull >] [< -no_use_skull >]
[< -avoid_eyes >] [< -no_avoid_eyes >]
[< -perc_int PERC_INT >]
[< -max_inter_iter MII >] [-mask_vol]
[< -debug DBG >] [< -node_dbg NODE_DBG >]
[< -demo_pause >]
NOTE: Program is in Beta mode, please report bugs and strange failures
to ziad@nih.gov
Mandatory parameters:
-input VOL: Input AFNI (or AFNI readable) volume.
Optional Parameters:
-o_TYPE PREFIX: prefix of output surface.
where TYPE specifies the format of the surface
and PREFIX is, well, the prefix.
TYPE is one of: fs, 1d (or vec), sf, ply.
More on that below.
-prefix VOL_PREFIX: prefix of output volume.
If not specified, the prefix is the same
as the one used with -o_TYPE.
The output volume is skull stripped version
of the input volume. In the earlier version
of the program, a mask volume was written out.
You can still get that mask volume instead of the
skull-stripped volume with the option -mask_vol .
-mask_vol: Output a mask volume instead of a skull-stripped
volume.
The mask volume containes:
0: Voxel outside surface
1: Voxel just outside the surface. This means the voxel
center is outside the surface but inside the
bounding box of a triangle in the mesh.
2: Voxel intersects the surface (a triangle), but center
lies outside.
3: Voxel contains a surface node.
4: Voxel intersects the surface (a triangle), center lies
inside surface.
5: Voxel just inside the surface. This means the voxel
center is inside the surface and inside the
bounding box of a triangle in the mesh.
6: Voxel inside the surface.
-spat_norm: (Default) Perform spatial normalization first.
This is a necessary step unless the volume has
been 'spatnormed' already.
-no_spatnorm: Do not perform spatial normalization.
Use this option only when the volume
has been run through the 'spatnorm' process
-spatnorm_dxyz DXYZ: Use DXY for the spatial resolution of the
spatially normalized volume. The default
is the lowest of all three dimensions.
For human brains, use DXYZ of 1.0, for
primate brain, use the default setting.
-write_spatnorm: Write the 'spatnormed' volume to disk.
-niter N_ITER: Number of iterations. Default is 250
For denser meshes, you need more iterations
N_ITER of 750 works for LD of 50.
-ld LD: Parameter to control the density of the surface.
Default is 20. See CreateIcosahedron -help
for details on this option.
-shrink_fac SF: Parameter controlling the brain vs non-brain
intensity threshold (tb). Default is 0.6.
tb = (Imax - t2) SF + t2
where t2 is the 2 percentile value and Imax is the local
maximum, limited to the median intensity value.
For more information on tb, t2, etc. read the BET paper
mentioned above. Note that in 3dSkullStrip, SF can vary across
iterations and might be automatically clipped in certain areas.
SF can vary between 0 and 1.
0: Intensities < median inensity are considered non-brain
1: Intensities < t2 are considered non-brain
-var_shrink_fac: Vary the shrink factor with the number of
iterations. This reduces the likelihood of a surface
getting stuck on large pools of CSF before reaching
the outer surface of the brain. (Default)
-no_var_shrink_fac: Do not use var_shrink_fac.
-shrink_fac_bot_lim SFBL: Do not allow the varying SF to go
below SFBL . Default 0.65.
This option helps reduce potential for leakage below
the cerebellum.
-pushout: Consider values above each node in addition to values
below the node when deciding on expansion. (Default)
-no_pushout: Do not use -pushout.
-exp_frac FRAC: Speed of expansion (see BET paper). Default is 0.1.
-touchup: Perform touchup operations at end to include
areas not covered by surface expansion.
Use -touchup -touchup for aggressive makeup.
(Default is -touchup)
-no_touchup: Do not use -touchup
-fill_hole R: Fill small holes that can result from small surface
intersections caused by the touchup operation.
R is the maximum number of pixels on the side of a hole
that can be filled. Big holes are not filled.
If you use -touchup, the default R is 10. Otherwise
the default is 0.
This is a less than elegant solution to the small
intersections which are usually eliminated
automatically.
-NN_smooth NN_SM: Perform Nearest Neighbor coordinate interpolation
every few iterations. Default is 72
-smooth_final SM: Perform final surface smoothing after all iterations.
Default is 20 smoothing iterations.
Smoothing is done using Taubin's method,
see SurfSmooth -help for detail.
-avoid_vent: avoid ventricles. Default.
-no_avoid_vent: Do not use -avoid_vent.
-avoid_eyes: avoid eyes. Default
-no_avoid_eyes: Do not use -avoid_eyes.
-use_skull: Use outer skull to limit expansion of surface into
the skull due to very strong shading artifacts.
This option is buggy at the moment, use it only
if you have leakage into skull.
-no_use_skull: Do not use -use_skull (Default).
-send_no_skull: Do not send the skull surface to SUMA if you are
using -talk_suma
-perc_int PERC_INT: Percentage of segments allowed to intersect
surface. Ideally this should be 0 (Default).
However, few surfaces might have small stubborn
intersections that produce a few holes.
PERC_INT should be a small number, typically
between 0 and 0.1
-max_inter_iter N_II: Number of iteration to remove intersection
problems. With each iteration, the program
automatically increases the amount of smoothing
to get rid of intersections. Default is 4
-blur_fwhm FWHM: Blur dset after spatial normalization.
Recommended when you have lots of CSF in brain
and when you have protruding gyri (finger like)
Recommended value is 2..4.
-interactive: Make the program stop at various stages in the
segmentation process for a prompt from the user
to continue or skip that stage of processing.
This option is best used in conjunction with options
-talk_suma and -feed_afni
-demo_pause: Pause at various step in the process to facilitate
interactive demo while 3dSkullStrip is communicating
with AFNI and SUMA. See 'Eye Candy' mode below and
-talk_suma option.
Specifying output surfaces using -o_TYPE options:
-o_TYPE outSurf specifies the output surface,
TYPE is one of the following:
fs: FreeSurfer ascii surface.
fsp: FeeSurfer ascii patch surface.
In addition to outSurf, you need to specify
the name of the parent surface for the patch.
using the -ipar_TYPE option.
This option is only for ConvertSurface
sf: SureFit surface.
For most programs, you are expected to specify prefix:
i.e. -o_sf brain. In some programs, you are allowed to
specify both .coord and .topo file names:
i.e. -o_sf XYZ.coord TRI.topo
The program will determine your choice by examining
the first character of the second parameter following
-o_sf. If that character is a '-' then you have supplied
a prefix and the program will generate the coord and topo names.
vec (or 1D): Simple ascii matrix format.
For most programs, you are expected to specify prefix:
i.e. -o_1D brain. In some programs, you are allowed to
specify both coord and topo file names:
i.e. -o_1D brain.1D.coord brain.1D.topo
coord contains 3 floats per line, representing
X Y Z vertex coordinates.
topo contains 3 ints per line, representing
v1 v2 v3 triangle vertices.
ply: PLY format, ascii or binary.
SUMA communication options:
-talk_suma: Send progress with each iteration to SUMA.
-refresh_rate rps: Maximum number of updates to SUMA per second.
The default is the maximum speed.
-send_kth kth: Send the kth element to SUMA (default is 1).
This allows you to cut down on the number of elements
being sent to SUMA.
-sh <SUMAHOST>: Name (or IP address) of the computer running SUMA.
This parameter is optional, the default is 127.0.0.1
-ni_text: Use NI_TEXT_MODE for data transmission.
-ni_binary: Use NI_BINARY_MODE for data transmission.
(default is ni_binary).
-feed_afni: Send updates to AFNI via SUMA's talk.
-visual: Equivalent to using -talk_suma -feed_afni -send_kth 5
-debug DBG: debug levels of 0 (default), 1, 2, 3.
This is no Rick Reynolds debug, which is oft nicer
than the results, but it will do.
-node_dbg NODE_DBG: Output lots of parameters for node
NODE_DBG for each iteration.
Tips:
I ran the program with the default parameters on 200+ datasets.
The results were quite good in all but a couple of instances, here
are some tips on fixing trouble spots:
Clipping in frontal areas, close to the eye balls:
+ Try -no_avoid_eyes option
Clipping in general:
+ Use lower -shrink_fac, start with 0.5 then 0.4
Some lobules are not included:
+ Use a denser mesh (like -ld 50) and increase iterations
(-niter 750). The program will take much longer to run in that case.
+ Instead of using denser meshes, you could try blurring the data
before skull stripping. Something like -blur_fwhm 2 did
wonders for some of my data with the default options of 3dSkullStrip
Blurring is a lot faster than increasing mesh density.
+ Use also a smaller -shrink_fac is you have lots of CSF between gyri.
Massive chunks missing:
+ If brain has very large ventricles and lots of CSF between gyri, the
ventricles will keep attracting the surface inwards. In such cases, use
the -visual option to see what is happening and try these options to
reduce the severity of the problem:
-blur_fwhm 2 -use_skull
Eye Candy Mode: (previous restrictions removed)
You can run BrainWarp and have it send successive iterations
to SUMA and AFNI. This is very helpful in following the
progression of the algorithm and determining the source
of trouble, if any.
Example:
afni -niml -yesplugouts &
suma -niml &
3dSkullStrip -input Anat+orig -o_ply anat_brain -talk_suma -feed_afni -send_kth 5
Common Debugging Options:
[-trace]: Turns on In/Out debug and Memory tracing.
For speeding up the tracing log, I recommend
you redirect stdout to a file when using this option.
For example, if you were running suma you would use:
suma -spec lh.spec -sv ... > TraceFile
This option replaces the old -iodbg and -memdbg.
[-TRACE]: Turns on extreme tracing.
[-nomall]: Turn off memory tracing.
[-yesmall]: Turn on memory tracing (default).
[-novolreg]: Ignore any Volreg or Tagalign transformations
present in the Surface Volume.
NOTE: For programs that output results to stdout
(that is to your shell/screen), the debugging info
might get mixed up with your results.
++ SUMA version 2004_12_29
CVS tag:
SUMA_2005_04_29_1733
Compile Date:
Aug 25 2005
Ziad S. Saad SSCC/NIMH/NIH ziad@nih.gov
This page auto-generated on Thu Aug 25 16:49:37 EDT 2005
|
| 3dSpatNorm |
**ERROR: -help is unknown option!This page auto-generated on Thu Aug 25 16:49:37 EDT 2005 |
| 3dStatClust |
Program: 3dStatClust
Author: B. Douglas Ward
Initial Release: 08 October 1999
Latest Revision: 15 August 2001
Perform agglomerative hierarchical clustering for user specified
parameter sub-bricks, for all voxels whose threshold statistic
is above a user specified value.
Usage: 3dStatClust options datasets
where the options are:
-prefix pname = Use 'pname' for the output dataset prefix name.
OR [default='SC']
-output pname
-session dir = Use 'dir' for the output dataset session directory.
[default='./'=current working directory]
-verb = Print out verbose output as the program proceeds.
Options for calculating distance between parameter vectors:
-dist_euc = Calculate Euclidean distance between parameters
-dist_ind = Statistical distance for independent parameters
-dist_cor = Statistical distance for correlated parameters
The default option is: Euclidean distance.
-thresh t tname = Use threshold statistic from file tname.
Only voxels whose threshold statistic is greater
than t in abolute value will be considered.
[If file tname contains more than 1 sub-brick,
the threshold stat. sub-brick must be specified!]
-nclust n = This specifies the maximum number of clusters for
output (= number of sub-bricks in output dataset).
Command line arguments after the above are taken as parameter datasets.
INPUT DATASET NAMES
-------------------
This program accepts datasets that are modified on input according to the
following schemes:
'r1+orig[3..5]' {sub-brick selector}
'r1+orig<100.200>' {sub-range selector}
'r1+orig[3..5]<100..200>' {both selectors}
'3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )' {calculation}
For the gruesome details, see the output of 'afni -help'.
This page auto-generated on Thu Aug 25 16:49:37 EDT 2005
|
| 3dSurf2Vol |
3dSurf2Vol - map data from a surface domain to an AFNI volume domain
usage: 3dSurf2Vol [options] -spec SPEC_FILE -surf_A SURF_NAME \
-grid_parent AFNI_DSET -sv SURF_VOL \
-map_func MAP_FUNC -prefix OUTPUT_DSET
This program is meant to take as input a pair of surfaces,
optionally including surface data, and an AFNI grid parent
dataset, and to output a new AFNI dataset consisting of the
surface data mapped to the dataset grid space. The mapping
function determines how to map the surface values from many
nodes to a single voxel.
Surfaces (from the spec file) are specified using '-surf_A'
(and '-surf_B', if a second surface is input). If two
surfaces are input, then the computed segments over node
pairs will be in the direction from surface A to surface B.
The basic form of the algorithm is:
o for each node pair (or single node)
o form a segment based on the xyz node coordinates,
adjusted by any '-f_pX_XX' options
o divide the segment up into N steps, according to
the '-f_steps' option
o for each segment point
o if the point is outside the space of the output
dataset, skip it
o locate the voxel in the output dataset which
corresponds to this segment point
o if the '-cmask' option was given, and the voxel
is outside the implied mask, skip it
o if the '-f_index' option is by voxel, and this
voxel has already been considered, skip it
o insert the surface node value, according to the
user-specified '-map_func' option
Surface Coordinates:
Surface coordinates are assumed to be in the Dicom
orientation. This information may come from the option
pair of '-spec' and '-sv', with which the user provides
the name of the SPEC FILE and the SURFACE VOLUME, along
with '-surf_A' and optionally '-surf_B', used to specify
actual surfaces by name. Alternatively, the surface
coordinates may come from the '-surf_xyz_1D' option.
See these option descriptions below.
Note that the user must provide either the three options
'-spec', '-sv' and '-surf_A', or the single option,
'-surf_xyz_1D'.
Surface Data:
Surface domain data can be input via the '-sdata_1D'
option. In such a case, the data is with respect to the
input surface. The first column of the sdata_1D file
should be a node index, and following columns are that
node's data. See the '-sdata_1D' option for more info.
If the surfaces have V values per node (pair), then the
resulting AFNI dataset will have V sub-bricks (unless the
user applies the '-data_expr' option).
Mapping Functions:
Mapping functions exist because a single volume voxel may
be occupied by multiple surface nodes or segment points.
Depending on how dense the surface mesh is, the number of
steps provided by the '-f_steps' option, and the indexing
type from '-f_index', even a voxel which is only 1 cubic
mm in volume may have quite a few contributing points.
The mapping function defines how multiple surface values
are combined to get a single result in each voxel. For
example, the 'max' function will take the maximum of all
surface values contributing to each given voxel.
Current mapping functions are listed under the '-map_func'
option, below.
------------------------------------------------------------
examples:
1. Map a single surface to an anatomical volume domain,
creating a simple mask of the surface. The output
dataset will be fred_surf+orig, and the orientation and
grid spacing will follow that of the grid parent. The
output voxels will be 1 where the surface exists, and 0
elsewhere.
3dSurf2Vol \
-spec fred.spec \
-surf_A pial \
-sv fred_anat+orig \
-grid_parent fred_anat+orig \
-map_func mask \
-prefix fred_surf
2. Map the cortical grey ribbon (between the white matter
surface and the pial surface) to an AFNI volume, where
the resulting volume is restriced to the mask implied by
the -cmask option.
Surface data will come from the file sdata_10.1D, which
has 10 values per node, and lists only a portion of the
entire set of surface nodes. Each node pair will be form
a segment of 15 equally spaced points, the values from
which will be applied to the output dataset according to
the 'ave' filter. Since the index is over points, each
of the 15 points will have its value applied to the
appropriate voxel, even multiple times. This weights the
resulting average by the fraction of each segment that
occupies a given voxel.
The output dataset will have 10 sub-bricks, according to
the 10 values per node index in sdata_10.1D.
3dSurf2Vol \
-spec fred.spec \
-surf_A smoothwm \
-surf_B pial \
-sv fred_anat+orig \
-grid_parent 'fred_func+orig[0]' \
-cmask '-a fred_func+orig[2] -expr step(a-0.6)' \
-sdata_1D sdata_10.1D \
-map_func ave \
-f_steps 15 \
-f_index points \
-prefix fred_surf_ave
3. The inputs in this example are identical to those in
example 2, including the surface dataset, sdata_10.1D.
Again, the output dataset will have 10 sub-bricks.
The surface values will be applied via the 'max_abs'
filter, with the intention of assigning to each voxel the
node value with the most significance. Here, the index
method does not matter, so it is left as the default,
'voxel'.
In this example, each node pair segment will be extended
by 20% into the white matter, and by 10% outside of the
grey matter, generating a "thicker" result.
3dSurf2Vol \
-spec fred.spec \
-surf_A smoothwm \
-surf_B pial \
-sv fred_anat+orig \
-grid_parent 'fred_func+orig[0]' \
-cmask '-a fred_func+orig[2] -expr step(a-0.6)' \
-sdata_1D sdata_10.1D \
-map_func max_abs \
-f_steps 15 \
-f_p1_fr -0.2 \
-f_pn_fr 0.1 \
-prefix fred_surf_max_abs
4. This is simliar to example 2. Here, the surface nodes
(coordinates) come from 'surf_coords_2.1D'. But these
coordinates do not happen to be in Dicomm orientation,
they are in the same orientation as the grid parent, so
the '-sxyz_orient_as_gpar' option is applied.
Even though the data comes from 'sdata_10.1D', the output
AFNI dataset will only have 1 sub-brick. That is because
of the '-data_expr' option. Here, each applied surface
value will be the average of the sines of the first 3
data values (columns of sdata_10.1D).
3dSurf2Vol \
-surf_xyz_1D surf_coords_2.1D \
-sxyz_orient_as_gpar \
-grid_parent 'fred_func+orig[0]' \
-sdata_1D sdata_10.1D \
-data_expr '(sin(a)+sin(b)+sin(c))/3' \
-map_func ave \
-f_steps 15 \
-f_index points \
-prefix fred_surf_ave_sine
5. In this example, voxels will get the maximum value from
column 3 of sdata_10.1D (as usual, column 0 is used for
node indices). The output dataset will have 1 sub-brick.
Here, the output dataset is forced to be of type 'short',
regardless of what the grid parent is. Also, there will
be no scaling factor applied.
To track the numbers for surface node #1234, the '-dnode'
option has been used, along with '-debug'. Additionally,
'-dvoxel' is used to track the results for voxel #6789.
3dSurf2Vol \
-spec fred.spec \
-surf_A smoothwm \
-surf_B pial \
-sv fred_anat+orig \
-grid_parent 'fred_func+orig[0]' \
-sdata_1D sdata_10.1D'[0,3]' \
-map_func max \
-f_steps 15 \
-datum short \
-noscale \
-debug 2 \
-dnode 1234 \
-dvoxel 6789 \
-prefix fred_surf_max
------------------------------------------------------------
REQUIRED COMMAND ARGUMENTS:
-spec SPEC_FILE : SUMA spec file
e.g. -spec fred.spec
The surface specification file contains the list of
mappable surfaces that are used.
See @SUMA_Make_Spec_FS and @SUMA_Make_Spec_SF.
Note: this option, along with '-sv', may be replaced
by the '-surf_xyz_1D' option.
-surf_A SURF_NAME : specify surface A (from spec file)
-surf_B SURF_NAME : specify surface B (from spec file)
e.g. -surf_A smoothwm
e.g. -surf_A lh.smoothwm
e.g. -surf_B lh.pial
This parameter is used to tell the program with surfaces
to use. The '-surf_A' parameter is required, but the
'-surf_B' parameter is an option.
The surface names must uniquely match those in the spec
file, though a sub-string match is good enough. The
surface names are compared with the names of the surface
node coordinate files.
For instance, given a spec file that has only the left
hemisphere in it, 'pial' should produce a unique match
with lh.pial.asc. But if both hemispheres are included,
then 'pial' would not be unique (matching rh.pail.asc,
also). In that case, 'lh.pial' would be better.
-sv SURFACE_VOLUME : AFNI dataset
e.g. -sv fred_anat+orig
This is the AFNI dataset that the surface is mapped to.
This dataset is used for the initial surface node to xyz
coordinate mapping, in the Dicom orientation.
Note: this option, along with '-spec', may be replaced
by the '-surf_xyz_1D' option.
-surf_xyz_1D SXYZ_NODE_FILE : 1D coordinate file
e.g. -surf_xyz_1D my_surf_coords.1D
This ascii file contains a list of xyz coordinates to be
considered as a surface, or 2 sets of xyz coordinates to
considered as a surface pair. As usual, these points
are assumed to be in Dicom orientation. Another option
for coordinate orientation is to use that of the grid
parent dataset. See '-sxyz_orient_as_gpar' for details.
This option is an alternative to the pair of options,
'-spec' and '-sv'.
The number of rows of the file should equal the number
of nodes on each surface. The number of columns should
be either 3 for a single surface, or 6 for two surfaces.
sample line of an input file (one surface):
11.970287 2.850751 90.896111
sample line of an input file (two surfaces):
11.97 2.85 90.90 12.97 2.63 91.45
-grid_parent AFNI_DSET : AFNI dataset
e.g. -grid_parent fred_function+orig
This dataset is used as a grid and orientation master
for the output AFNI dataset.
-map_func MAP_FUNC : surface to dataset function
e.g. -map_func max
e.g. -map_func mask -f_steps 20
This function applies to the case where multiple data
points get mapped to a single voxel, which is expected
since surfaces tend to have a much higher resolution
than AFNI volumes. In the general case data points come
from each point on each partitioned line segment, with
one segment per node pair. Note that these segments may
have length zero, such as when only a single surface is
input.
See "Mapping Functions" above, for more information.
The current mapping function for one surface is:
mask : For each xyz location, set the corresponding
voxel to 1.
The current mapping functions for two surfaces are as
follows. These descriptions are per output voxel, and
over the values of all points mapped to a given voxel.
mask2 : if any points are mapped to the voxel, set
the voxel value to 1
ave : average all values
count : count the number of mapped data points
min : find the minimum value from all mapped points
max : find the maximum value from all mapped points
max_abs: find the number with maximum absolute value
(the resulting value will retain its sign)
-prefix OUTPUT_PREFIX : prefix for the output dataset
e.g. -prefix anat_surf_mask
This is used to specify the prefix of the resulting AFNI
dataset.
------------------------------
SUB-SURFACE DATA FILE OPTIONS:
-sdata_1D SURF_DATA.1D : 1D sub-surface file, with data
e.g. -sdata_1D roi3.1D
This is used to specify a 1D file, which contains
surface indices and data. The indices refer to the
surface(s) read from the spec file.
The format of this data file is a surface index and a
list of data values on each row. To be a valid 1D file,
each row must have the same number of columns.
------------------------------
OPTIONS SPECIFIC TO SEGMENT SELECTION:
(see "The basic form of the algorithm" for more details)
-f_steps NUM_STEPS : partition segments
e.g. -f_steps 10
default: -f_steps 2 (or 1, the number of surfaces)
This option specifies the number of points to divide
each line segment into, before mapping the points to the
AFNI volume domain. The default is the number of input
surfaces (usually, 2). The default operation is to have
the segment endpoints be the actual surface nodes,
unless they are altered with the -f_pX_XX options.
-f_index TYPE : index by points or voxels
e.g. -f_index points
e.g. -f_index voxels
default: -f_index voxels
Along a single segment, the default operation is to
apply only those points mapping to a new voxel. The
effect of the default is that a given voxel will have
at most one value applied per voxel pair.
If the user applies this option with 'points' or 'nodes'
as the argument, then every point along the segment will
be applied. This may be preferred if, for example, the
user wishes to have the average weighted by the number
of points occupying a voxel, not just the number of node
pair segments.
Note: the following -f_pX_XX options are used to alter the
locations of the segment endpoints, per node pair.
The segments are directed, from the node on the first
surface to the node on the second surface. To modify
the first endpoint, use a -f_p1_XX option, and use
-f_pn_XX to modify the second.
-f_p1_fr FRACTION : offset p1 by a length fraction
e.g. -f_p1_fr -0.2
e.g. -f_p1_fr -0.2 -f_pn_fr 0.2
This option moves the first endpoint, p1, by a distance
of the FRACTION times the original segment length. If
the FRACTION is positive, it moves in the direction of
the second endpoint, pn.
In the example, p1 is moved by 20% away from pn, which
will increase the length of each segment.
-f_pn_fr FRACTION : offset pn by a length fraction
e.g. -f_pn_fr 0.2
e.g. -f_p1_fr -0.2 -f_pn_fr 0.2
This option moves pn by a distance of the FRACTION times
the original segment length, in the direction from p1 to
pn. So a positive fraction extends the segment, and a
negative fraction reduces it.
In the example above, using 0.2 adds 20% to the segment
length past the original pn.
-f_p1_mm DISTANCE : offset p1 by a distance in mm.
e.g. -f_p1_mm -1.0
e.g. -f_p1_mm -1.0 -f_pn_fr 1.0
This option moves p1 by DISTANCE mm., in the direction
of pn. If the DISTANCE is positive, the segment gets
shorter. If DISTANCE is negative, the segment will get
longer.
In the example, p1 is moved away from pn, extending the
segment by 1 millimeter.
-f_pn_mm DISTANCE : offset pn by a distance in mm.
e.g. -f_pn_mm 1.0
e.g. -f_p1_mm -1.0 -f_pn_fr 1.0
This option moves pn by DISTANCE mm., in the direction
from the first point to the second. So if DISTANCE is
positive, the segment will get longer. If DISTANCE is
negative, the segment will get shorter.
In the example, pn is moved 1 millimeter farther from
p1, extending the segment by that distance.
------------------------------
GENERAL OPTIONS:
-cmask MASK_COMMAND : command for dataset mask
e.g. -cmask '-a fred_func+orig[2] -expr step(a-0.8)'
This option will produce a mask to be applied to the
output dataset. Note that this mask should form a
single sub-brick.
This option follows the style of 3dmaskdump (since the
code for it was, uh, borrowed from there (thanks Bob!)).
See '3dmaskdump -help' for more information.
-data_expr EXPRESSION : apply expression to surface input
e.g. -data_expr 17
e.g. -data_expr '(a+b+c+d)/4'
e.g. -data_expr '(sin(a)+sin(b))/2'
This expression is applied to the list of data values
from the surface data file input via '-sdata_1D'. The
expression is applied for each node or node pair, to the
list of data values corresponding to that node.
The letters 'a' through 'z' may be used as input, and
refer to columns 1 through 26 of the data file (where
column 0 is a surface node index). The data file must
have enough columns to support the expression. Is is
valid to have a constant expression without a data file.
-datum DTYPE : set data type in output dataset
e.g. -datum short
default: same as that of grid parent
This option specifies the data type for the output AFNI
dataset. Valid choices are byte, short and float, which
are 1, 2 and 4 bytes for each data point, respectively.
-debug LEVEL : verbose output
e.g. -debug 2
This option is used to print out status information
during the execution of the program. Current levels are
from 0 to 5.
-dnode DEBUG_NODE : extra output for that node
e.g. -dnode 123456
This option requests additional debug output for the
given surface node. This index is with respect to the
input surface (included in the spec file, or through the
'-surf_xyz_1D' option).
This will have no effect without the '-debug' option.
-dvoxel DEBUG_VOXEL : extra output for that voxel
e.g. -dvoxel 234567
This option requests additional debug output for the
given volume voxel. This 1-D index is with respect to
the output AFNI dataset. One good way to find a voxel
index to supply is from output via the '-dnode' option.
This will have no effect without the '-debug' option.
-hist : show revision history
Display module history over time.
-help : show this help
If you can't get help here, please get help somewhere.
-noscale : no scale factor in output dataset
If the output dataset is an integer type (byte, shorts
or ints), then the output dataset may end up with a
scale factor attached (see 3dcalc -help). With this
option, the output dataset will not be scaled.
-sxyz_orient_as_gpar : assume gpar orientation for sxyz
This option specifies that the surface coordinate points
in the '-surf_xyz_1D' option file have the orientation
of the grid parent dataset.
When the '-surf_xyz_1D' option is applied the surface
coordinates are assumed to be in Dicom orientation, by
default. This '-sxyz_orient_as_gpar' option overrides
the Dicom default, specifying that the node coordinates
are in the same orientation as the grid parent dataset.
See the '-surf_xyz_1D' option for more information.
-version : show version information
Show version and compile date.
------------------------------------------------------------
Author: R. Reynolds - version 3.6a (March 22, 2005)
(many thanks to Z. Saad and R.W. Cox)
This page auto-generated on Thu Aug 25 16:49:37 EDT 2005
|
| 3dSurfMask |
Usage: 3dSurfMask <-i_TYPE SURFACE> <-prefix PREFIX>
<-grid_parent GRID_VOL> [-sv SURF_VOL] [-mask_only]
Creates a volumetric dataset that marks the inside
of the surface. Voxels in the output dataset are set to the following
values:
0: Voxel outside surface
1: Voxel just outside the surface. This means the voxel
center is outside the surface but inside the
bounding box of a triangle in the mesh.
2: Voxel intersects the surface (a triangle), but center lies outside.
3: Voxel contains a surface node.
4: Voxel intersects the surface (a triangle), center lies inside surface.
5: Voxel just inside the surface. This means the voxel
center is inside the surface and inside the
bounding box of a triangle in the mesh.
6: Voxel inside the surface.
Mandatory Parameters:
-i_TYPE SURFACE: Specify input surface.
You can also use -t* and -spec and -surf
methods to input surfaces. See below
for more details.
-prefix PREFIX: Prefix of output dataset.
-grid_parent GRID_VOL: Specifies the grid for the
output volume.
Other parameters:
-mask_only: Produce an output dataset where voxels
are 1 inside the surface and 0 outside,
instead of the more nuanced output above.
Specifying input surfaces using -i_TYPE options:
-i_TYPE inSurf specifies the input surface,
TYPE is one of the following:
fs: FreeSurfer surface.
If surface name has .asc it is assumed to be
in ASCII format. Otherwise it is assumed to be
in BINARY_BE (Big Endian) format.
Patches in Binary format cannot be read at the moment.
sf: SureFit surface.
You must specify the .coord followed by the .topo file.
vec (or 1D): Simple ascii matrix format.
You must specify the coord (NodeList) file followed by
the topo (FaceSetList) file.
coord contains 3 floats per line, representing
X Y Z vertex coordinates.
topo contains 3 ints per line, representing
v1 v2 v3 triangle vertices.
ply: PLY format, ascii or binary.
Only vertex and triangulation info is preserved.
bv: BrainVoyager format.
Only vertex and triangulation info is preserved.
dx: OpenDX ascii mesh format.
Only vertex and triangulation info is preserved.
Requires presence of 3 objects, the one of class
'field' should contain 2 components 'positions'
and 'connections' that point to the two objects
containing node coordinates and topology, respectively.
Specifying surfaces using -t* options:
-tn TYPE NAME: specify surface type and name.
See below for help on the parameters.
-tsn TYPE STATE NAME: specify surface type state and name.
TYPE: Choose from the following (case sensitive):
1D: 1D format
FS: FreeSurfer ascii format
PLY: ply format
SF: Caret/SureFit format
BV: BrainVoyager format
NAME: Name of surface file.
For SF and 1D formats, NAME is composed of two names
the coord file followed by the topo file
STATE: State of the surface.
Default is S1, S2.... for each surface.
Specifying a Surface Volume:
-sv SurfaceVolume [VolParam for sf surfaces]
If you supply a surface volume, the coordinates of the input surface.
are modified to SUMA's convention and aligned with SurfaceVolume.
You must also specify a VolParam file for SureFit surfaces.
Specifying a surface specification (spec) file:
-spec SPEC: specify the name of the SPEC file.
Common Debugging Options:
[-trace]: Turns on In/Out debug and Memory tracing.
For speeding up the tracing log, I recommend
you redirect stdout to a file when using this option.
For example, if you were running suma you would use:
suma -spec lh.spec -sv ... > TraceFile
This option replaces the old -iodbg and -memdbg.
[-TRACE]: Turns on extreme tracing.
[-nomall]: Turn off memory tracing.
[-yesmall]: Turn on memory tracing (default).
[-novolreg]: Ignore any Volreg or Tagalign transformations
present in the Surface Volume.
NOTE: For programs that output results to stdout
(that is to your shell/screen), the debugging info
might get mixed up with your results.
++ SUMA version 2004_12_29
CVS tag:
SUMA_2005_04_29_1733
Compile Date:
Aug 25 2005
Ziad S. Saad SSCC/NIMH/NIH ziad@nih.gov
This page auto-generated on Thu Aug 25 16:49:37 EDT 2005
|
| 3dSurfMaskDump |
3dSurfMaskDump - dump ascii dataset values corresponding to a surface
This program is used to display AFNI dataset values that
correspond to a surface. The surface points are mapped to xyz
coordinates, according to the SURF_VOL (surface volume) AFNI
dataset. These coordinates are then matched to voxels in other
AFNI datasets. So given any other AFNI dataset, this program
can output all of the sub-brick values that correspond to each
of the suface locations. The user also has options to mask
regions for output.
Different mappings are allowed from the surface(s) to the grid
parent dataset. The mapping function is a required parameter to
the program.
The current mapping functions are:
ave : for each node pair (from 2 surfaces), output the
average of all voxel values along that line
segment
mask : each node in the surface is mapped to one voxel
midpoint : for each node pair (from 2 surfaces), output the
dataset value at their midpoint (in xyz space)
usage: 3dSurfMaskDump [options] -spec SPEC_FILE -sv SURF_VOL \
-grid_parent AFNI_DSET -map_func MAP_FUNC
examples:
3dSurfMaskDump \
-spec fred.spec \
-sv fred_anat+orig \
-grid_parent fred_anat+orig \
-map_func mask \
3dSurfMaskDump \
-spec fred.spec \
-sv fred_anat+orig \
-grid_parent 'fred_epi+orig[0]' \
-map_func mask \
-cmask '-a fred_func+orig[2] -expr step(a-0.6)' \
-debug 2 \
-output fred_surf_vals.txt
3dSurfMaskDump \
-spec fred.spec \
-sv fred_anat+orig \
-grid_parent fred_anat+orig \
-map_func ave \
-m2_steps 10 \
-m2_index nodes \
-cmask '-a fred_func+orig[2] -expr step(a-0.6)' \
-output fred_surf_ave.txt
REQUIRED COMMAND ARGUMENTS:
-spec SPEC_FILE : SUMA spec file
e.g. -spec fred.spec
The surface specification file contains the list of
mappable surfaces that are used.
See @SUMA_Make_Spec_FS and @SUMA_Make_Spec_SF.
-sv SURFACE_VOLUME : AFNI dataset
e.g. -sv fred_anat+orig
This is the AFNI dataset that the surface is mapped to.
This dataset is used for the intial surface node to xyz
coordinate mapping, in the Dicomm orientation.
-grid_parent AFNI_DSET : AFNI dataset
e.g. -grid_parent fred_function+orig
This dataset is used as a grid and orientation master
for the output. Output coordinates are based upon
this dataset.
-map_func MAP_FUNC : surface to dataset function
e.g. -map_func ave
e.g. -map_func ave -m2_steps 10
e.g. -map_func ave -m2_steps 10 -m2_index nodes
e.g. -map_func mask
e.g. -map_func midpoint
Given one or more surfaces, there are many ways to
select voxel locations, and to select corresponding
values for the output dataset. Some of the functions
will have separate options.
The current mapping functions are:
ave : Given 2 related surfaces, for each node
pair, output the average of the dataset
values located along the segment joining
those nodes.
-m2_steps NUM_STEPS :
The -m2_steps option may be added here, to
specify the number of points to use in the
average. The default and minimum is 2.
e.g. -map_func ave -m2_steps 10
default: -m2_steps 2
-m2_index TYPE :
The -m2_index options is used to specify
whether the average is taken by indexing
over distict nodes or over distict voxels.
For instance, when taking the average along
one node pair segment using 10 node steps,
perhaps 3 of those nodes may occupy one
particular voxel. In this case, does the
user want the voxel counted only once, or 3
times? Each case makes sense.
Note that this will only make sense when
used along with the '-m2_steps' option.
Possible values are "nodes", "voxels".
The default value is voxels. So each voxel
along a segment will be counted only once.
e.g. -m2_index nodes
e.g. -m2_index voxels
default: -m2_index voxels
mask : For each surface xyz location, output the
dataset values of each sub-brick.
midpoint : Given 2 related surfaces, for each node
pair, output the dataset value with xyz
coordinates at the midpoint of the nodes.
options:
-cmask MASK_COMMAND : (optional) command for dataset mask
e.g. -cmask '-a fred_func+orig[2] -expr step(a-0.8)'
This option will produce a mask to be applied to the
output dataset. Note that this mask should form a
single sub-brick.
This option follows the style of 3dmaskdump (since the
code for it was, uh, borrowed from there (thanks Bob!)).
See '3dmaskdump -help' for more information.
-debug LEVEL : (optional) verbose output
e.g. -debug 2
This option is used to print out status information
during the execution of the program. Current levels are
from 0 to 4.
-help : show this help
If you can't get help here, please get help somewhere.
-outfile OUTPUT_FILE : specify a file for the output
e.g. -outfile some_output_file
e.g. -outfile mask_values_over_dataset.txt
e.g. -outfile stderr
default: write to stdout
This is where the user will specify which file they want
the output to be written to. Note that the output file
should not yet exist.
Two special (valid) cases are stdout and stderr, either
of which may be specified.
-noscale : no scale factor in output dataset
If the output dataset is an integer type (byte, shorts
or ints), then the output dataset may end up with a
scale factor attached (see 3dcalc -help). With this
option, the output dataset will not be scaled.
-version : show version information
Show version and compile date.
Author: R. Reynolds - version 2.3 (July 21, 2003)
(many thanks to Z. Saad and R.W. Cox)
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|
| 3dTagalign |
Usage: 3dTagalign [options] dset
Rotates/translates dataset 'dset' to be aligned with the master,
using the tagsets embedded in their .HEAD files.
Options:
-master mset = Use dataset 'mset' as the master dataset
[this is a nonoptional option]
-nokeeptags = Don't put transformed locations of dset's tags
into the output dataset [default = keep tags]
-matvec mfile = Write the matrix+vector of the transformation to
file 'mfile'. This can be used as input to the
'-matvec_out2in' option of 3dWarp, if you want
to align other datasets in the same way (e.g.,
functional datasets).
-rotate = Compute the best transformation as a rotation + shift.
This is the default.
-affine = Compute the best transformation as a general affine
map rather than just a rotation + shift. In all
cases, the transformation from input to output
coordinates is of the form
[out] = [R] [in] + [V]
where [R] is a 3x3 matrix and [V] is a 3-vector.
By default, [R] is computed as a proper (det=1)
rotation matrix (3 parameters). The '-affine'
option says to fit [R] as a general matrix
(9 parameters).
N.B.: An affine transformation can rotate, rescale, and
shear the volume. Be sure to look at the dataset
before and after to make sure things are OK.
-rotscl = Compute transformation as a rotation times an isotropic
scaling; that is, [R] is an orthogonal matrix times
a scalar.
N.B.: '-affine' and '-rotscl' do unweighted least squares.
-prefix pp = Use 'pp' as the prefix for the output dataset.
[default = 'tagalign']
-verb = Print progress reports
-dummy = Don't actually rotate the dataset, just compute
the transformation matrix and vector. If
'-matvec' is used, the mfile will be written.
Nota Bene:
* Cubic interpolation is used. The transformation is carried out
using the same methods as program 3dWarp.
Author: RWCox - 16 Jul 2000, etc.
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|
| 3dTcat |
Concatenate sub-bricks from input datasets into one big 3D+time dataset.
Usage: 3dTcat options
where the options are:
-prefix pname = Use 'pname' for the output dataset prefix name.
OR -output pname [default='tcat']
-session dir = Use 'dir' for the output dataset session directory.
[default='./'=current working directory]
-glueto fname = Append bricks to the end of the 'fname' dataset.
This command is an alternative to the -prefix
and -session commands.
-dry = Execute a 'dry run'; that is, only print out
what would be done. This is useful when
combining sub-bricks from multiple inputs.
-verb = Print out some verbose output as the program
proceeds (-dry implies -verb).
Using -verb twice results in quite lengthy output.
-rlt = Remove linear trends in each voxel time series loaded
from each input dataset, SEPARATELY. That is, the
data from each dataset is detrended separately.
At least 3 sub-bricks from a dataset must be input
for this option to apply.
Notes: (1) -rlt removes the least squares fit of 'a+b*t'
to each voxel time series; this means that
the mean is removed as well as the trend.
This effect makes it impractical to compute
the % Change using AFNI's internal FIM.
(2) To have the mean of each dataset time series added
back in, use this option in the form '-rlt+'.
In this case, only the slope 'b*t' is removed.
(3) To have the overall mean of all dataset time
series added back in, use this option in the
form '-rlt++'. In this case, 'a+b*t' is removed
from each input dataset separately, and the
mean of all input datasets is added back in at
the end. (This option will work properly only
if all input datasets use at least 3 sub-bricks!)
(4) -rlt can be used on datasets that contain shorts
or floats, but not on complex- or byte-valued
datasets.
Command line arguments after the above are taken as input datasets.
A dataset is specified using one of these forms:
'prefix+view', 'prefix+view.HEAD', or 'prefix+view.BRIK'.
SUB-BRICK SELECTION:
You can also add a sub-brick selection list after the end of the
dataset name. This allows only a subset of the sub-bricks to be
included into the output (by default, all of the input dataset
is copied into the output). A sub-brick selection list looks like
one of the following forms:
fred+orig[5] ==> use only sub-brick #5
fred+orig[5,9,17] ==> use #5, #9, and #12
fred+orig[5..8] or [5-8] ==> use #5, #6, #7, and #8
fred+orig[5..13(2)] or [5-13(2)] ==> use #5, #7, #9, #11, and #13
Sub-brick indexes start at 0. You can use the character '$'
to indicate the last sub-brick in a dataset; for example, you
can select every third sub-brick by using the selection list
fred+orig[0..$(3)]
NOTES:
* The TR and other time-axis properties are taken from the
first input dataset that is itself 3D+time. If no input
datasets contain such information, then TR is set to 1.0.
This can be altered using the 3drefit program.
* The sub-bricks are output in the order specified, which may
not be the order in the original datasets. For example, using
fred+orig[0..$(2),1..$(2)]
will cause the sub-bricks in fred+orig to be output into the
new dataset in an interleaved fashion. Using
fred+orig[$..0]
will reverse the order of the sub-bricks in the output.
If the -rlt option is used, the sub-bricks selected from each
input dataset will be re-ordered into the output dataset, and
then this sequence will be detrended.
* You can use the '3dinfo' program to see how many sub-bricks
a 3D+time or a bucket dataset contains.
* The '$', '(', ')', '[', and ']' characters are special to
the shell, so you will have to escape them. This is most easily
done by putting the entire dataset plus selection list inside
single quotes, as in 'fred+orig[5..7,9]'.
* You may wish to use the 3drefit program on the output dataset
to modify some of the .HEAD file parameters.
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|
| 3dTcorrelate |
Usage: 3dTcorrelate [options] xset yset
Computes the correlation coefficient between corresponding voxel
time series in two input 3D+time datasets 'xset' and 'yset', and
stores the output in a new 1 sub-brick dataset.
Options:
-pearson = Correlation is the normal Pearson (product moment)
correlation coefficient [default].
-spearman = Correlation is the Spearman (rank) correlation
coefficient.
-quadrant = Correlation is the quadrant correlation coefficient.
-polort m = Remove polynomical trend of order 'm', for m=-1..3.
[default is m=1; removal is by least squares].
Using m=-1 means no detrending; this is only useful
for data/information that has been pre-processed.
-ort r.1D = Also detrend using the columns of the 1D file 'r.1D'.
Only one -ort option can be given. If you want to use
more than one, create a temporary file using 1dcat.
-autoclip = Clip off low-intensity regions in the two datasets,
-automask = so that the correlation is only computed between
high-intensity (presumably brain) voxels. The
intensity level is determined the same way that
3dClipLevel works.
-prefix p = Save output into dataset with prefix 'p'
[default prefix is 'Tcorr'].
Notes:
* The output dataset is functional bucket type, with one
sub-brick, stored in floating point format.
* Because both time series are detrended prior to correlation,
the results will not be identical to using FIM or FIM+ to
calculate correlations (whose ideal vector is not detrended).
* This is a quick hack for Mike Beauchamp. Thanks for you-know-what.
-- RWCox - Aug 2001
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|
| 3dThreetoRGB |
Usage #1: 3dThreetoRGB [options] dataset
Usage #2: 3dThreetoRGB [options] dataset1 dataset2 dataset3
Converts 3 sub-bricks of input to an RGB-valued dataset.
* If you have 1 input dataset, then sub-bricks [0..2] are
used to form the RGB components of the output.
* If you have 3 input datasets, then the [0] sub-brick of
each is used to form the RGB components, respectively.
* RGB datasets have 3 bytes per voxel, with values ranging
from 0..255.
Options:
-prefix ppp = Write output into dataset with prefix 'ppp'.
[default='rgb']
-scale fac = Multiply input values by 'fac' before using
as RGB [default=1]. If you have floating
point inputs in range 0..1, then using
'-scale 255' would make a lot of sense.
-mask mset = Only output nonzero values where the mask
dataset 'mset' is nonzero.
-fim = Write result as a 'fim' type dataset.
[this is the default]
-anat = Write result as a anatomical type dataset.
Notes:
* Input datasets must be byte-, short-, or float-valued.
* You might calculate the component datasets using 3dcalc.
* You can also create RGB-valued datasets in to3d, using
2D raw PPM image files as input, or the 3Dr: format.
* RGB fim overlays are transparent in AFNI in voxels where all
3 bytes are zero - that is, it won't overlay solid black.
* At present, there is limited support for RGB datasets.
About the only thing you can do is display them in 2D
slice windows in AFNI.
-- RWCox - April 2002
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|
| 3dToutcount |
Usage: 3dToutcount [options] dataset
Calculates number of 'outliers' a 3D+time dataset, at each
time point, and writes the results to stdout.
Options:
-mask mset = Only count voxels in the mask dataset.
-qthr q = Use 'q' instead of 0.001 in the calculation
of alpha (below): 0 < q < 1.
-autoclip }= Clip off 'small' voxels (as in 3dClipLevel);
-automask }= you can't use this with -mask!
-range = Print out median+3.5*MAD of outlier count with
each time point; use with 1dplot as in
3dToutcount -range fred+orig | 1dplot -stdin -one
-save ppp = Make a new dataset, and save the outlier Q in each
voxel, where Q is calculated from voxel value v by
Q = -log10(qg(abs((v-median)/(sqrt(PI/2)*MAD))))
or Q = 0 if v is 'close' to the median (not an outlier).
That is, 10**(-Q) is roughly the p-value of value v
under the hypothesis that the v's are iid normal.
The prefix of the new dataset (float format) is 'ppp'.
-polort nn = Detrend each voxel time series with polynomials of
order 'nn' prior to outlier estimation. Default
value of nn=0, which means just remove the median.
Detrending is done with L1 regression, not L2.
OUTLIERS are defined as follows:
* The trend and MAD of each time series are calculated.
- MAD = median absolute deviation
= median absolute value of time series minus trend.
* In each time series, points that are 'far away' from the
trend are called outliers, where 'far' is defined by
alpha * sqrt(PI/2) * MAD
alpha = qginv(0.001/N) (inverse of reversed Gaussian CDF)
N = length of time series
* Some outliers are to be expected, but if a large fraction of the
voxels in a volume are called outliers, you should investigate
the dataset more fully.
Since the results are written to stdout, you probably want to redirect
them to a file or another program, as in this example:
3dToutcount -automask v1+orig | 1dplot -stdin
NOTE: also see program 3dTqual for a similar quality check.
INPUT DATASET NAMES
-------------------
This program accepts datasets that are modified on input according to the
following schemes:
'r1+orig[3..5]' {sub-brick selector}
'r1+orig<100.200>' {sub-range selector}
'r1+orig[3..5]<100..200>' {both selectors}
'3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )' {calculation}
For the gruesome details, see the output of 'afni -help'.
This page auto-generated on Thu Aug 25 16:49:38 EDT 2005
|
| 3dTqual |
Usage: 3dTqual [options] dataset
Computes a `quality index' for each sub-brick in a 3D+time dataset.
The output is a 1D time series with the index for each sub-brick.
The results are written to stdout.
Note that small values of the index are 'good', indicating that
the sub-brick is not very different from the norm. The purpose
of this program is to provide a crude way of screening FMRI
time series for sporadic abnormal images, such as might be
caused by large subject head motion or scanner glitches.
Do not take the results of this program too literally. It
is intended as a GUIDE to help you find data problems, and no
more. It is not an assurance that the dataset is good, and
it may indicate problems where nothing is wrong.
Sub-bricks with index values much higher than others should be
examined for problems. How you determine what 'much higher' means
is mostly up to you. I suggest graphical inspection of the indexes
(cf. EXAMPLE, infra). As a guide, the program will print (stderr)
the median quality index and the range median-3.5*MAD .. median+3.5*MAD
(MAD=Median Absolute Deviation). Values well outside this range might
be considered suspect; if the quality index were normally distributed,
then values outside this range would occur only about 1% of the time.
OPTIONS:
-spearman = Quality index is 1 minus the Spearman (rank)
correlation coefficient of each sub-brick
with the median sub-brick.
[This is the default method.]
-quadrant = Similar to -spearman, but using 1 minus the
quadrant correlation coefficient as the
quality index.
-autoclip = Clip off low-intensity regions in the median sub-brick,
-automask = so that the correlation is only computed between
high-intensity (presumably brain) voxels. The
intensity level is determined the same way that
3dClipLevel works. This prevents the vast number
of nearly 0 voxels outside the brain from biasing
the correlation coefficient calculations.
-clip val = Clip off values below 'val' in the median sub-brick.
-range = Print the median-3.5*MAD and median+3.5*MAD values
out with EACH quality index, so that they
can be plotted (cf. Example, infra).
Notes: * These values are printed to stderr in any case.
* This is only useful for plotting with 1dplot.
* The lower value median-3.5*MAD is never allowed
to go below 0.
EXAMPLE:
3dTqual -range -automask fred+orig | 1dplot -one -stdin
will calculate the time series of quality indexes and plot them
to an X11 window, along with the median+/-3.5*MAD bands.
NOTE: cf. program 3dToutcount for a somewhat different quality check.
-- RWCox - Aug 2001
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|
| 3dTSgen |
Program: 3dTSgen
Author: B. Douglas Ward
Date: 09 September 1999
This program generates an AFNI 3d+time data set. The time series for
each voxel is generated according to a user specified signal + noise
model.
Usage:
3dTSgen
-input fname fname = filename of prototype 3d + time data file
[-inTR] set the TR of the created timeseries to be the TR
of the prototype dataset
[The default is to compute with TR = 1.]
[The model functions are called for a ]
[time grid of 0, TR, 2*TR, 3*TR, .... ]
-signal slabel slabel = name of (non-linear) signal model
-noise nlabel nlabel = name of (linear) noise model
-sconstr k c d constraints for kth signal parameter:
c <= gs[k] <= d
-nconstr k c d constraints for kth noise parameter:
c+b[k] <= gn[k] <= d+b[k]
-sigma s s = std. dev. of additive Gaussian noise
[-voxel num] screen output for voxel #num
-output fname fname = filename of output 3d + time data file
The following commands generate individual AFNI 1 sub-brick datasets:
[-scoef k fname] write kth signal parameter gs[k];
output 'fim' is written to prefix filename fname
[-ncoef k fname] write kth noise parameter gn[k];
output 'fim' is written to prefix filename fname
The following commands generate one AFNI 'bucket' type dataset:
[-bucket n prefixname] create one AFNI 'bucket' dataset containing
n sub-bricks; n=0 creates default output;
output 'bucket' is written to prefixname
The mth sub-brick will contain:
[-brick m scoef k label] kth signal parameter regression coefficient
[-brick m ncoef k label] kth noise parameter regression coefficient
This page auto-generated on Thu Aug 25 16:49:38 EDT 2005
|
| 3dTshift |
Usage: 3dTshift [options] dataset
Shifts voxel time series from the input dataset so that the separate
slices are aligned to the same temporal origin. By default, uses the
slicewise shifting information in the dataset header (from the 'tpattern'
input to program to3d).
Method: detrend -> interpolate -> retrend (optionally)
The input dataset can have a sub-brick selector attached, as documented
in '3dcalc -help'.
The output dataset time series will be interpolated from the input to
the new temporal grid. This may not be the best way to analyze your
data, but it can be convenient.
Warnings:
* Please recall the phenomenon of 'aliasing': frequencies above 1/(2*TR) can't
be properly interpolated. For most 3D FMRI data, this means that cardiac
and respiratory effects will not be treated properly by this program.
* The images at the beginning of a high-speed FMRI imaging run are usually
of a different quality than the later images, due to transient effects
before the longitudinal magnetization settles into a steady-state value.
These images should not be included in the interpolation! For example,
if you wish to exclude the first 4 images, then the input dataset should
be specified in the form 'prefix+orig[4..$]'. Alternatively, you can
use the '-ignore ii' option.
* It seems to be best to use 3dTshift before using 3dvolreg.
Options:
-verbose = print lots of messages while program runs
-TR ddd = use 'ddd' as the TR, rather than the value
stored in the dataset header using to3d.
You may attach the suffix 's' for seconds,
or 'ms' for milliseconds.
-tzero zzz = align each slice to time offset 'zzz';
the value of 'zzz' must be between the
minimum and maximum slice temporal offsets.
N.B.: The default alignment time is the average
of the 'tpattern' values (either from the
dataset header or from the -tpattern option)
-slice nnn = align each slice to the time offset of slice
number 'nnn' - only one of the -tzero and
-slice options can be used.
-prefix ppp = use 'ppp' for the prefix of the output file;
the default is 'tshift'.
-ignore ii = Ignore the first 'ii' points. (Default is ii=0.)
The first ii values will be unchanged in the output
(regardless of the -rlt option). They also will
not be used in the detrending or time shifting.
-rlt = Before shifting, the mean and linear trend
-rlt+ = of each time series is removed. The default
action is to add these back in after shifting.
-rlt means to leave both of these out of the output
-rlt+ means to add only the mean back into the output
(cf. '3dTcat -help')
-Fourier = Use a Fourier method (the default: most accurate; slowest).
-linear = Use linear (1st order polynomial) interpolation (least accurate).
-cubic = Use the cubic (3rd order) Lagrange polynomial interpolation.
-quintic = Use the quintic (5th order) Lagrange polynomial interpolation.
-heptic = Use the heptic (7th order) Lagrange polynomial interpolation.
-tpattern ttt = use 'ttt' as the slice time pattern, rather
than the pattern in the input dataset header;
'ttt' can have any of the values that would
go in the 'tpattern' input to to3d, described below:
alt+z = altplus = alternating in the plus direction
alt+z2 = alternating, starting at slice #1 instead of #0
alt-z = altminus = alternating in the minus direction
alt-z2 = alternating, starting at slice #nz-2 instead of #nz-1
seq+z = seqplus = sequential in the plus direction
seq-z = seqminus = sequential in the minus direction
@filename = read temporal offsets from 'filename'
For example if nz = 5 and TR = 1000, then the inter-slice
time is taken to be dt = TR/nz = 200. In this case, the
slices are offset in time by the following amounts:
S L I C E N U M B E R
tpattern 0 1 2 3 4 Comment
--------- --- --- --- --- --- -------------------------------
altplus 0 600 200 800 400 Alternating in the +z direction
alt+z2 400 0 600 200 800 Alternating, but starting at #1
altminus 400 800 200 600 0 Alternating in the -z direction
alt-z2 800 200 600 0 400 Alternating, starting at #nz-2
seqplus 0 200 400 600 800 Sequential in the -z direction
seqplus 800 600 400 200 0 Sequential in the -z direction
If @filename is used for tpattern, then nz ASCII-formatted numbers
are read from the file. These indicate the time offsets for each
slice. For example, if 'filename' contains
0 600 200 800 400
then this is equivalent to 'altplus' in the above example.
(nz = number of slices in the input dataset)
N.B.: if you are using -tpattern, make sure that the units supplied
match the units of TR in the dataset header, or provide a
new TR using the -TR option.
As a test of how well 3dTshift interpolates, you can take a dataset
that was created with '-tpattern alt+z', run 3dTshift on it, and
then run 3dTshift on the new dataset with '-tpattern alt-z' -- the
effect will be to reshift the dataset back to the original time
grid. Comparing the original dataset to the shifted-then-reshifted
output will show where 3dTshift does a good job and where it does
a bad job.
-- RWCox - 31 October 1999
INPUT DATASET NAMES
-------------------
This program accepts datasets that are modified on input according to the
following schemes:
'r1+orig[3..5]' {sub-brick selector}
'r1+orig<100.200>' {sub-range selector}
'r1+orig[3..5]<100..200>' {both selectors}
'3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )' {calculation}
For the gruesome details, see the output of 'afni -help'.
This page auto-generated on Thu Aug 25 16:49:38 EDT 2005
|
| 3dTsmooth |
Usage: 3dTsmooth [options] dataset
Smooths each voxel time series in a 3D+time dataset and produces
as output a new 3D+time dataset (e.g., lowpass filter in time).
General Options:
-prefix ppp = Sets the prefix of the output dataset to be 'ppp'.
[default = 'smooth']
-datum type = Coerce output dataset to be stored as the given type.
[default = input data type]
Three Point Filtering Options [07 July 1999]
--------------------------------------------
The following options define the smoothing filter to be used.
All these filters use 3 input points to compute one output point:
Let a = input value before the current point
b = input value at the current point
c = input value after the current point
[at the left end, a=b; at the right end, c=b]
-lin = 3 point linear filter: 0.15*a + 0.70*b + 0.15*c
[This is the default smoother]
-med = 3 point median filter: median(a,b,c)
-osf = 3 point order statistics filter:
0.15*min(a,b,c) + 0.70*median(a,b,c) + 0.15*max(a,b,c)
-3lin m = 3 point linear filter: 0.5*(1-m)*a + m*b + 0.5*(1-m)*c
Here, 'm' is a number strictly between 0 and 1.
General Linear Filtering Options [03 Mar 2001]
----------------------------------------------
-hamming N = Use N point Hamming or Blackman windows.
-blackman N (N must be odd and bigger than 1.)
-custom coeff_filename.1D (odd # of coefficients must be in a
single column in ASCII file)
(-custom added Jan 2003)
WARNING: If you use long filters, you do NOT want to include the
large early images in the program. Do something like
3dTsmooth -hamming 13 'fred+orig[4..$]'
to eliminate the first 4 images (say).
The following options determing how the general filters treat
time points before the beginning and after the end:
-EXTEND = BEFORE: use the first value; AFTER: use the last value
-ZERO = BEFORE and AFTER: use zero
-TREND = compute a linear trend, and extrapolate BEFORE and AFTER
The default is -EXTEND. These options do NOT affect the operation
of the 3 point filters described above, which always use -EXTEND.
INPUT DATASET NAMES
-------------------
This program accepts datasets that are modified on input according to the
following schemes:
'r1+orig[3..5]' {sub-brick selector}
'r1+orig<100.200>' {sub-range selector}
'r1+orig[3..5]<100..200>' {both selectors}
'3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )' {calculation}
For the gruesome details, see the output of 'afni -help'.
This page auto-generated on Thu Aug 25 16:49:38 EDT 2005
|
| 3dTstat |
Usage: 3dTstat [options] dataset
Computes one or more voxel-wise statistics for a 3D+time dataset
and stores them in a bucket dataset.
Options:
-mean = compute mean of input voxels [DEFAULT]
-slope = compute mean slope of input voxels vs. time
-stdev = compute standard deviation of input voxels
[N.B.: this is computed after ]
[ the slope has been removed]
-cvar = compute coefficient of variation of input
voxels = stdev/fabs(mean)
**N.B.: You can add NOD to the end of the above 2
options to turn off detrending, as in
-stdevNOD or -cvarNOD
-MAD = compute MAD (median absolute deviation) of
input voxels = median(|voxel-median(voxel)|)
[N.B.: the trend is NOT removed for this]
-DW = compute Durbin-Watson Statistic of
input voxels
[N.B.: the trend is removed for this]
-median = compute median of input voxels [undetrended]
-min = compute minimum of input voxels [undetrended]
-max = compute maximum of input voxels [undetrended]
-absmax = compute absolute maximum of input voxels [undetrended]
-argmin = index of minimum of input voxels [undetrended]
-argmax = index of maximum of input voxels [undetrended]
-argabsmax = index of absolute maximum of input voxels [undetrended]
-prefix p = use string 'p' for the prefix of the
output dataset [DEFAULT = 'stat']
-datum d = use data type 'd' for the type of storage
of the output, where 'd' is one of
'byte', 'short', or 'float' [DEFAULT=float]
-autocorr n = compute autocorrelation function and return
first n coefficients
-autoreg n = compute autoregression coefficients and return
first n coefficients
[N.B.: -autocorr 0 and/or -autoreg 0 will return coefficients
equal to the length of the input data
The output is a bucket dataset. The input dataset
may use a sub-brick selection list, as in program 3dcalc.
INPUT DATASET NAMES
-------------------
This program accepts datasets that are modified on input according to the
following schemes:
'r1+orig[3..5]' {sub-brick selector}
'r1+orig<100.200>' {sub-range selector}
'r1+orig[3..5]<100..200>' {both selectors}
'3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )' {calculation}
For the gruesome details, see the output of 'afni -help'.
This page auto-generated on Thu Aug 25 16:49:38 EDT 2005
|
| 3dttest |
Gosset (Student) t-test sets of 3D datasets
Usage 1: 3dttest [options] -set1 datasets ... -set2 datasets ...
for comparing the means of 2 sets of datasets (voxel by voxel).
Usage 2: 3dttest [options] -base1 bval -set2 datasets ...
for comparing the mean of 1 set of datasets against a constant.
OUTPUTS:
A single dataset is created that is the voxel-by-voxel difference
of the mean of set2 minus the mean of set1 (or minus 'bval').
The output dataset will be of the intensity+Ttest ('fitt') type.
The t-statistic at each voxel can be used as an interactive
thresholding tool in AFNI.
t-TESTING OPTIONS:
-set1 datasets ... = Specifies the collection of datasets to put into
the first set. The mean of set1 will be tested
with a 2-sample t-test against the mean of set2.
N.B.: -set1 and -base1 are mutually exclusive!
-base1 bval = 'bval' is a numerical value that the mean of set2
will be tested against with a 1-sample t-test.
-set2 datasets ... = Specifies the collection of datasets to put into
the second set. There must be at least 2 datasets
in each of set1 (if used) and set2.
-paired = Specifies the use of a paired-sample t-test to
compare set1 and set2. If this option is used,
set1 and set2 must have the same cardinality.
N.B.: A paired test is intended for use when the set1 and set2
dataset function values may be pairwise correlated.
If they are in fact uncorrelated, this test has less
statistical 'power' than the unpaired (default) t-test.
This loss of power is the price that is paid for
insurance against pairwise correlations.
-unpooled = Specifies that the variance estimates for set1 and
set2 be computed separately (not pooled together).
This only makes sense if -paired is NOT given.
N.B.: If this option is used, the number of degrees
of freedom per voxel is a variable, rather
than a constant.
-dof_prefix ddd = If '-unpooled' is also used, then a dataset with
prefix 'ddd' will be created that contains the
degrees of freedom (DOF) in each voxel.
You can convert the t-value in the -prefix
dataset to a z-score using the -dof_prefix dataset
using commands like so:
3dcalc -a 'pname+orig[1]' -b ddd+orig \
-datum float -prefix ddd_zz -expr 'fitt_t2z(a,b)'
3drefit -substatpar 0 fizt ddd_zz+orig
At present, AFNI is incapable of directly dealing
with datasets whose DOF parameter varies between
voxels. Converting to a z-score (with no parameters)
is one way of getting around this difficulty.
-workmem mega = 'mega' specifies the number of megabytes of RAM
to use for statistical workspace. It defaults
to 12. The program will run faster if this is
larger (see the NOTES section below).
The -base1 or -set1 command line switches must follow all other options
(including those described below) except for the -set2 switch.
INPUT EDITING OPTIONS: The same as are available in 3dmerge.
OUTPUT OPTIONS: these options control the output files.
-session dirname = Write output into given directory (default=./)
-prefix pname = Use 'pname' for the output directory prefix
(default=tdif)
-datum type = Use 'type' to store the output difference
in the means; 'type' may be short or float.
How the default is determined is described
in the notes below.
NOTES:
** To economize on memory, 3dttest makes multiple passes through
the input datasets. On each pass, the entire editing process
will be carried out again. For efficiency's sake, it is
better to carry out the editing using 3dmerge to produce
temporary datasets, and then run 3dttest on them. This applies
with particular force if a 'blurring' option is used.
Note also that editing a dataset requires that it be read into
memory in its entirety (so that the disk file is not altered).
This will increase the memory needs of the program far beyond
the level set by the -workmem option.
** The input datasets are specified by their .HEAD files,
but their .BRIK files must exist also! This program cannot
'warp-on-demand' from other datasets.
** This program cannot deal with time-dependent or complex-valued datasets!
By default, the output dataset function values will be shorts if the
first input dataset is byte- or short-valued; otherwise they will be
floats. This behavior may be overridden using the -datum option.
INPUT DATASET NAMES
-------------------
This program accepts datasets that are modified on input according to the
following schemes:
'r1+orig[3..5]' {sub-brick selector}
'r1+orig<100.200>' {sub-range selector}
'r1+orig[3..5]<100..200>' {both selectors}
'3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )' {calculation}
For the gruesome details, see the output of 'afni -help'.
This page auto-generated on Thu Aug 25 16:49:38 EDT 2005
|
| 3dUndump |
Usage: 3dUndump [options] infile ...
Assembles a 3D dataset from an ASCII list of coordinates and
(optionally) values.
Options:
-prefix ppp = 'ppp' is the prefix for the output dataset
[default = undump].
-master mmm = 'mmm' is the master dataset, whose geometry
*OR* will determine the geometry of the output.
-dimen I J K = Sets the dimensions of the output dataset to
be I by J by K voxels. (Each I, J, and K
must be >= 2.) This option can be used to
create a dataset of a specific size for test
purposes, when no suitable master exists.
** N.B.: Exactly one of -master or -dimen must be given.
-mask kkk = This option specifies a mask dataset 'kkk', which
will control which voxels are allowed to get
values set. If the mask is present, only
voxels that are nonzero in the mask can be
set in the new dataset.
* A mask can be created with program 3dAutomask.
* Combining a mask with sphere insertion makes
a lot of sense (to me, at least).
-datum type = 'type' determines the voxel data type of the
output, which may be byte, short, or float
[default = short].
-dval vvv = 'vvv' is the default value stored in each
input voxel that does not have a value
supplied in the input file [default = 1].
-fval fff = 'fff' is the fill value, used for each voxel
in the output dataset that is NOT listed
in the input file [default = 0].
-ijk = Coordinates in the input file are (i,j,k) index
*OR* triples, as might be output by 3dmaskdump.
-xyz = Coordinates in the input file are (x,y,z)
spatial coordinates, in mm. If neither
-ijk or -xyz is given, the default is -ijk.
** N.B.: -xyz can only be used with -master. If -dimen
is used to specify the size of the output dataset,
(x,y,z) coordinates are not defined (until you
use 3drefit to define the spatial structure).
-srad rrr = Specifies that a sphere of radius 'rrr' will be
filled about each input (x,y,z) or (i,j,k) voxel.
If the radius is not given, or is 0, then each
input data line sets the value in only one voxel.
* If '-master' is used, then 'rrr' is in mm.
* If '-dimen' is used, then 'rrr' is in voxels.
-orient code = Specifies the coordinate order used by -xyz.
The code must be 3 letters, one each from the pairs
{R,L} {A,P} {I,S}. The first letter gives the
orientation of the x-axis, the second the orientation
of the y-axis, the third the z-axis:
R = right-to-left L = left-to-right
A = anterior-to-posterior P = posterior-to-anterior
I = inferior-to-superior S = superior-to-inferior
If -orient isn't used, then the coordinate order of the
-master dataset is used to interpret (x,y,z) inputs.
** N.B.: If -dimen is used (which implies -ijk), then the
only use of -orient is to specify the axes ordering
of the output dataset. If -master is used instead,
the output dataset's axes ordering is the same as the
-master dataset's, regardless of -orient.
Input File Format:
The input file(s) are ASCII files, with one voxel specification per
line. A voxel specification is 3 numbers (-ijk or -xyz coordinates),
with an optional 4th number giving the voxel value. For example:
1 2 3
3 2 1 5
5.3 6.2 3.7
// this line illustrates a comment
The first line puts a voxel (with value given by -dval) at point
(1,2,3). The second line puts a voxel (with value 5) at point (3,2,1).
The third line puts a voxel (with value given by -dval) at point
(5.3,6.2,3.7). If -ijk is in effect, and fractional coordinates
are given, they will be rounded to the nearest integers; for example,
the third line would be equivalent to (i,j,k) = (5,6,4).
Notes:
* This program creates a 1 sub-brick file. You can 'glue' multiple
files together using 3dbucket or 3dTcat to make multi-brick datasets.
* If an input filename is '-', then stdin is used for input.
* By default, the output dataset is of type '-fim', unless the -master
dataset is an anat type. You can change the output type using 3drefit.
* You could use program 1dcat to extract specific columns from a
multi-column rectangular file (e.g., to get a specific sub-brick
from the output of 3dmaskdump), and use the output of 1dcat as input
to this program.
* [19 Feb 2004] The -mask and -srad options were added this day.
Also, a fifth value on an input line, if present, is taken as a
sphere radius to be used for that input point only. Thus, input
3.3 4.4 5.5 6.6 7.7
means to put the value 6.6 into a sphere of radius 7.7 mm centered
about (x,y,z)=(3.3,4.4,5.5).
-- RWCox -- October 2000
This page auto-generated on Thu Aug 25 16:49:38 EDT 2005
|
| 3dUniformize |
Program: 3dUniformize
Author: B. D. Ward
Initial Release: 28 January 2000
Latest Revision: 16 April 2003
This program corrects for image intensity non-uniformity.
Usage:
3dUniformize
-anat filename Filename of anat dataset to be corrected
[-quiet] Suppress output to screen
-prefix pname Prefix name for file to contain corrected image
INPUT DATASET NAMES
-------------------
This program accepts datasets that are modified on input according to the
following schemes:
'r1+orig[3..5]' {sub-brick selector}
'r1+orig<100.200>' {sub-range selector}
'r1+orig[3..5]<100..200>' {both selectors}
'3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )' {calculation}
For the gruesome details, see the output of 'afni -help'.
This page auto-generated on Thu Aug 25 16:49:38 EDT 2005
|
| 3dVol2Surf |
3dVol2Surf - map data from a volume domain to a surface domain
usage: 3dVol2Surf [options] -spec SPEC_FILE -sv SURF_VOL \
-grid_parent AFNI_DSET -map_func MAP_FUNC
This program is used to map data values from an AFNI volume
dataset to a surface dataset. A filter may be applied to the
volume data to produce the value(s) for each surface node.
The surface and volume domains are spacially matched via the
'surface volume' AFNI dataset. This gives each surface node xyz
coordinates, which are then matched to the input 'grid parent'
dataset. This grid parent is an AFNI dataset containing the
data values destined for output.
Typically, two corresponding surfaces will be input (via the
spec file and the '-surf_A' and '-surf_B' options), along with
a mapping function and relevant options. The mapping function
will act as a filter over the values in the AFNI volume.
Note that an alternative to using a second surface with the
'-surf_B' option is to define the second surface by using the
normals from the first surface. By default, the second surface
would be defined at a distance of 1mm along the normals, but the
user may modify the applied distance (and direction). See the
'-use_norms' and '-norm_len' options for more details.
For each pair of corresponding surface nodes, let NA be the node
on surface A (such as a white/grey boundary) and NB be the
corresponding node on surface B (such as a pial surface). The
filter is applied to the volume data values along the segment
from NA to NB (consider the average or maximum as examples of
filters).
Note: if either endpoint of a segment is outside the grid parent
volume, that node (pair) will be skipped.
Note: surface A corresponds to the required '-surf_A' argument,
while surface B corresponds to '-surf_B'.
By default, this segment only consists of the endpoints, NA and
NB (the actual nodes on the two surfaces). However the number
of evenly spaced points along the segment may be specified with
the -f_steps option, and the actual locations of NA and NB may
be altered with any of the -f_pX_XX options, covered below.
As an example, for each node pair, one could output the average
value from some functional dataset along a segment of 10 evenly
spaced points, where the segment endpoints are defined by the
xyz coordinates of the nodes. This is example 3, below.
The mapping function (i.e. filter) is a required parameter to
the program.
Brief descriptions of the current mapping functions are as
follows. These functions are defined over a segment of points.
ave : output the average of all voxel values along the
segment
mask : output the voxel value for the trivial case of a
segment - defined by a single surface point
median : output the median value from the segment
midpoint : output the dataset value at the segment midpoint
mode : output the mode of the values along the segment
max : output the maximum volume value over the segment
max_abs : output the dataset value with max abs over seg
min : output the minimum volume value over the segment
seg_vals : output _all_ volume values over the segment (one
sub-brick only)
--------------------------------------------------
examples:
1. Apply a single surface mask to output volume values over
each surface node. Output is one value per sub-brick
(per surface node).
3dVol2Surf \
-spec fred.spec \
-surf_A smoothwm \
-sv fred_anat+orig \
-grid_parent fred_anat+orig \
-map_func mask \
-out_1D fred_anat_vals.1D
2. Apply a single surface mask to output volume values over
each surface node. In this case restrict input to the
mask implied by the -cmask option. Supply additional
debug output, and more for surface node 1874
3dVol2Surf \
-spec fred.spec \
-surf_A smoothwm \
-sv fred_anat+orig \
-grid_parent 'fred_epi+orig[0]' \
-cmask '-a fred_func+orig[2] -expr step(a-0.6)' \
-map_func mask \
-debug 2 \
-dnode 1874 \
-out_niml fred_epi_vals.niml
3. Given a pair of related surfaces, for each node pair,
break the connected line segment into 10 points, and
compute the average dataset value over those points.
Since the index is nodes, each of the 10 points will be
part of the average. This could be changed so that only
values from distinct volume nodes are considered (by
changing the -f_index from nodes to voxels). Restrict
input voxels to those implied by the -cmask option
Output is one average value per sub-brick (per surface
node).
3dVol2Surf \
-spec fred.spec \
-surf_A smoothwm \
-surf_B pial \
-sv fred_anat+orig \
-grid_parent fred_func+orig \
-cmask '-a fred_func+orig[2] -expr step(a-0.6)' \
-map_func ave \
-f_steps 10 \
-f_index nodes \
-out_1D fred_func_ave.1D
4. Similar to example 3, but restrict the output columns to
only node indices and values (i.e. skip 1dindex, i, j, k
and vals).
3dVol2Surf \
-spec fred.spec \
-surf_A smoothwm \
-surf_B pial \
-sv fred_anat+orig \
-grid_parent fred_func+orig \
-cmask '-a fred_func+orig[2] -expr step(a-0.6)' \
-map_func ave \
-f_steps 10 \
-f_index nodes \
-skip_col_1dindex \
-skip_col_i \
-skip_col_j \
-skip_col_k \
-skip_col_vals \
-out_1D fred_func_ave_short.1D
5. Similar to example 3, but each of the node pair segments
has grown by 10% on the inside of the first surface,
and 20% on the outside of the second. This is a 30%
increase in the length of each segment. To shorten the
node pair segment, use a '+' sign for p1 and a '-' sign
for pn.
As an interesting side note, '-f_p1_fr 0.5 -f_pn_fr -0.5'
would give a zero length vector identical to that of the
'midpoint' filter.
3dVol2Surf \
-spec fred.spec \
-surf_A smoothwm \
-surf_B pial \
-sv fred_anat+orig \
-grid_parent fred_func+orig \
-cmask '-a fred_func+orig[2] -expr step(a-0.6)' \
-map_func ave \
-f_steps 10 \
-f_index voxels \
-f_p1_fr -0.1 \
-f_pn_fr 0.2 \
-out_1D fred_func_ave2.1D
6. Similar to example 3, instead of computing the average
across each segment (one average per sub-brick), output
the volume value at _every_ point across the segment.
The output here would be 'f_steps' values per node pair,
though the output could again be restricted to unique
voxels along each segment with '-f_index voxels'.
Note that only sub-brick 0 will be considered here.
3dVol2Surf \
-spec fred.spec \
-surf_A smoothwm \
-surf_B pial \
-sv fred_anat+orig \
-grid_parent fred_func+orig \
-cmask '-a fred_func+orig[2] -expr step(a-0.6)' \
-map_func seg_vals \
-f_steps 10 \
-f_index nodes \
-out_1D fred_func_segvals_10.1D
7. Similar to example 6, but make sure there is output for
every node pair in the surfaces. Since it is expected
that some nodes are out of bounds (meaning that they lie
outside the domain defined by the grid parent dataset),
the '-oob_value' option is added to include a default
value of 0.0 in such cases. And since it is expected
that some node pairs are "out of mask" (meaning that
their resulting segment lies entirely outside the cmask),
the '-oom_value' was added to output the same default
value of 0.0.
3dVol2Surf \
-spec fred.spec \
-surf_A smoothwm \
-surf_B pial \
-sv fred_anat+orig \
-grid_parent fred_func+orig \
-cmask '-a fred_func+orig[2] -expr step(a-0.6)' \
-map_func seg_vals \
-f_steps 10 \
-f_index nodes \
-oob_value 0.0 \
-oom_value 0.0 \
-out_1D fred_func_segvals_10_all.1D
8. This is a basic example of calculating the average along
each segment, but where the segment is produced by only
one surface, along with its set of surface normals. The
segments will be 2.5 mm in length.
3dVol2Surf \
-spec fred.spec \
-surf_A smoothwm \
-sv fred_anat+orig \
-grid_parent fred_anat+orig \
-use_norms \
-norm_len 2.5 \
-map_func ave \
-f_steps 10 \
-f_index nodes \
-out_1D fred_anat_norm_ave.2.5.1D
9. This is the same as example 8, but where the surface
nodes are restricted to the range 1000..1999 via the
options '-first_node' and '-last_node'.
3dVol2Surf \
-spec fred.spec \
-surf_A smoothwm \
-sv fred_anat+orig \
-grid_parent fred_anat+orig \
-first_node 1000 \
-last_node 1999 \
-use_norms \
-norm_len 2.5 \
-map_func ave \
-f_steps 10 \
-f_index nodes \
-out_1D fred_anat_norm_ave.2.5.1D
--------------------------------------------------
REQUIRED COMMAND ARGUMENTS:
-spec SPEC_FILE : SUMA spec file
e.g. -spec fred.spec
The surface specification file contains the list of
mappable surfaces that are used.
See @SUMA_Make_Spec_FS and @SUMA_Make_Spec_SF.
-surf_A SURF_NAME : name of surface A (from spec file)
-surf_B SURF_NAME : name of surface B (from spec file)
e.g. -surf_A smoothwm
e.g. -surf_A lh.smoothwm
e.g. -surf_B lh.pial
This is used to specify which surface(s) will be used by
the program. The '-surf_A' parameter is required, as it
specifies the first surface, whereas since '-surf_B' is
used to specify an optional second surface, it is not
required.
Note that any need for '-surf_B' may be fulfilled using
the '-use_norms' option.
Note that any name provided must be in the spec file,
uniquely matching the name of a surface node file (such
as lh.smoothwm.asc, for example). Note that if both
hemispheres are represented in the spec file, then there
may be both lh.pial.asc and rh.pial.asc, for instance.
In such a case, 'pial' would not uniquely determine a
a surface, but the name 'lh.pial' would.
-sv SURFACE_VOLUME : AFNI volume dataset
e.g. -sv fred_anat+orig
This is the AFNI dataset that the surface is mapped to.
This dataset is used for the initial surface node to xyz
coordinate mapping, in the Dicom orientation.
-grid_parent AFNI_DSET : AFNI volume dataset
e.g. -grid_parent fred_function+orig
This dataset is used as a grid and orientation master
for the output (i.e. it defines the volume domain).
It is also the source of the output data values.
-map_func MAP_FUNC : filter for values along the segment
e.g. -map_func ave
e.g. -map_func ave -f_steps 10
e.g. -map_func ave -f_steps 10 -f_index nodes
The current mapping function for 1 surface is:
mask : For each surface xyz location, output the
dataset values of each sub-brick.
Most mapping functions are defined for 2 related input
surfaces (such as white/grey boundary and pial). For
each node pair, the function will be performed on the
values from the 'grid parent dataset', and along the
segment connecting the nodes.
ave : Output the average of the dataset values
along the segment.
max : Output the maximum dataset value along the
connecting segment.
max_abs : Output the dataset value with the maximum
absolute value along the segment.
median : Output the median of the dataset values
along the connecting segment.
midpoint : Output the dataset value with xyz
coordinates at the midpoint of the nodes.
min : Output the minimum dataset value along the
connecting segment.
mode : Output the mode of the dataset values along
the connecting segment.
seg_vals : Output all of the dataset values along the
connecting segment. Here, only sub-brick
number 0 will be considered.
------------------------------
options specific to functions on 2 surfaces:
-f_steps NUM_STEPS :
Use this option to specify the number of
evenly spaced points along each segment.
The default is 2 (i.e. just use the two
surface nodes as endpoints).
e.g. -f_steps 10
default: -f_steps 2
-f_index TYPE :
This option specifies whether to use all
segment point values in the filter (using
the 'nodes' TYPE), or to use only those
corresponding to unique volume voxels (by
using the 'voxel' TYPE).
For instance, when taking the average along
one node pair segment using 10 node steps,
perhaps 3 of those nodes may occupy one
particular voxel. In this case, does the
user want the voxel counted only once, or 3
times? Each way makes sense.
Note that this will only make sense when
used along with the '-f_steps' option.
Possible values are "nodes", "voxels".
The default value is voxels. So each voxel
along a segment will be counted only once.
e.g. -f_index nodes
e.g. -f_index voxels
default: -f_index voxels
-f_keep_surf_order :
Depreciated.
See required arguments -surf_A and -surf_B,
above.
Note: The following -f_pX_XX options are used to alter
the lengths and locations of the computational
segments. Recall that by default, segments are
defined using the node pair coordinates as
endpoints. And the direction from p1 to pn is
from the inner surface to the outer surface.
-f_p1_mm DISTANCE :
This option is used to specify a distance
in millimeters to add to the first point of
each line segment (in the direction of the
second point). DISTANCE can be negative
(which would set p1 to be farther from pn
than before).
For example, if a computation is over the
grey matter (from the white matter surface
to the pial), and it is wished to increase
the range by 1mm, set this DISTANCE to -1.0
and the DISTANCE in -f_pn_mm to 1.0.
e.g. -f_p1_mm -1.0
e.g. -f_p1_mm -1.0 -f_pn_mm 1.0
-f_pn_mm DISTANCE :
Similar to -f_p1_mm, this option is used
to specify a distance in millimeters to add
to the second point of each line segment.
Note that this is in the same direction as
above, from point p1 to point pn.
So a positive DISTANCE, for this option,
would set pn to be farther from p1 than
before, and a negative DISTANCE would set
it to be closer.
e.g. -f_pn_mm 1.0
e.g. -f_p1_mm -1.0 -f_pn_mm 1.0
-f_p1_fr FRACTION :
Like the -f_pX_mm options above, this
is used to specify a change to point p1, in
the direction of point pn, but the change
is a fraction of the original distance,
not a pure change in millimeters.
For example, suppose one wishes to do a
computation based on the segments spanning
the grey matter, but to add 20% to either
side. Then use -0.2 and 0.2:
e.g. -f_p1_fr -0.2
e.g. -f_p1_fr -0.2 -f_pn_fr 0.2
-f_pn_fr FRACTION :
See -f_p1_fr above. Note again that the
FRACTION is in the direction from p1 to pn.
So to extend the segment past pn, this
FRACTION will be positive (and to reduce
the segment back toward p1, this -f_pn_fr
FRACTION will be negative).
e.g. -f_pn_fr 0.2
e.g. -f_p1_fr -0.2 -f_pn_fr 0.2
Just for entertainment, one could reverse
the order that the segment points are
considered by adjusting p1 to be pn, and
pn to be p1. This could be done by adding
a fraction of 1.0 to p1 and by subtracting
a fraction of 1.0 from pn.
e.g. -f_p1_fr 1.0 -f_pn_fr -1.0
------------------------------
options specific to use of normals:
Notes:
o Using a single surface with its normals for segment
creation can be done in lieu of using two surfaces.
o Normals at surface nodes are defined by the average of
the normals of the triangles including the given node.
o The default normals have a consistent direction, but it
may be opposite of what is should be. For this reason,
the direction is verified by default, and may be negated
internally. See the '-keep_norm_dir' option for more
information.
-use_norms : use normals for second surface
Segments are usually defined by connecting corresponding
node pairs from two surfaces. With this options the
user can use one surface, along with its normals, to
define the segments.
By default, each segment will be 1.0 millimeter long, in
the direction of the normal. The '-norm_len' option
can be used to alter this default action.
-keep_norm_dir : keep the direction of the normals
Normal directions are verified by checking that the
normals of the outermost 6 points point away from the
center of mass. If they point inward instead, then
they are negated.
This option will override the directional check, and
use the normals as they come.
See also -reverse_norm_dir, below.
-norm_len LENGTH : use LENGTH for node normals
e.g. -norm_len 3.0
e.g. -norm_len -3.0
default: -norm_len 1.0
For use with the '-use_norms' option, this allows the
user to specify a directed distance to use for segments
based on the normals. So for each node on a surface,
the computation segment will be from the node, in the
direction of the normal, a signed distance of LENGTH.
A negative LENGTH means to use the opposite direction
from the normal.
The '-surf_B' option is not allowed with the use of
normals.
-reverse_norm_dir : reverse the normal directions
Normal directions are verified by checking that the
normals of the outermost 6 points point away from the
center of mass. If they point inward instead, then
they are negated.
This option will override the directional check, and
reverse the direction of the normals as they come.
See also -keep_norm_dir, above.
------------------------------
general options:
-cmask MASK_COMMAND : (optional) command for dataset mask
e.g. -cmask '-a fred_func+orig[2] -expr step(a-0.8)'
This option will produce a mask to be applied to the
input AFNI dataset. Note that this mask should form a
single sub-brick.
This option follows the style of 3dmaskdump (since the
code for it was, uh, borrowed from there (thanks Bob!)).
See '3dmaskdump -help' for more information.
-debug LEVEL : (optional) verbose output
e.g. -debug 2
This option is used to print out status information
during the execution of the program. Current levels are
from 0 to 5.
-first_node NODE_NUM : skip all previous nodes
e.g. -first_node 1000
e.g. -first_node 1000 -last_node 1999
Restrict surface node output to those with indices as
large as NODE_NUM. In the first example, the first 1000
nodes are ignored (those with indices from 0 through
999).
See also, '-last_node'.
-dnode NODE_NUM : (optional) node for debug
e.g. -dnode 1874
This option is used to print out status information
for node NODE_NUM.
-gp_index SUB_BRICK : choose grid_parent sub-brick
e.g. -gp_index 3
This option allows the user to choose only a single
sub-brick from the grid_parent dataset for computation.
Note that this option is virtually useless when using
the command-line, as the user can more directly do this
via brick selectors, e.g. func+orig'[3]'.
This option was written for the afni interface.
-help : show this help
If you can't get help here, please get help somewhere.
-hist : show revision history
Display module history over time.
See also, -v2s_hist
-last_node NODE_NUM : skip all following nodes
e.g. -last_node 1999
e.g. -first_node 1000 -last_node 1999
Restrict surface node output to those with indices no
larger than NODE_NUM. In the first example, nodes above
1999 are ignored (those with indices from 2000 on up).
See also, '-first_node'.
-no_headers : do not output column headers
Column header lines all begin with the '#' character.
With the '-no_headers' option, these lines will not be
output.
-oob_index INDEX_NUM : specify default index for oob nodes
e.g. -oob_index -1
default: -oob_index 0
By default, nodes which lie outside the box defined by
the -grid_parent dataset are considered out of bounds,
and are skipped. If an out of bounds index is provided,
or an out of bounds value is provided, such nodes will
not be skipped, and will have indices and values output,
according to the -oob_index and -oob_value options.
This INDEX_NUM will be used for the 1dindex field, along
with the i, j and k indices.
-oob_value VALUE : specify default value for oob nodes
e.g. -oob_value -999.0
default: -oob_value 0.0
See -oob_index, above.
VALUE will be output for nodes which are out of bounds.
-oom_value VALUE : specify default value for oom nodes
e.g. -oom_value -999.0
e.g. -oom_value 0.0
By default, node pairs defining a segment which gets
completely obscured by a command-line mask (see -cmask)
are considered "out of mask", and are skipped.
If an out of mask value is provided, such nodes will not
be skipped. The output indices will come from the first
segment point, mapped to the AFNI volume. All output vN
values will be the VALUE provided with this option.
This option is meaningless without a '-cmask' option.
-out_1D OUTPUT_FILE : specify a 1D file for the output
e.g. -out_1D mask_values_over_dataset.1D
This is where the user will specify which file they want
the output to be written to. In this case, the output
will be in readable, column-formatted ASCII text.
Note : the output file should not yet exist.
: -out_1D or -out_niml must be used
-out_niml OUTPUT_FILE : specify a niml file for the output
e.g. -out_niml mask_values_over_dataset.niml
The user may use this option to get output in the form
of a niml element, with binary data. The output will
contain (binary) columns of the form:
node_index value_0 value_1 value_2 ...
A major difference between 1D output and niml output is
that the value_0 column number will be 6 in the 1D case,
but will be 2 in the niml case. The index columns will
not be used for niml output.
Note : the output file should not yet exist.
: -out_1D or -out_niml must be used
-skip_col_nodes : do not output node column
-skip_col_1dindex : do not output 1dindex column
-skip_col_i : do not output i column
-skip_col_j : do not output j column
-skip_col_k : do not output k column
-skip_col_vals : do not output vals column
-skip_col_results : only output ONE result column
(seems to make the most sense)
-skip_col_non_results : skip everything but the results
(i.e. only output result columns)
These options are used to restrict output. Each option
will prevent the program from writing that column of
output to the 1D file.
For now, the only effect that these options can have on
the niml output is by skipping nodes or results (all
other columns are skipped by default).
-v2s_hist : show revision history for library
Display vol2surf library history over time.
See also, -hist
-version : show version information
Show version and compile date.
--------------------------------------------------
Output from the program defaults to 1D format, in ascii text.
For each node (pair) that results in output, there will be one
line, consisting of:
node : the index of the current node (or node pair)
1dindex : the global index of the AFNI voxel used for output
Note that for some filters (min, max, midpoint,
median and mode) there is a specific location (and
therefore voxel) that the result comes from. It
will be accurate (though median may come from one
of two voxels that are averaged).
For filters without a well-defined source (such as
average or seg_vals), the 1dindex will come from
the first point on the corresponding segment.
Note: this will _not_ be output in the niml case.
i j k : the i j k indices matching 1dindex
These indices are based on the orientation of the
grid parent dataset.
Note: these will _not_ be output in the niml case.
vals : the number of segment values applied to the filter
Note that when -f_index is 'nodes', this will
always be the same as -f_steps, except when using
the -cmask option. In that case, along a single
segment, some points may be in the mask, and some
may not.
When -f_index is 'voxels' and -f_steps is used,
vals will often be much smaller than -f_steps.
This is because many segment points may in a
single voxel.
Note: this will _not_ be output in the niml case.
v0, ... : the requested output values
These are the filtered values, usually one per
AFNI sub-brick. For example, if the -map_func
is 'ave', then there will be one segment-based
average output per sub-brick of the grid parent.
In the case of the 'seg_vals' filter, however,
there will be one output value per segment point
(possibly further restricted to voxels). Since
output is not designed for a matrix of values,
'seg_vals' is restricted to a single sub-brick.
Author: R. Reynolds - version 6.4 (June 2, 2005)
(many thanks to Z. Saad and R.W. Cox)
This page auto-generated on Thu Aug 25 16:49:38 EDT 2005
|
| 3dvolreg |
Usage: 3dvolreg [options] dataset
Registers each 3D sub-brick from the input dataset to the base brick.
'dataset' may contain a sub-brick selector list.
OPTIONS:
-verbose Print progress reports. Use twice for LOTS of output.
-Fourier Perform the alignments using Fourier interpolation.
-heptic Use heptic polynomial interpolation.
-quintic Use quintic polynomical interpolation.
-cubic Use cubic polynomial interpolation.
Default = Fourier [slowest and most accurate interpolator]
-clipit Clips the values in each output sub-brick to be in the same
range as the corresponding input volume.
The interpolation schemes can produce values outside
the input range, which is sometimes annoying.
[16 Apr 2002: -clipit is now the default]
-noclip Turns off -clipit
-zpad n Zeropad around the edges by 'n' voxels during rotations
(these edge values will be stripped off in the output)
N.B.: Unlike to3d, in this program '-zpad' adds zeros in
all directions.
N.B.: The environment variable AFNI_ROTA_ZPAD can be used
to set a nonzero default value for this parameter.
-prefix fname Use 'fname' for the output dataset prefix.
The program tries not to overwrite an existing dataset.
Default = 'volreg'.
-base n Sets the base brick to be the 'n'th sub-brick
from the input dataset (indexing starts at 0).
Default = 0 (first sub-brick).
-base 'bset[n]' Sets the base brick to be the 'n'th sub-brick
from the dataset specified by 'bset', as in
-base 'elvis+orig[4]'
The quotes are needed because the '[]' characters
are special to the shell.
-dfile dname Save the motion parameters in file 'dname'.
The output is in 9 ASCII formatted columns:
n roll pitch yaw dS dL dP rmsold rmsnew
where: n = sub-brick index
roll = rotation about the I-S axis }
pitch = rotation about the R-L axis } degrees CCW
yaw = rotation about the A-P axis }
dS = displacement in the Superior direction }
dL = displacement in the Left direction } mm
dP = displacement in the Posterior direction }
rmsold = RMS difference between input brick and base brick
rmsnew = RMS difference between output brick and base brick
N.B.: If the '-dfile' option is not given, the parameters aren't saved.
N.B.: The motion parameters are those needed to bring the sub-brick
back into alignment with the base. In 3drotate, it is as if
the following options were applied to each input sub-brick:
-rotate <ROLL>I <PITCH>R <YAW>A -ashift <DS>S <DL>L <DP>P
-1Dfile ename Save the motion parameters ONLY in file 'ename'.
The output is in 6 ASCII formatted columns:
roll pitch yaw dS dL dP
This file can be used in FIM as an 'ort', to detrend
the data against correlation with the movements.
This type of analysis can be useful in removing
errors made in the interpolation.
-rotcom Write the fragmentary 3drotate commands needed to
perform the realignments to stdout; for example:
3drotate -rotate 7.2I 3.2R -5.7A -ashift 2.7S -3.8L 4.9P
The purpose of this is to make it easier to shift other
datasets using exactly the same parameters.
-tshift ii If the input dataset is 3D+time and has slice-dependent
time-offsets (cf. the output of 3dinfo -v), then this
option tells 3dvolreg to time shift it to the average
slice time-offset prior to doing the spatial registration.
The integer 'ii' is the number of time points at the
beginning to ignore in the time shifting. The results
should like running program 3dTshift first, then running
3dvolreg -- this is primarily a convenience option.
N.B.: If the base brick is taken from this dataset, as in
'-base 4', then it will be the time shifted brick.
If for some bizarre reason this is undesirable, you
could use '-base this+orig[4]' instead.
-rotparent rset
Specifies that AFTER the registration algorithm finds the best
transformation for each sub-brick of the input, an additional
rotation+translation should be performed before computing the
final output dataset; this extra transformation is taken from
the first 3dvolreg transformation found in dataset 'rset'.
-gridparent gset
Specifies that the output dataset of 3dvolreg should be shifted to
match the grid of dataset 'gset'. Can only be used with -rotparent.
This dataset should be one this is properly aligned with 'rset' when
overlaid in AFNI.
* If 'gset' has a different number of slices than the input dataset,
then the output dataset will be zero-padded in the slice direction
to match 'gset'.
* These options are intended to be used to align datasets between sessions:
S1 = SPGR from session 1 E1 = EPI from session 1
S2 = SPGR from session 2 E2 = EPI from session 2
3dvolreg -twopass -twodup -base S1+orig -prefix S2reg S2+orig
3dvolreg -rotparent S2reg+orig -gridparent E1+orig -prefix E2reg \
-base 4 E2+orig
Each sub-brick in E2 is registered to sub-brick E2+orig[4], then the
rotation from S2 to S2reg is also applied, which shifting+padding
applied to properly overlap with E1.
* A similar effect could be done by using commands
3dvolreg -twopass -twodup -base S1+orig -prefix S2reg S2+orig
3dvolreg -prefix E2tmp -base 4 E2+orig
3drotate -rotparent S2reg+orig -gridparent E1+orig -prefix E2reg E2tmp+orig
The principal difference is that the latter method results in E2
being interpolated twice to make E2reg: once in the 3dvolreg run to
produce E2tmp, then again when E2tmp is rotated to make E2reg. Using
3dvolreg with the -rotparent and -gridparent options simply skips the
intermediate interpolation.
*** Please read file README.registration for more ***
*** information on the use of 3dvolreg and 3drotate ***
Algorithm: Iterated linearized weighted least squares to make each
sub-brick as like as possible to the base brick.
This method is useful for finding SMALL MOTIONS ONLY.
See program 3drotate for the volume shift/rotate algorithm.
The following options can be used to control the iterations:
-maxite m = Allow up to 'm' iterations for convergence
[default = 19].
-x_thresh x = Iterations converge when maximum movement
is less than 'x' voxels [default=0.020000],
-rot_thresh r = And when maximum rotation is less than
'r' degrees [default=0.030000].
-delta d = Distance, in voxel size, used to compute
image derivatives using finite differences
[default=0.700000].
-final mode = Do the final interpolation using the method
defined by 'mode', which is one of the
strings 'NN', 'cubic', 'quintic', 'heptic',
or 'Fourier'
[default=mode used to estimate parameters].
-weight 'wset[n]' = Set the weighting applied to each voxel
proportional to the brick specified here
[default=smoothed base brick].
N.B.: if no weight is given, and -twopass is
engaged, then the first pass weight is the
blurred sum of the base brick and the first
data brick to be registered.
-edging ee = Set the size of the region around the edges of
the base volume where the default weight will
be set to zero. If 'ee' is a plain number,
then it is a voxel count, giving the thickness
along each face of the 3D brick. If 'ee' is
of the form '5%', then it is a fraction of
of each brick size. For example, '5%' of
a 256x256x124 volume means that 13 voxels
on each side of the xy-axes will get zero
weight, and 6 along the z-axis. If this
option is not used, then 'ee' is read from
the environment variable AFNI_VOLREG_EDGING.
If that variable is not set, then 5% is used.
N.B.: This option has NO effect if the -weight
option is used.
N.B.: The largest % value allowed is 25%.
-twopass = Do two passes of the registration algorithm:
(1) with smoothed base and data bricks, with
linear interpolation, to get a crude
alignment, then
(2) with the input base and data bricks, to
get a fine alignment.
This method is useful when aligning high-
resolution datasets that may need to be
moved more than a few voxels to be aligned.
-twoblur bb = 'bb' is the blurring factor for pass 1 of
the -twopass registration. This should be
a number >= 2.0 (which is the default).
Larger values would be reasonable if pass 1
has to move the input dataset a long ways.
Use '-verbose -verbose' to check on the
iterative progress of the passes.
N.B.: when using -twopass, and you expect the
data bricks to move a long ways, you might
want to use '-heptic' rather than
the default '-Fourier', since you can get
wraparound from Fourier interpolation.
-twodup = If this option is set, along with -twopass,
then the output dataset will have its
xyz-axes origins reset to those of the
base dataset. This is equivalent to using
'3drefit -duporigin' on the output dataset.
-sinit = When using -twopass registration on volumes
whose magnitude differs significantly, the
least squares fitting procedure is started
by doing a zero-th pass estimate of the
scale difference between the bricks.
Use this option to turn this feature OFF.
-coarse del num = When doing the first pass, the first step is
to do a number of coarse shifts in order to
find a starting point for the iterations.
'del' is the size of these steps, in voxels;
'num' is the number of these steps along
each direction (+x,-x,+y,-y,+z,-z). The
default values are del=10 and num=2. If
you don't want this step performed, set
num=0. Note that the amount of computation
grows as num**3, so don't increase num
past 4, or the program will run forever!
N.B.: The 'del' parameter cannot be larger than
10% of the smallest dimension of the input
dataset.
-wtinp = Use sub-brick[0] of the input dataset as the
weight brick in the final registration pass.
N.B.: * This program can consume VERY large quantities of memory.
(Rule of thumb: 40 bytes per input voxel.)
Use of '-verbose -verbose' will show the amount of workspace,
and the steps used in each iteration.
* ALWAYS check the results visually to make sure that the program
wasn't trapped in a 'false optimum'.
* The default rotation threshold is reasonable for 64x64 images.
You may want to decrease it proportionally for larger datasets.
* -twopass resets the -maxite parameter to 66; if you want to use
a different value, use -maxite AFTER the -twopass option.
* The -twopass option can be slow; several CPU minutes for a
256x256x124 volume is a typical run time.
* After registering high-resolution anatomicals, you may need to
set their origins in 3D space to match. This can be done using
the '-duporigin' option to program 3drefit, or by using the
'-twodup' option to this program.
</DL>
This page auto-generated on Thu Aug 25 16:49:38 EDT 2005
|
| 3dWarp |
Usage: 3dWarp [options] dataset
Warp (spatially transform) a 3D dataset.
--------------------------
Transform Defining Options: [exactly one of these must be used]
--------------------------
-matvec_in2out mmm = Read a 3x4 affine transform matrix+vector
from file 'mmm':
x_out = Matrix x_in + Vector
-matvec_out2in mmm = Read a 3x4 affine transform matrix+vector
from file 'mmm':
x_in = Matrix x_out + Vector
** N.B.: The coordinate vectors described above are
defined in DICOM ('RAI') coordinate order.
(Also see the '-fsl_matvec option, below.)
** N.B.: Using the special name 'IDENTITY' for 'mmm'
means to use the identity matrix.
** N.B.: You can put the matrix on the command line
directly by using an argument of the form
'MATRIX(a11,a12,a13,a14,a21,a22,a23,a24,a31,a32,a33,a34)'
in place of 'mmm', where the aij values are the
matrix entries (aij = i-th row, j-th column),
separated by commas.
* You will need the 'forward single quotes' around
the argument.
-tta2mni = Transform a dataset in Talairach-Tournoux Atlas
coordinates to MNI-152 coordinates.
-mni2tta = Transform a dataset in MNI-152 coordinates to
Talairach-Tournoux Atlas coordinates.
-matparent mset = Read in the matrix from WARPDRIVE_MATVEC_*
attributes in the header of dataset 'mset',
which must have been created by program
3dWarpDrive. In this way, you can apply
a transformation matrix computed from
in 3dWarpDrive to another dataset.
** N.B.: The above option is analogous to the -rotparent
option in program 3drotate. Use of -matparent
should be limited to datasets whose spatial
coordinate system corresponds to that which
was used for input to 3dWarpDrive (i.e., the
input to 3dWarp should overlay properly with
the input to 3dWarpDrive that generated the
-matparent dataset).
Sample usages:
3dWarpDrive -affine_general -base d1+orig -prefix d2WW -twopass -input d2+orig
3dWarp -matparent d2WW+orig -prefix epi2WW epi2+orig
-----------------------
Other Transform Options:
-----------------------
-linear }
-cubic } = Chooses spatial interpolation method.
-NN } = [default = linear]
-quintic }
-fsl_matvec = Indicates that the matrix file 'mmm' uses FSL
ordered coordinates ('LPI'). For use with
matrix files from FSL and SPM.
-newgrid ddd = Tells program to compute new dataset on a
new 3D grid, with spacing of 'ddd' mmm.
* If this option is given, then the new
3D region of space covered by the grid
is computed by warping the 8 corners of
the input dataset, then laying down a
regular grid with spacing 'ddd'.
* If this option is NOT given, then the
new dataset is computed on the old
dataset's grid.
-gridset ggg = Tells program to compute new dataset on the
same grid as dataset 'ggg'.
-zpad N = Tells program to pad input dataset with 'N'
planes of zeros on all sides before doing
transformation.
---------------------
Miscellaneous Options:
---------------------
-prefix ppp = Sets the prefix of the output dataset.
This page auto-generated on Thu Aug 25 16:49:38 EDT 2005
|
| 3dWarpDrive |
Usage: 3dWarpDrive [options] dataset
Warp a dataset to match another one (the base).
This program is a generalization of 3dvolreg. It tries to find
a spatial transformation that warps a given dataset to match an
input dataset (given by the -base option). It will be slow.
--------------------------
Transform Defining Options: [exactly one of these must be used]
--------------------------
-shift_only = 3 parameters (shifts)
-shift_rotate = 6 parameters (shifts + angles)
-shift_rotate_scale = 9 parameters (shifts + angles + scale factors)
-affine_general = 12 parameters (3 shifts + 3x3 matrix)
-bilinear_general = 39 parameters (3 + 3x3 + 3x3x3)
N.B.: At this time, the image intensity is NOT
adjusted for the Jacobian of the transformation.
N.B.: -bilinear_general is not yet implemented.
-------------
Other Options:
-------------
-linear }
-cubic } = Chooses spatial interpolation method.
-NN } = [default = linear; inaccurate but fast]
-quintic } [for accuracy, try '-cubic -final quintic']
-base bbb = Load dataset 'bbb' as the base to which the
input dataset will be matched.
[This is a mandatory option]
-verb = Print out lots of information along the way.
-prefix ppp = Sets the prefix of the output dataset.
-input ddd = You can put the input dataset anywhere in the
command line option list by using the '-input'
option, instead of always putting it last.
-----------------
Technical Options:
-----------------
-maxite m = Allow up to 'm' iterations for convergence.
-delta d = Distance, in voxel size, used to compute
image derivatives using finite differences.
[Default=1.0]
-weight wset = Set the weighting applied to each voxel
proportional to the brick specified here.
[Default=computed by program from base]
-thresh t = Set the convergence parameter to be RMS 't' voxels
movement between iterations. [Default=0.03]
-twopass = Do the parameter estimation in two passes,
coarse-but-fast first, then fine-but-slow second
(much like the same option in program 3dvolreg).
This is useful if large-ish warping is needed to
align the volumes.
-final 'mode' = Set the final warp to be interpolated using 'mode'
instead of the spatial interpolation method used
to find the warp parameters.
-parfix n v = Fix the n'th parameter of the warp model to
the value 'v'. More than one -parfix option
can be used, to fix multiple parameters.
-1Dfile ename = Write out the warping parameters to the file
named 'ename'. Each sub-brick of the input
dataset gets one line in this file. Each
parameter in the model gets one column.
-float = Write output dataset in float format, even if
input dataset is short or byte.
----------------------
AFFINE TRANSFORMATIONS:
----------------------
The options below control how the affine tranformations
(-shift_rotate, -shift_rotate_scale, -affine_general)
are structured in terms of 3x3 matrices:
-SDU or -SUD }= Set the order of the matrix multiplication
-DSU or -DUS }= for the affine transformations:
-USD or -UDS }= S = triangular shear (params #10-12)
D = diagonal scaling matrix (params #7-9)
U = rotation matrix (params #4-6)
Default order is '-SDU', which means that
the U matrix is applied first, then the
D matrix, then the S matrix.
-Supper }= Set the S matrix to be upper or lower
-Slower }= triangular [Default=lower triangular]
-ashift OR }= Apply the shift parameters (#1-3) after OR
-bshift }= before the matrix transformation. [Default=after]
The matrices are specified in DICOM-ordered (x=-R+L,y=-A+P,z=-I+S)
coordinates as:
[U] = [Rotate_y(param#6)] [Rotate_x(param#5)] [Rotate_z(param #4)]
(angles are in degrees)
[D] = diag( param#7 , param#8 , param#9 )
[ 1 0 0 ] [ 1 param#10 param#11 ]
[S] = [ param#10 1 0 ] OR [ 0 1 param#12 ]
[ param#11 param#12 1 ] [ 0 0 1 ]
For example, the default (-SDU/-ashift/-Slower) has the warp
specified as [x]_warped = [S] [D] [U] [x]_in + [shift].
The shift vector comprises parameters #1, #2, and #3.
The goal of the program is to find the warp parameters such that
I([x]_warped) = s * J([x]_in)
as closely as possible in a weighted least squares sense, where
's' is a scaling factor (an extra, invisible, parameter), J(x)
is the base image, I(x) is the input image, and the weight image
is a blurred copy of J(x).
Using '-parfix', you can specify that some of these parameters
are fixed. For example, '-shift_rotate_scale' is equivalent
'-affine_general -parfix 10 0 -parfix 11 0 -parfix 12 0'.
Don't attempt to use the '-parfix' option unless you understand
this example!
-------------------------
RWCox - November 2004
-------------------------
This page auto-generated on Thu Aug 25 16:49:38 EDT 2005
|
| 3dWavelets |
Program: 3dWavelets
Author: B. Douglas Ward
Initial Release: 28 March 2000
Latest Revision: 02 December 2002
Program to perform wavelet analysis of an FMRI 3d+time dataset.
Usage:
3dWavelets
-type wname wname = name of wavelet to use for the analysis
At present, there are only two choices for wname:
Haar --> Haar wavelets
Daub --> Daubechies wavelets
-input fname fname = filename of 3d+time input dataset
[-input1D dname] dname = filename of single (fMRI) .1D time series
[-mask mname] mname = filename of 3d mask dataset
[-nfirst fnum] fnum = number of first dataset image to use in
the wavelet analysis. (default = 0)
[-nlast lnum] lnum = number of last dataset image to use in
the wavelet analysis. (default = last)
[-fdisp fval] Write (to screen) results for those voxels
whose F-statistic is >= fval
Filter options:
[-filt_stop band mintr maxtr] Specify wavelet coefs. to set to zero
[-filt_base band mintr maxtr] Specify wavelet coefs. for baseline model
[-filt_sgnl band mintr maxtr] Specify wavelet coefs. for signal model
where band = frequency band
mintr = min. value for time window (in TR)
maxtr = max. value for time window (in TR)
Output options:
[-coefts cprefix] cprefix = prefix of 3d+time output dataset which
will contain the forward wavelet transform
coefficients
[-fitts fprefix] fprefix = prefix of 3d+time output dataset which
will contain the full model time series fit
to the input data
[-sgnlts sprefix] sprefix = prefix of 3d+time output dataset which
will contain the signal model time series fit
to the input data
[-errts eprefix] eprefix = prefix of 3d+time output dataset which
will contain the residual error time series
from the full model fit to the input data
The following options control the contents of the bucket dataset:
[-fout] Flag to output the F-statistics
[-rout] Flag to output the R^2 statistics
[-cout] Flag to output the full model wavelet coefficients
[-vout] Flag to output the sample variance (MSE) map
[-stat_first] Flag to specify that the full model statistics will
appear prior to the wavelet coefficients in the
bucket dataset output
[-bucket bprefix] bprefix = prefix of AFNI 'bucket' dataset containing
parameters of interest, such as the F-statistic
for significance of the wavelet signal model.
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|
| 3dWilcoxon |
Program: 3dWilcoxon
Author: B. Douglas Ward
Initial Release: 23 July 1997
Latest Revision: 02 Dec 2002
This program performs the nonparametric Wilcoxon signed-rank test
for paired comparisons of two samples.
Usage:
3dWilcoxon
-dset 1 filename data set for X observations
. . . . . .
-dset 1 filename data set for X observations
-dset 2 filename data set for Y observations
. . . . . .
-dset 2 filename data set for Y observations
[-workmem mega] number of megabytes of RAM to use
for statistical workspace
[-voxel num] screen output for voxel # num
-out prefixname estimated population delta and
Wilcoxon signed-rank statistics are
written to file prefixname
N.B.: For this program, the user must specify 1 and only 1 sub-brick
with each -dset command. That is, if an input dataset contains
more than 1 sub-brick, a sub-brick selector must be used, e.g.:
-dset 2 'fred+orig[3]'
INPUT DATASET NAMES
-------------------
This program accepts datasets that are modified on input according to the
following schemes:
'r1+orig[3..5]' {sub-brick selector}
'r1+orig<100.200>' {sub-range selector}
'r1+orig[3..5]<100..200>' {both selectors}
'3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )' {calculation}
For the gruesome details, see the output of 'afni -help'.
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|
| 3dWinsor |
Usage: 3dWinsor [options] dataset
Apply a 3D 'Winsorizing' filter to a short-valued dataset.
Options:
-irad rr = include all points within 'distance'
rr in the operation, where distance
is defined as sqrt(i*i+j*j+k*k), and
(i,j,k) are voxel index offsets
[default rr=1.5]
-cbot bb = set bottom clip index to bb
[default = 20% of the number of points]
-ctop tt = set top clip index to tt
[default = 80% of the number of points]
-nrep nn = repeat filter nn times [default nn=1]
if nn < 0, means to repeat filter until
less than abs(n) voxels change
-keepzero = don't filter voxels that are zero
-clip xx = set voxels at or below 'xx' to zero
-prefix pp = use 'pp' as the prefix for the output
dataset [default pp='winsor']
-mask mmm = use 'mmm' as a mask dataset - voxels NOT
in the mask won't be filtered
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|
| 3dZcat |
Usage: 3dZcat [options] dataset dataset ...
Concatenates datasets in the slice (z) direction. Each input
dataset must have the same number of voxels in each slice, and
must have the same number of sub-bricks.
Options:
-prefix pname = Use 'pname' for the output dataset prefix name.
[default='zcat']
-datum type = Coerce the output data to be stored as the given
type, which may be byte, short, or float.
-fscale = Force scaling of the output to the maximum integer
range. This only has effect if the output datum
is byte or short (either forced or defaulted).
This option is sometimes necessary to eliminate
unpleasant truncation artifacts.
-nscale = Don't do any scaling on output to byte or short datasets.
This may be especially useful when operating on mask
datasets whose output values are only 0's and 1's.
-verb = Print out some verbositiness as the program
proceeds.
Command line arguments after the above are taken as input datasets.
A dataset is specified using one of these forms:
'prefix+view', 'prefix+view.HEAD', or 'prefix+view.BRIK'.
INPUT DATASET NAMES
-------------------
This program accepts datasets that are modified on input according to the
following schemes:
'r1+orig[3..5]' {sub-brick selector}
'r1+orig<100.200>' {sub-range selector}
'r1+orig[3..5]<100..200>' {both selectors}
'3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )' {calculation}
For the gruesome details, see the output of 'afni -help'.
Notes:
* You can use the '3dinfo' program to see how many slices a
dataset comprises.
* There must be at least two datasets input (otherwise, the
program doesn't make much sense, does it?).
* Each input dataset must have the same number of voxels in each
slice, and must have the same number of sub-bricks.
* This program does not deal with complex-valued datasets.
* See the output of '3dZcutup -help' for a C shell script that
can be used to take a dataset apart into single slice datasets,
analyze them separately, and then assemble the results into
new 3D datasets.
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|
| 3dZcutup |
Usage: 3dZcutup [options] dataset
Cuts slices off a dataset in its z-direction, and writes a new
dataset. The z-direction and number of slices in a dataset
can be determined using the 3dinfo program.
Options:
-keep b t = Keep slices numbered 'b' through 't', inclusive.
This is a mandatory option. If you want to
create a single-slice dataset, this is allowed,
but AFNI may not display such datasets properly.
A single slice dataset would have b=t. Slice
numbers start at 0.
-prefix ppp = Write result into dataset with prefix 'ppp'
[default = 'zcutup']
Notes:
* You can use a sub-brick selector on the input dataset.
* 3dZcutup won't overwrite an existing dataset (I hope).
* This program is adapted from 3dZeropad, which does the
same thing, but along all 3 axes.
* You can glue datasets back together in the z-direction
using program 3dZcat. A sample C shell script that
uses these progams to carry out an analysis of a large
dataset is:
#!/bin/csh
# Cut 3D+time dataset epi07+orig into individual slices
foreach sl ( `count -dig 2 0 20` )
3dZcutup -prefix zcut${sl} -keep $sl $sl epi07+orig
# Analyze this slice with 3dDeconvolve separately
3dDeconvolve -input zcut${sl}+orig.HEAD \
-num_stimts 3 \
-stim_file 1 ann_response_07.1D \
-stim_file 2 antiann_response_07.1D \
-stim_file 3 righthand_response_07.1D \
-stim_label 1 annulus \
-stim_label 2 antiann \
-stim_label 3 motor \
-stim_minlag 1 0 -stim_maxlag 1 0 \
-stim_minlag 2 0 -stim_maxlag 2 0 \
-stim_minlag 3 0 -stim_maxlag 3 0 \
-fitts zcut${sl}_fitts \
-fout -bucket zcut${sl}_stats
end
# Assemble slicewise outputs into final datasets
time 3dZcat -verb -prefix zc07a_fitts zcut??_fitts+orig.HEAD
time 3dZcat -verb -prefix zc07a_stats zcut??_stats+orig.HEAD
# Remove individual slice datasets
/bin/rm -f zcut*
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|
| 3dZeropad |
Usage: 3dZeropad [options] dataset
Adds planes of zeros to a dataset (i.e., pads it out).
Options:
-I n = adds 'n' planes of zero at the Inferior edge
-S n = adds 'n' planes of zero at the Superior edge
-A n = adds 'n' planes of zero at the Anterior edge
-P n = adds 'n' planes of zero at the Posterior edge
-L n = adds 'n' planes of zero at the Left edge
-R n = adds 'n' planes of zero at the Right edge
-z n = adds 'n' planes of zeros on EACH of the
dataset z-axis (slice-direction) faces
-RL a = These options specify that planes should be added/cut
-AP b = symmetrically to make the resulting volume have
-IS c = 'a', 'b', and 'c' slices in the respective directions.
-mm = pad counts 'n' are in mm instead of slices:
* each 'n' is an integer
* at least 'n' mm of slices will be added/removed:
n = 3 and slice thickness = 2.5 mm ==> 2 slices added
n = -6 and slice thickness = 2.5 mm ==> 3 slices removed
-master mset = match the volume described in dataset 'mset':
* mset must have the same orientation and grid
spacing as dataset to be padded
* the goal of -master is to make the output dataset
from 3dZeropad match the spatial 'extents' of
mset (cf. 3dinfo output) as much as possible,
by adding/subtracting slices as needed.
* you can't use -I,-S,..., or -mm with -master
-prefix ppp = write result into dataset with prefix 'ppp'
[default = 'zeropad']
Nota Bene:
* You can use negative values of n to cut planes off the edges
of a dataset. At least one plane must be added/removed
or the program won't do anything.
* Anat parent and Talairach markers are NOT preserved in the
new dataset.
* If the old dataset has z-slice-dependent time offsets, and
if new (zero filled) z-planes are added, the time offsets
of the new slices will be set to zero.
* You can use program '3dinfo' to find out how many planes
a dataset has in each direction.
* Program works for byte-, short-, float-, and complex-valued
datasets.
* You can use a sub-brick selector on the input dataset.
* 3dZeropad won't overwrite an existing dataset (I hope).
Author: RWCox - July 2000
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|
| 3dZregrid |
Usage: 3dZregrid [option] dataset
Alters the input dataset's slice thickness and/or number.
OPTIONS:
-dz D = sets slice thickness to D mm
-nz N = sets slice count to N
-zsize Z = sets thickness of dataset (center-to-center of
first and last slices) to Z mm
-prefix P = write result in dataset with prefix P
-verb = write progress reports to stderr
At least one of '-dz', '-nz', or '-zsize' must be given.
On the other hand, using all 3 is over-specification.
The following combinations make sense:
-dz only ==> N stays fixed from input dataset
and then is like setting Z = N*D
-dz and -nz together ==> like setting Z = N*D
-dz and -zsize together ==> like setting N = Z/D
-nz only ==> D stays fixed from input dataset
and then is like setting Z = N*D
-zsize only ==> D stays fixed from input dataset
and then is like setting N = Z/D
-nsize and -zsize together ==> like setting D = Z/N
NOTES:
* If the input is a 3D+time dataset with slice-dependent time
offsets, the output will have its time offsets cleared.
It probably makes sense to do 3dTshift BEFORE using this
program in such a case.
* The output of this program is centered around the same
location as the input dataset. Slices outside the
original volume (e.g., when Z is increased) will be
zero. This is NOT the same as using 3dZeropad, which
only adds zeros, and does not interpolate to a new grid.
* Linear interpolation is used between slices. However,
new slice positions outside the old volume but within
0.5 old slice thicknesses will get a copy of the last slice.
New slices outside this buffer zone will be all zeros.
EXAMPLE:
You have two 3D anatomical datasets from the same subject that
need to be registered. Unfortunately, the first one has slice
thickness 1.2 mm and the second 1.3 mm. Assuming they have
the same number of slices, then do something like
3dZregrid -dz 1.2 -prefix ElvisZZ Elvis2+orig
3dvolreg -base Elvis1+orig -prefix Elvis2reg ElvisZZ+orig
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|
| @4Daverage |
********************************** This script is somewhat outdated. I suggest you use 3dMean which is faster, meaner and not limited to the alphabet. ZSS, 03/14/03 ********************************** \012Usage : @4Daverage <AVERAGE prefix brick 3D+t> <3D+t brik names...> \012This script file uses 3Dcalc to compute average 3D+time bricks example : @4Daverage NPt1av NPt1r1+orig NPt1r2+orig NPt1r3+orig The output NPt1av+orig is the average of the three bricks NPt1r1+orig, NPt1r2+orig and NPt1r3+orig You can use wildcards such as @4Daverage test ADzst2*.HEAD AFzst2r*.HEAD Make sure you do not pass both .HEAD and .BRIK names. If you do so they will be counted twice.\012 The bricks to be averaged must be listed individually. The total number of bricks that can be averaged at once (26) is determined by 3dcalc. \012Ziad Saad Nov 21 97, Marquette University Modified to accept wild cards Jan 24 01, FIM/LBC/NIH Ziad S. Saad (ziad@nih.gov)This page auto-generated on Thu Aug 25 16:49:38 EDT 2005 |
| 4swap |
Usage: 4swap [-q] file ... -- Swaps byte quadruples on the files listed. The -q option means to work quietly.This page auto-generated on Thu Aug 25 16:49:38 EDT 2005 |
| abut |
ABUT: put noncontiguous FMRI slices together [for to3d]
method: put zero valued slices in the gaps, then
replicate images to simulate thinner slices
Usage:
abut [-dzin thickness] [-dzout thickness] [-root name]
[-linear | -blocky] [-verbose] [-skip n+gap] ... images ...
-dzin the thickness value in mm; if not given,
taken to be 1.0 (in which case, the output
thickness and gap sizes are simply relative
to the slice thickness, rather than absolute)
-dzout the output slice thickness, usually smaller than
the input thickness; if not given, the program
will compute a value (the smaller the ratio
dzout/dzin is, the more slices will be output)
-root 'name' is the root (or prefix) for the output
slice filename; for example, '-root fred.'
will result in files fred.0001, fred.0002, ...
-linear if present, this flag indicates that subdivided slices
will be linearly interpolated rather than simply
replicated -- this will make the results smoother
in the through-slice direction (if dzout < dzin)
-blocky similar to -linear, but uses AFNI's 'blocky' interpolation
when possible to put out intermediate slices.
Both interpolation options only apply when dzout < dzin
and when an output slice has a non-gappy neighbor.
-skip 'n+gap' indicates that a gap is to be inserted
between input slices #n and #n+1, where n=1,2,...;
for example, -skip 6+5.5 means put a gap of 5.5 mm
between slices 6 and 7.
More than one -skip option is allowed. They must all occur
before the list of input image filenames.
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|
| adwarp |
Program: adwarp.c
Author: R. W. Cox and B. D. Ward
Initial Release: 02 April 1999
Latest Revision: 15 August 2001
Usage: adwarp [options]
Resamples a 'data parent' dataset to the grid defined by an
'anat parent' dataset. The anat parent dataset must contain
in its .HEAD file the coordinate transformation (warp) needed
to bring the data parent dataset to the output grid. This
program provides a batch implementation of the interactive
AFNI 'Write' buttons, one dataset at a time.
Example: adwarp -apar anat+tlrc -dpar func+orig
This will create dataset func+tlrc (.HEAD and .BRIK).
Options (so to speak):
----------------------
-apar aset = Set the anat parent dataset to 'aset'. This
is a nonoptional option (must be present).
-dpar dset = Set the data parent dataset to 'dset'. This
is a nonoptional option (must be present).
Note: dset may contain a sub-brick selector,
e.g., -dpar 'dset+orig[2,5,7]'
-prefix ppp = Set the prefix for the output dataset to 'ppp'.
The default is the prefix of 'dset'.
-dxyz ddd = Set the grid spacing in the output datset to
'ddd' mm. The default is 1 mm.
-verbose = Print out progress reports.
-force = Write out result even if it means deleting
an existing dataset. The default is not
to overwrite.
-resam rrr = Set resampling mode to 'rrr' for all sub-bricks
--- OR ---
-thr rrr = Set resampling mode to 'rrr' for threshold sub-bricks
-func rrr = Set resampling mode to 'rrr' for functional sub-bricks
The resampling mode 'rrr' must be one of the following:
NN = Nearest Neighbor
Li = Linear Interpolation
Cu = Cubic Interpolation
Bk = Blocky Interpolation
NOTE: The default resampling mode is Li for all sub-bricks.
This page auto-generated on Thu Aug 25 16:49:38 EDT 2005
|
| afni |
GPL AFNI: Analysis of Functional NeuroImages, by RW Cox (rwcox@nih.gov)
This is Version AFNI_2005_08_24_1751
[[Precompiled binary linux_gcc32: Aug 25 2005]]
** This software was designed to be used only for research purposes. **
** Clinical uses are not recommended, and have never been evaluated. **
** This software comes with no warranties of any kind whatsoever, **
** and may not be useful for anything. Use it at your own risk! **
** If these terms are not acceptable, you aren't allowed to use AFNI.**
** See 'Define Datamode->Misc->License Info' for more details. **
----------------------------------------------------------------
USAGE 1: read in sessions of 3D datasets (created by to3d, etc.)
----------------------------------------------------------------
afni [options] [session_directory ...]
-purge Conserve memory by purging data to disk.
[Use this if you run out of memory when running AFNI.]
[This will slow the code down, so use only if needed.]
-posfunc Set up the color 'pbar' to use only positive function values.
-R Recursively search each session_directory for more session
subdirectories.
WARNING: This will descend the entire filesystem hierarchy from
each session_directory given on the command line. On a
large disk, this may take a long time. To limit the
recursion to 5 levels (for example), use -R5.
-ignore N Tells the program to 'ignore' the first N points in
time series for graphs and FIM calculations.
-im1 N Tells the program to use image N as the first one for
graphs and FIM calculations (same as '-ignore N-1')
-tlrc_small These options set whether to use the 'small' or 'big'
-tlrc_big Talairach brick size. The compiled in default for
the program is now 'big', unlike AFNI 1.0x.
-no1D Tells AFNI not to read *.1D timeseries files from
the dataset directories. The *.1D files in the
directories listed in the AFNI_TSPATH environment
variable will still be read (if this variable is
not set, then './' will be scanned for *.1D files.)
-noqual Tells AFNI not to enforce the 'quality' checks when
making the transformations to +acpc and +tlrc.
-unique Tells the program to create a unique set of colors
for each AFNI controller window. This allows
different datasets to be viewed with different
grayscales or colorscales. Note that -unique
will only work on displays that support 12 bit
PseudoColor (e.g., SGI workstations) or TrueColor.
-orient code Tells afni the orientation in which to display
x-y-z coordinates (upper left of control window).
The code must be 3 letters, one each from the
pairs {R,L} {A,P} {I,S}. The first letter gives
the orientation of the x-axis, the second the
orientation of the y-axis, the third the z-axis:
R = right-to-left L = left-to-right
A = anterior-to-posterior P = posterior-to-anterior
I = inferior-to-superior S = superior-to-inferior
The default code is RAI ==> DICOM order. This can
be set with the environment variable AFNI_ORIENT.
As a special case, using the code 'flipped' is
equivalent to 'LPI' (this is for Steve Rao).
-noplugins Tells the program not to load plugins.
(Plugins can also be disabled by setting the
environment variable AFNI_NOPLUGINS.)
-yesplugouts Tells the program to listen for plugouts.
(Plugouts can also be enabled by setting the
environment variable AFNI_YESPLUGOUTS.)
-YESplugouts Makes the plugout code print out lots of messages
(useful for debugging a new plugout).
-noplugouts Tells the program NOT to listen for plugouts.
(This option is available to override
the AFNI_YESPLUGOUTS environment variable.)
-skip_afnirc Tells the program NOT to read the file .afnirc
in the home directory. See README.setup for
details on the use of .afnirc for initialization.
-layout fn Tells AFNI to read the initial windows layout from
file 'fn'. If this option is not given, then
environment variable AFNI_LAYOUT_FILE is used.
If neither is present, then AFNI will do whatever
it feels like.
-niml If present, turns on listening for NIML-formatted
data from SUMA. Can also be turned on by setting
environment variable AFNI_NIML_START to YES.
-np port If present, sets the NIML socket port number to 'port'.
This must be an integer between 1024 and 65535,
and must be the same as the '-np port' number given
to SUMA. [default = 53211]
-com ccc This option lets you specify 'command strings' to
drive AFNI after the program startup is completed.
Legal command strings are described in the file
README.driver. More than one '-com' option can
be used, and the commands will be executed in
the order they are given on the command line.
N.B.: Most commands to AFNI contain spaces, so the 'ccc'
command strings will need to be enclosed in quotes.
* If no session_directories are given, then the program will use
the current working directory (i.e., './').
* The maximum number of sessions is now set to 80.
* The maximum number of datasets per session is 4096.
* To change these maximums, you must edit file '3ddata.h' and then
recompile this program.
-----------------------------------------------------
USAGE 2: read in images for 'quick and dirty' viewing
-----------------------------------------------------
(Most advanced features of AFNI will be disabled.)
afni -im [options] im1 im2 im3 ...
-im Flag to read in images instead of 3D datasets
(Talaraich and functional stuff won't work)
-dy yratio Tells afni the downscreen pixel size is 'yratio' times
the across-screen (x) pixel dimension (default=1.0)
-dz zratio Tells afni the slice thickness is 'zratio' times
the x pixel dimension (default=1.0)
-orient code Tells afni the orientation of the input images.
The code must be 3 letters, one each from the
pairs {R,L} {A,P} {I,S}. The first letter gives
the orientation of the x-axis, the second the
orientation of the y-axis, the third the z-axis:
R = right-to-left L = left-to-right
A = anterior-to-posterior P = posterior-to-anterior
I = inferior-to-superior S = superior-to-inferior
(the default code is ASL ==> sagittal images).
Note that this use of '-orient' is different from
the use when viewing datasets.
-resize Tells afni that all images should be resized to fit
the size of the first one, if they don't already fit
(by default, images must all 'fit' or afni will stop)
-datum type Tells afni to convert input images into the type given:
byte, short, float, complex are the legal types.
The image files (im1 ...) are the same formats as accepted by to3d.
New image display options (alternatives to -im) [19 Oct 1999]:
-tim These options tell AFNI to arrange the input images
-tim:<NT> into a internal time-dependent dataset. Suppose that
-zim:<NZ> there are N input 2D slices on the command line.
* -tim alone means these are N points in time (1 slice).
* -tim:<NT> means there are nt points in time (nt is
an integer > 1), so there are N/nt slices in space,
and the images on the command line are input in
time order first (like -time:tz in to3d).
* -zim:<NZ> means there are nz slices in space (nz is
an integer > 1), so there are N/nz points in time,
and the images on the command line are input in
slice order first (like -time:zt in to3d).
N.B.: You may wish to use the -ignore option to set the number of
initial points to ignore in the time series graph if you use
-tim or -zim, since there is no way to change this from
within an AFNI run (the FIM menus are disabled).
N.B.: The program 'aiv' (AFNI image viewer) can also be used to
look at images.
-------------------------------------------------------
USAGE 3: read in datasets specified on the command line
-------------------------------------------------------
afni -dset [options] dname1 dname2 ...
where 'dname1' is the name of a dataset, etc. With this option, only
the chosen datasets are read in, and they are all put in the same
'session'. Follower datasets are not created.
INPUT DATASET NAMES
-------------------
An input dataset is specified using one of these forms:
'prefix+view', 'prefix+view.HEAD', or 'prefix+view.BRIK'.
You can also add a sub-brick selection list after the end of the
dataset name. This allows only a subset of the sub-bricks to be
read in (by default, all of a dataset's sub-bricks are input).
A sub-brick selection list looks like one of the following forms:
fred+orig[5] ==> use only sub-brick #5
fred+orig[5,9,17] ==> use #5, #9, and #12
fred+orig[5..8] or [5-8] ==> use #5, #6, #7, and #8
fred+orig[5..13(2)] or [5-13(2)] ==> use #5, #7, #9, #11, and #13
Sub-brick indexes start at 0. You can use the character '$'
to indicate the last sub-brick in a dataset; for example, you
can select every third sub-brick by using the selection list
fred+orig[0..$(3)]
N.B.: The sub-bricks are read in the order specified, which may
not be the order in the original dataset. For example, using
fred+orig[0..$(2),1..$(2)]
will cause the sub-bricks in fred+orig to be input into memory
in an interleaved fashion. Using
fred+orig[$..0]
will reverse the order of the sub-bricks.
N.B.: You may also use the syntax <A..B> after the name of an input
dataset to restrict the range of values read in to the numerical
values in a..b, inclusive. For example,
fred+orig[5..7]<100..200>
creates a 3 sub-brick dataset with values less than 100 or
greater than 200 from the original set to zero.
If you use the <> sub-range selection without the [] sub-brick
selection, it is the same as if you had put [0..$] in front of
the sub-range selection.
N.B.: Datasets using sub-brick/sub-range selectors are treated as:
- 3D+time if the dataset is 3D+time and more than 1 brick is chosen
- otherwise, as bucket datasets (-abuc or -fbuc)
(in particular, fico, fitt, etc datasets are converted to fbuc!)
N.B.: The characters '$ ( ) [ ] < >' are special to the shell,
so you will have to escape them. This is most easily done by
putting the entire dataset plus selection list inside forward
single quotes, as in 'fred+orig[5..7,9]', or double quotes "x".
CALCULATED DATASETS
-------------------
Datasets may also be specified as runtime-generated results from
program 3dcalc. This type of dataset specifier is enclosed in
quotes, and starts with the string '3dcalc(':
'3dcalc( opt opt ... opt )'
where each 'opt' is an option to program 3dcalc; this program
is run to generate a dataset in the directory given by environment
variable TMPDIR (default=/tmp). This dataset is then read into
memory, locked in place, and deleted from disk. For example
afni -dset '3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )'
will let you look at the average of datasets r1+orig and r2+orig.
N.B.: using this dataset input method will use lots of memory!
-------------------------------
GENERAL OPTIONS (for any usage)
-------------------------------
-q Tells afni to be 'quiet' on startup
-Dname=val Sets environment variable 'name' to 'val' inside AFNI;
will supersede any value set in .afnirc.
-gamma gg Tells afni that the gamma correction factor for the
monitor is 'gg' (default gg is 1.0; greater than
1.0 makes the image contrast larger -- this may
also be adjusted interactively)
-install Tells afni to install a new X11 Colormap. This only
means something for PseudoColor displays. Also, it
usually cause the notorious 'technicolor' effect.
-ncolors nn Tells afni to use 'nn' gray levels for the image
displays (default is 80)
-xtwarns Tells afni to show any Xt warning messages that may
occur; the default is to suppress these messages.
-tbar name Uses 'name' instead of 'AFNI' in window titlebars.
-flipim and The '-flipim' option tells afni to display images in the
-noflipim 'flipped' radiology convention (left on the right).
The '-noflipim' option tells afni to display left on
the left, as neuroscientists generally prefer. This
latter mode can also be set by the Unix environment
variable 'AFNI_LEFT_IS_LEFT'. The '-flipim' mode is
the default.
-trace Turns routine call tracing on, for debugging purposes.
-TRACE Turns even more verbose tracing on, for more debugging.
-nomall Disables use of the mcw_malloc() library routines.
N.B.: Many of these options, as well as the initial color set up,
can be controlled by appropriate X11 resources. See the
file AFNI.Xdefaults for instructions and examples.
----------
REFERENCES
----------
The following papers describe some of the components of the AFNI package.
RW Cox. AFNI: Software for analysis and visualization of functional
magnetic resonance neuroimages. Computers and Biomedical Research,
29: 162-173, 1996.
* The first AFNI paper, and the one I prefer you cite if you want to
refer to the AFNI package as a whole.
RW Cox, A Jesmanowicz, and JS Hyde. Real-time functional magnetic
resonance imaging. Magnetic Resonance in Medicine, 33: 230-236, 1995.
* The first paper on realtime FMRI; describes the algorithm used in
3dfim+, the interactive FIM calculations, and in the realtime plugin.
RW Cox and JS Hyde. Software tools for analysis and visualization of
FMRI Data. NMR in Biomedicine, 10: 171-178, 1997.
* A second paper about AFNI and design issues for FMRI software tools.
RW Cox and A Jesmanowicz. Real-time 3D image registration for
functional MRI. Magnetic Resonance in Medicine, 42: 1014-1018, 1999.
* Describes the algorithm used for image registration in 3dvolreg
and in the realtime plugin.
ZS Saad, KM Ropella, RW Cox, and EA DeYoe. Analysis and use of FMRI
response delays. Human Brain Mapping, 13: 74-93, 2001.
* Describes the algorithm used in 3ddelay (cf. '3ddelay -help').
This page auto-generated on Thu Aug 25 16:49:38 EDT 2005
|
| @AfniOrient2RAImap |
Usage: @AfniOrient2RAImap <ORIENTATION code> ..... returns the index map fo the RAI directions examples: @AfniOrient2RAImap RAI returns: 1 2 3 @AfniOrient2RAImap LSP returns: -1 -3 -2 Ziad Saad (ziad@nih.gov) SSCC/NIMH/ National Institutes of Health, Bethesda MarylandThis page auto-generated on Thu Aug 25 16:49:39 EDT 2005 |
| afni_vcheck |
Usage: afni_version
Prints out the AFNI version with which it was compiled,
and checks across the Web for the latest version available.
N.B.: Doing the check across the Web will mean that your
computer's access to our server will be logged here.
If you don't want this, don't use this program!
This page auto-generated on Thu Aug 25 16:49:39 EDT 2005
|
| aiv |
Usage: aiv [-v] [-p xxxx ] image ...
AFNI Image Viewer program.
Shows the 2D images on the command line in an AFNI-like image viewer.
Can also read images in NIML '<MRI_IMAGE...>' format from a TCP/IP socket.
Image file formats are those supported by to3d:
* various MRI formats (e.g., DICOM, GEMS I.xxx)
* raw PPM or PGM
* JPEG (if djpeg is in the path)
* GIF, TIFF, BMP, and PNG (if netpbm is in the path)
The '-v' option will make aiv print out the image filenames
as it reads them - this can be a useful progress meter if
the program starts up slowly.
The '-p xxxx' option will make aiv listen to TCP/IP port 'xxxx'
for incoming images in the NIML '<MRI_IMAGE...>' format. The
port number must be between 1024 and 65535, inclusive. For
conversion to NIML '<MRI_IMAGE...>' format, see program im2niml.
Normally, at least one image must be given on the command line.
If the '-p xxxx' option is used, then you don't have to input
any images this way; however, since the program requires at least
one image to start up, a crude 'X' will be displayed. When the
first image arrives via the socket, the 'X' image will be replaced.
Subsequent images arriving by socket will be added to the sequence.
-----------------------------------------------------------------
Sample program fragment, for sending images from one program
into a copy of aiv (which that program also starts up):
#include "mrilib.h"
NI_stream ns; MRI_IMAGE *im; float *far; int nx,ny;
system("aiv -p 4444 &"); /* start aiv */
ns = NI_stream_open( "tcp:localhost:4444" , "w" ); /* connect to it */
while(1){
/** ......... create 2D nx X ny data into the far array .........**/
im = mri_new_vol_empty( nx , ny , 1 , MRI_float ); /* fake image */
mri_fix_data_pointer( far , im ); /* attach data */
NI_element nel = mri_to_niml(im); /* convert to NIML element */
NI_write_element( ns , nel , NI_BINARY_MODE ); /* send to aiv */
NI_free_element(nel); mri_clear_data_pointer(im); mri_free(im);
}
NI_stream_writestring( ns , "<NI_DO ni_verb="QUIT">" ) ;
NI_stream_close( ns ) ; /* do this, or the above, if done with aiv */
-- Author: RW Cox
This page auto-generated on Thu Aug 25 16:49:39 EDT 2005
|
| @Align_Centers |
Usage: @Align_Centers <VOL1> <VOL2> Creates a copy of Vol1 (Vol1_Shft) with a modified origin to make the centers Vol1_Shft and Vol2 coincide. Vol1_Shft is written out to the directory containing Vol2. Requires 3drefit newer than Oct. 02/02. Ziad Saad (ziad@nih.gov) SSCC/NIMH/ National Institutes of Health, Bethesda MarylandThis page auto-generated on Thu Aug 25 16:49:39 EDT 2005 |
| AlphaSim |
Program: AlphaSim
Author: B. Douglas Ward
Initial Release: 18 June 1997
Latest Revision: 02 December 2002
This program performs alpha probability simulations.
Usage:
AlphaSim
-nx n1 n1 = number of voxels along x-axis
-ny n2 n2 = number of voxels along y-axis
-nz n3 n3 = number of voxels along z-axis
-dx d1 d1 = voxel size (mm) along x-axis
-dy d2 d2 = voxel size (mm) along y-axis
-dz d3 d3 = voxel size (mm) along z-axis
[-mask mset] Use the 0 sub-brick of dataset 'mset' as a mask
to indicate which voxels to analyze (a sub-brick
selector is allowed) [default = use all voxels]
Note: The -mask command REPLACES the -nx, -ny, -nz,
-dx, -dy, and -dz commands.
[-fwhm s] s = Gaussian filter width (FWHM)
[-fwhmx sx] sx = Gaussian filter width, x-axis (FWHM)
[-fwhmy sy] sy = Gaussian filter width, y-axis (FWHM)
[-fwhmz sz] sz = Gaussian filter width, z-axis (FWHM)
[-sigma s] s = Gaussian filter width (1 sigma)
[-sigmax sx] sx = Gaussian filter width, x-axis (1 sigma)
[-sigmay sy] sy = Gaussian filter width, y-axis (1 sigma)
[-sigmaz sz] sz = Gaussian filter width, z-axis (1 sigma)
[-power] perform statistical power calculations
[-ax n1] n1 = extent of active region (in voxels) along x-axis
[-ay n2] n2 = extent of active region (in voxels) along y-axis
[-az n3] n3 = extent of active region (in voxels) along z-axis
[-zsep z] z = z-score separation between signal and noise
-rmm r r = cluster connection radius (mm)
-pthr p p = individual voxel threshold probability
-iter n n = number of Monte Carlo simulations
[-quiet] suppress screen output
[-out file] file = name of output file
This page auto-generated on Thu Aug 25 16:49:39 EDT 2005
|
| byteorder |
Usage: byteorder Prints out a string indicating the byte order of the CPU on which the program is running. For this computer, we have: CPU byte order = LSB_FIRSTThis page auto-generated on Thu Aug 25 16:49:40 EDT 2005 |
| cat_matvec |
Usage: cat_matvec [-MATRIX] matvec_spec matvec_spec ...
Catenates 3D rotation+shift matrix+vector transformations.
Each matvec_spec is of the form
mfile [-opkey]
'mfile' specifies the matrix, and can take 4 forms:
=== FORM 1 ===
mfile is the name of an ASCII file with 12 numbers arranged
in 3 lines:
u11 u12 u13 v1
u21 u22 u23 v2
u31 u32 u33 v3
where each 'uij' and 'vi' is a number. The 3x3 matrix [uij]
is the matrix of the transform, and the 3-vector [vi] is the
shift. The transform is [xnew] = [uij]*[xold] + [vi].
=== FORM 2 ===
mfile is of the form 'dataset::attribute', where 'dataset'
is the name of an AFNI dataset, and 'attribute' is the name
of an attribute in the dataset's header that contains a
matrix+vector. Examples:
'fred+orig::VOLREG_MATVEC_000000' = fred+orig from 3dvolreg
'fred+acpc::WARP_DATA' = fred+acpc warped in AFNI
'fred+orig::WARPDRIVE_MATVEC_FOR_000000' = fred+orig from 3dWarpDrive
'fred+orig::ROTATE_MATVEC_000000' = fred+orig from 3drotate
=== FORM 3 ===
mfile is of the form
'MATRIX(u11,u12,u13,v1,u21,u22,u23,v2,u31,u32,u33,v3)'
directly giving all 12 numbers on the command line. You will
need the 'forward single quotes' around this argument.
=== FORM 4 ===
mfile is of the form
'-rotate xI yR zA'
where 'x', 'y', and 'z' are angles in degrees, specifying rotations
about the I, R, and A axes respectively. The letters 'I', 'R', 'A'
specify the axes, and can be altered as in program 3drotate.
(The 'quotes' are mandatory here because the argument contains spaces.)
=== COMPUTATIONS ===
If [U] [v] are the matrix/vector for the first mfile, and
[A] [b] are the matrix/vector for the second mfile, then
the catenated transformation is
matrix = [A][U] vector = [A][v] + [b]
That is, the second mfile transformation follows the first.
The optional 'opkey' (operation key) following each mfile
starts with a '-', and then is a set of letters telling how
to treat the input. The only opkey currently defined is
-I = invert the transformation:
-1 -1
[xold] = [uij] [xnew] - [uij] [vi]
The transformation resulting by catenating the transformations
is written to stdout in the same 3x4 ASCII file format. This can
be used as input to '3drotate -matvec_dicom' (provided [uij] is a
proper orthogonal matrix), or to '3dWarp -matvec_xxx'.
N.B.: If only 9 numbers can be read from an mfile, then those
values form the [uij] matrix, and the vector is set to zero.
N.B.: The '-MATRIX' option indicates that the resulting matrix will
be written to stdout in the 'MATRIX(...)' format (FORM 3).
This feature could be used, with clever scripting, to input
a matrix directly on the command line to program 3dWarp.
This page auto-generated on Thu Aug 25 16:49:40 EDT 2005
|
| ccalc |
Usage: ccalc [-eval <EXPR>] With no command line parameters: Interactive numerical calculator, using the same expression syntax as 3dcalc. Mostly for playing. With -eval <EXPR> option: Calculates expr and quits. Do not use variables in expr. Example: ccalc -eval '3 + 5 * sin(22)' or: ccalc -eval 3 +5 '*' 'sin(22)'This page auto-generated on Thu Aug 25 16:49:40 EDT 2005 |
| cdf |
Usage 1: cdf [-v] -t2p statname t params
Usage 2: cdf [-v] -p2t statname p params
Usage 3: cdf [-v] -t2z statname t params
This program does various conversions using the cumulative distribution
function (cdf) of certain canonical probability functions. The optional
'-v' indicates to be verbose -- this is for debugging purposes, mostly.
Usage 1: Converts a statistic 't' to a tail probability.
Usage 2: Converts a tail probability 'p' to a statistic.
Usage 3: Converts a statistic 't' to a N(0,1) value (or z-score)
that has the same tail probability.
The parameter 'statname' refers to the type of distribution to be used.
The numbers in the params list are the auxiliary parameters for the
particular distribution. The following table shows the available
distribution functions and their parameters:
statname Description PARAMETERS
-------- ----------- ----------------------------------------
fico Cor SAMPLES FIT-PARAMETERS ORT-PARAMETERS
fitt Ttest DEGREES-of-FREEDOM
fift Ftest NUMERATOR and DENOMINATOR DEGREES-of-FREEDOM
fizt Ztest N/A
fict ChiSq DEGREES-of-FREEDOM
fibt Beta A (numerator) and B (denominator)
fibn Binom NUMBER-of-TRIALS and PROBABILITY-per-TRIAL
figt Gamma SHAPE and SCALE
fipt Poisson MEAN
This page auto-generated on Thu Aug 25 16:49:40 EDT 2005
|
| @CheckForAfniDset |
Usage: @CheckForAfniDset <NAME> .....
example: @CheckForAfniDset /Data/stuff/Hello+orig.HEAD
returns 0 if neither .HEAD nor .BRIK(.gz) exist
1 if only .HEAD exists
2 if both .HEAD and .BRIK(.gz) exist
Ziad Saad (ziad@nih.gov)
SSCC/NIMH/ National Institutes of Health, Bethesda Maryland
This page auto-generated on Thu Aug 25 16:49:40 EDT 2005
|
| cjpeg |
usage: /var/www/html/pub/dist/bin/linux_gcc32/cjpeg [switches] [inputfile] Switches (names may be abbreviated): -quality N Compression quality (0..100; 5-95 is useful range) -grayscale Create monochrome JPEG file -optimize Optimize Huffman table (smaller file, but slow compression) -progressive Create progressive JPEG file -targa Input file is Targa format (usually not needed) Switches for advanced users: -dct int Use integer DCT method (default) -dct fast Use fast integer DCT (less accurate) -dct float Use floating-point DCT method -restart N Set restart interval in rows, or in blocks with B -smooth N Smooth dithered input (N=1..100 is strength) -maxmemory N Maximum memory to use (in kbytes) -outfile name Specify name for output file -verbose or -debug Emit debug output Switches for wizards: -baseline Force baseline quantization tables -qtables file Use quantization tables given in file -qslots N[,...] Set component quantization tables -sample HxV[,...] Set component sampling factors -scans file Create multi-scan JPEG per script fileThis page auto-generated on Thu Aug 25 16:49:40 EDT 2005 |
| @clip_volume |
Usage 1: A script to clip regions of a volume
@clip_volume <-input VOL> <-below Zmm> [ [-and/-or] <-above Zmm> ]
Mandatory parameters:
-input VOL: Volume to clip
+ At least one of the options below:
-below Zmm: Set to 0 slices below Zmm
Zmm (and all other coordinates) are in RAI
as displayed by AFNI on the top left corner
of the AFNI controller
-above Zmm: Set to 0 slices above Zmm
-left Xmm: Set to 0 slices left of Xmm
-right Xmm: Set to 0 slices right of Xmm
-anterior Ymm: Set to 0 slices anterior to Ymm
-posterior Ymm: Set to 0 slices posterior to Ymm
Optional parameters:
-and (default): Combine with next clipping planes using 'and'
-or : Combine with next clipping planes using 'or'
-verb : Verbose, show command
-prefix PRFX : Use PRFX for output prefix. Default is the
input prefix with _clp suffixed to it.
Example:
@clip_volume -below -30 -above 53 -left 20 -right -13 -anterior -15 \
-posterior 42 -input ABanat+orig. -verb -prefix sample
Written by Ziad S. Saad (ziad@nih.gov)
SSCC/NIMH/NIH/DHHS
This page auto-generated on Thu Aug 25 16:49:40 EDT 2005
|
| @CommandGlobb |
Usage: @CommandGlobb -com <PROGRAM line Command> -session <OUTPUT> -newxt <EXTENSION> -list <BRICK 1> <BRICK 2> ... <PROGRAM line Command> : The entire command line for the program desired The command is best put between single quotes, do not use the \ to break a long line within the quotes <BRIK*> : a list of bricks (or anything) <EXTENSION> : if the program requires a -prefix option, then you can specify the extension which will get appended to the Brick names before +orig <OUTPUT> : The output directory example @CommandGlobb -com '3dinfo -v' -list *.HEAD will execute 3dinfo -v on each of the A*.HEAD headers @CommandGlobb -com '3dZeropad -z 4' -newxt _zpd4 -list ADzst*vr+orig.BRIK will run 3dZeropad with the -z 4 option on all the bricks ADzst*vr+orig.BRIK Ziad S. Saad (ziad@nih.gov). FIM/LBC/NIMH/NIH. Wed Jan 24This page auto-generated on Thu Aug 25 16:49:40 EDT 2005 |
| CompareSurfaces |
Usage: CompareSurfaces
-spec <SPEC file>
-hemi <L R or>
-sv1 <VOLPARENTALIGNED1.BRIK>
-sv2 <VOLPARENTALIGNED2.BRIK>
[-prefix <FILEPREFIX>]
NOTE: This program is now superseded by SurfToSurf
This program calculates the distance, at each node in Surface 1 (S1) to Surface 2 (S2)
The distances are computed along the local surface normal at each node in S1.
S1 and S2 are the first and second surfaces encountered in the spec file, respectively.
-spec <SPEC file>: File containing surface specification. This file is typically
generated by @SUMA_Make_Spec_FS (for FreeSurfer surfaces) or
@SUMA_Make_Spec_SF (for SureFit surfaces).
-hemi <LEFT or right>: specify the hemisphere being processed
-sv1 <VOLUME BRIK parent>:volume parent BRIK for first surface
-sv2 <VOLUME BRIK parent>:volume parent BRIK for second surface
Optional parameters:
[-prefix <FILEPREFIX>]: Prefix for distance and node color output files.
Existing file will not be overwritten.
[-onenode <INDEX>]: output results for node index only.
This option is for debugging.
[-noderange <ISTART> <ISTOP>]: output results from node istart to node istop only.
This option is for debugging.
NOTE: -noderange and -onenode are mutually exclusive
[-nocons]: Skip mesh orientation consistency check.
This speeds up the start time so it is useful
for debugging runs.
Common Debugging Options:
[-trace]: Turns on In/Out debug and Memory tracing.
For speeding up the tracing log, I recommend
you redirect stdout to a file when using this option.
For example, if you were running suma you would use:
suma -spec lh.spec -sv ... > TraceFile
This option replaces the old -iodbg and -memdbg.
[-TRACE]: Turns on extreme tracing.
[-nomall]: Turn off memory tracing.
[-yesmall]: Turn on memory tracing (default).
[-novolreg]: Ignore any Volreg or Tagalign transformations
present in the Surface Volume.
NOTE: For programs that output results to stdout
(that is to your shell/screen), the debugging info
might get mixed up with your results.
For more help: http://afni.nimh.nih.gov/ssc/ziad/SUMA/SUMA_doc.htm
If you can't get help here, please get help somewhere.
++ SUMA version 2004_12_29
CVS tag:
SUMA_2005_04_29_1733
Compile Date:
Aug 25 2005
Shruti Japee LBC/NIMH/NIH shruti@codon.nih.gov Ziad S. Saad SSSC/NIMH/NIH ziad@nih.gov
This page auto-generated on Thu Aug 25 16:49:40 EDT 2005
|
| ConvertDset |
Usage:
ConvertDset -o_TYPE -input DSET [-i_TYPE] [-prefix OUT_PREF]
Converts a surface dataset from one format to another.
Mandatory parameters:
-o_TYPE: TYPE of output datasets
where TYPE is one of:
niml_asc (or niml): for ASCII niml format.
niml_bi: for BINARY niml format.
1D: for AFNI's 1D ascii format.
-input DSET: Input dataset to be converted.
Optional parameters:
-i_TYPE: TYPE of input datasets
where TYPE is one of:
niml: for niml data sets.
1D: for AFNI's 1D ascii format.
1Dp: like 1D but with no comments
or other 1D formatting gimmicks.
dx: OpenDX format, expects to work on 1st
object only.
If no format is specified, the program will
guess however that might slow
operations down considerably.
-prefix OUT_PREF: Output prefix for data set.
Default is something based
on the input prefix.
Notes:
-This program will not overwrite pre-existing files.
-The new data set is given a new idcode.
Common Debugging Options:
[-trace]: Turns on In/Out debug and Memory tracing.
For speeding up the tracing log, I recommend
you redirect stdout to a file when using this option.
For example, if you were running suma you would use:
suma -spec lh.spec -sv ... > TraceFile
This option replaces the old -iodbg and -memdbg.
[-TRACE]: Turns on extreme tracing.
[-nomall]: Turn off memory tracing.
[-yesmall]: Turn on memory tracing (default).
[-novolreg]: Ignore any Volreg or Tagalign transformations
present in the Surface Volume.
NOTE: For programs that output results to stdout
(that is to your shell/screen), the debugging info
might get mixed up with your results.
++ SUMA version 2004_12_29
CVS tag:
SUMA_2005_04_29_1733
Compile Date:
Aug 25 2005
Ziad S. Saad SSCC/NIMH/NIH ziad@nih.gov Thu Apr 8 16:15:02 EDT 2004
This page auto-generated on Thu Aug 25 16:49:40 EDT 2005
|
| ConvertSurface |
Usage: ConvertSurface <-i_TYPE inSurf> <-o_TYPE outSurf>
[<-sv SurfaceVolume [VolParam for sf surfaces]>] [-tlrc] [-MNI_rai/-MNI_lpi]
reads in a surface and writes it out in another format.
Note: This is a not a general utility conversion program.
Only fields pertinent to SUMA are preserved.
Specifying input surfaces using -i_TYPE options:
-i_TYPE inSurf specifies the input surface,
TYPE is one of the following:
fs: FreeSurfer surface.
If surface name has .asc it is assumed to be
in ASCII format. Otherwise it is assumed to be
in BINARY_BE (Big Endian) format.
Patches in Binary format cannot be read at the moment.
sf: SureFit surface.
You must specify the .coord followed by the .topo file.
vec (or 1D): Simple ascii matrix format.
You must specify the coord (NodeList) file followed by
the topo (FaceSetList) file.
coord contains 3 floats per line, representing
X Y Z vertex coordinates.
topo contains 3 ints per line, representing
v1 v2 v3 triangle vertices.
ply: PLY format, ascii or binary.
Only vertex and triangulation info is preserved.
bv: BrainVoyager format.
Only vertex and triangulation info is preserved.
dx: OpenDX ascii mesh format.
Only vertex and triangulation info is preserved.
Requires presence of 3 objects, the one of class
'field' should contain 2 components 'positions'
and 'connections' that point to the two objects
containing node coordinates and topology, respectively.
-ipar_TYPE ParentSurf specifies the parent surface. Only used
when -o_fsp is used, see -o_TYPE options.
Specifying a Surface Volume:
-sv SurfaceVolume [VolParam for sf surfaces]
If you supply a surface volume, the coordinates of the input surface.
are modified to SUMA's convention and aligned with SurfaceVolume.
You must also specify a VolParam file for SureFit surfaces.
Specifying output surfaces using -o_TYPE options:
-o_TYPE outSurf specifies the output surface,
TYPE is one of the following:
fs: FreeSurfer ascii surface.
fsp: FeeSurfer ascii patch surface.
In addition to outSurf, you need to specify
the name of the parent surface for the patch.
using the -ipar_TYPE option.
This option is only for ConvertSurface
sf: SureFit surface.
For most programs, you are expected to specify prefix:
i.e. -o_sf brain. In some programs, you are allowed to
specify both .coord and .topo file names:
i.e. -o_sf XYZ.coord TRI.topo
The program will determine your choice by examining
the first character of the second parameter following
-o_sf. If that character is a '-' then you have supplied
a prefix and the program will generate the coord and topo names.
vec (or 1D): Simple ascii matrix format.
For most programs, you are expected to specify prefix:
i.e. -o_1D brain. In some programs, you are allowed to
specify both coord and topo file names:
i.e. -o_1D brain.1D.coord brain.1D.topo
coord contains 3 floats per line, representing
X Y Z vertex coordinates.
topo contains 3 ints per line, representing
v1 v2 v3 triangle vertices.
ply: PLY format, ascii or binary.
-orient_out STR: Output coordinates in STR coordinate system.
STR is a three character string following AFNI's
naming convention. The program assumes that the native
orientation of the surface is RAI, unless you use the
-MNI_lpi option. The coordinate transformation is carried
out last, just before writing the surface to disk.
-make_consistent: Check the consistency of the surface's mesh (triangle
winding). This option will write out a new surface even
if the mesh was consistent.
See SurfQual -help for mesh checks.
-acpc: Apply acpc transform (which must be in acpc version of
SurfaceVolume) to the surface vertex coordinates.
This option must be used with the -sv option.
-tlrc: Apply Talairach transform (which must be a talairach version of
SurfaceVolume) to the surface vertex coordinates.
This option must be used with the -sv option.
-MNI_rai/-MNI_lpi: Apply Andreas Meyer Lindenberg's transform to turn
AFNI tlrc coordinates (RAI) into MNI coord space
in RAI (with -MNI_rai) or LPI (with -MNI_lpi)).
NOTE: -MNI_lpi option has not been tested yet (I have no data
to test it on. Verify alignment with AFNI and please report
any bugs.
This option can be used without the -tlrc option.
But that assumes that surface nodes are already in
AFNI RAI tlrc coordinates .
NOTE: The vertex coordinates coordinates of the input surfaces are only
transformed if -sv option is used. If you do transform surfaces,
take care not to load them into SUMA with another -sv option.
Options for applying arbitrary affine transform:
[xyz_new] = [Mr] * [xyz_old - cen] + D + cen
-xmat_1D mat: Apply transformation specified in 1D file mat.1D.
to the surface's coordinates.
[mat] = [Mr][D] is of the form:
r11 r12 r13 D1
r21 r22 r23 D2
r31 r32 r33 D3
-xcenter x y z: Use vector cen = [x y z]' for rotation center.
Default is cen = [0 0 0]'
Common Debugging Options:
[-trace]: Turns on In/Out debug and Memory tracing.
For speeding up the tracing log, I recommend
you redirect stdout to a file when using this option.
For example, if you were running suma you would use:
suma -spec lh.spec -sv ... > TraceFile
This option replaces the old -iodbg and -memdbg.
[-TRACE]: Turns on extreme tracing.
[-nomall]: Turn off memory tracing.
[-yesmall]: Turn on memory tracing (default).
[-novolreg]: Ignore any Volreg or Tagalign transformations
present in the Surface Volume.
NOTE: For programs that output results to stdout
(that is to your shell/screen), the debugging info
might get mixed up with your results.
++ SUMA version 2004_12_29
CVS tag:
SUMA_2005_04_29_1733
Compile Date:
Aug 25 2005
Ziad S. Saad SSCC/NIMH/NIH ziad@nih.gov Wed Jan 8 13:44:29 EST 2003
This page auto-generated on Thu Aug 25 16:49:40 EDT 2005
|
| ConvexHull |
Usage: A program to find the convex hull of a set of points.
This program is a wrapper for the Qhull program.
see copyright notice by running suma -sources.
ConvexHull
usage 1: < -input VOL >
< -isoval V | -isorange V0 V1 | -isocmask MASK_COM >
[<-xform XFORM>]
usage 2: < i_TYPE input surface >
[<-sv SURF_VOL>]
usage 3: < -input_1D XYZ >
common optional:
[< -o_TYPE PREFIX>]
[< -debug DBG >]
Mandatory parameters, choose one of three usage modes:
Usage 1:
You must use one of the following two options:
-input VOL: Input AFNI (or AFNI readable) volume.
You must use one of the following iso* options:
-isoval V: Create isosurface where volume = V
-isorange V0 V1: Create isosurface where V0 <= volume < V1
-isocmask MASK_COM: Create isosurface where MASK_COM != 0
For example: -isocmask '-a VOL+orig -expr (1-bool(a-V))'
is equivalent to using -isoval V.
NOTE: -isorange and -isocmask are only allowed with -xform mask
See -xform below for details.
Usage 2:
-i_TYPE SURF: Use the nodes of a surface model
for input. See help for i_TYPE usage
below.
Usage 3:
-input_1D XYZ: Construct the convex hull of the points
contained in 1D file XYZ. If the file has
more than 3 columns, use AFNI's [] selectors
to specify the XYZ columns.
Optional Parameters:
Usage 1 only:
-xform XFORM: Transform to apply to volume values
before searching for sign change
boundary. XFORM can be one of:
mask: values that meet the iso* conditions
are set to 1. All other values are set
to -1. This is the default XFORM.
shift: subtract V from the dataset and then
search for 0 isosurface. This has the
effect of constructing the V isosurface
if your dataset has a continuum of values.
This option can only be used with -isoval V.
none: apply no transforms. This assumes that
your volume has a continuum of values
from negative to positive and that you
are seeking to 0 isosurface.
This option can only be used with -isoval 0.
Usage 2 only:
-sv SURF_VOL: Specify a surface volume which contains
a transform to apply to the surface node
coordinates prior to constructing the
convex hull.
All Usage:
-o_TYPE PREFIX: prefix of output surface.
where TYPE specifies the format of the surface
and PREFIX is, well, the prefix.
TYPE is one of: fs, 1d (or vec), sf, ply.
Default is: -o_ply
Specifying input surfaces using -i_TYPE options:
-i_TYPE inSurf specifies the input surface,
TYPE is one of the following:
fs: FreeSurfer surface.
If surface name has .asc it is assumed to be
in ASCII format. Otherwise it is assumed to be
in BINARY_BE (Big Endian) format.
Patches in Binary format cannot be read at the moment.
sf: SureFit surface.
You must specify the .coord followed by the .topo file.
vec (or 1D): Simple ascii matrix format.
You must specify the coord (NodeList) file followed by
the topo (FaceSetList) file.
coord contains 3 floats per line, representing
X Y Z vertex coordinates.
topo contains 3 ints per line, representing
v1 v2 v3 triangle vertices.
ply: PLY format, ascii or binary.
Only vertex and triangulation info is preserved.
bv: BrainVoyager format.
Only vertex and triangulation info is preserved.
dx: OpenDX ascii mesh format.
Only vertex and triangulation info is preserved.
Requires presence of 3 objects, the one of class
'field' should contain 2 components 'positions'
and 'connections' that point to the two objects
containing node coordinates and topology, respectively.
Specifying a Surface Volume:
-sv SurfaceVolume [VolParam for sf surfaces]
If you supply a surface volume, the coordinates of the input surface.
are modified to SUMA's convention and aligned with SurfaceVolume.
You must also specify a VolParam file for SureFit surfaces.
Specifying output surfaces using -o_TYPE options:
-o_TYPE outSurf specifies the output surface,
TYPE is one of the following:
fs: FreeSurfer ascii surface.
fsp: FeeSurfer ascii patch surface.
In addition to outSurf, you need to specify
the name of the parent surface for the patch.
using the -ipar_TYPE option.
This option is only for ConvertSurface
sf: SureFit surface.
For most programs, you are expected to specify prefix:
i.e. -o_sf brain. In some programs, you are allowed to
specify both .coord and .topo file names:
i.e. -o_sf XYZ.coord TRI.topo
The program will determine your choice by examining
the first character of the second parameter following
-o_sf. If that character is a '-' then you have supplied
a prefix and the program will generate the coord and topo names.
vec (or 1D): Simple ascii matrix format.
For most programs, you are expected to specify prefix:
i.e. -o_1D brain. In some programs, you are allowed to
specify both coord and topo file names:
i.e. -o_1D brain.1D.coord brain.1D.topo
coord contains 3 floats per line, representing
X Y Z vertex coordinates.
topo contains 3 ints per line, representing
v1 v2 v3 triangle vertices.
ply: PLY format, ascii or binary.
Common Debugging Options:
[-trace]: Turns on In/Out debug and Memory tracing.
For speeding up the tracing log, I recommend
you redirect stdout to a file when using this option.
For example, if you were running suma you would use:
suma -spec lh.spec -sv ... > TraceFile
This option replaces the old -iodbg and -memdbg.
[-TRACE]: Turns on extreme tracing.
[-nomall]: Turn off memory tracing.
[-yesmall]: Turn on memory tracing (default).
[-novolreg]: Ignore any Volreg or Tagalign transformations
present in the Surface Volume.
NOTE: For programs that output results to stdout
(that is to your shell/screen), the debugging info
might get mixed up with your results.
++ SUMA version 2004_12_29
CVS tag:
SUMA_2005_04_29_1733
Compile Date:
Aug 25 2005
Ziad S. Saad SSCC/NIMH/NIH ziad@nih.gov
This page auto-generated on Thu Aug 25 16:49:40 EDT 2005
|
| count |
Usage: count [options] bot top [step]
* Produces many numbered copies of the root and/or suffix,
counting from 'bot' to 'top' with stride 'step'.
* If 'bot' > 'top', counts backwards with stride '-step'.
* If step is of the form 'R#', then '#' random counts are produced
in the range 'bot..top' (inclusive).
* 'bot' and 'top' must not be negative; step must be positive.
Options:
-digits n prints numbers with 'n' digits [default=4]
-root rrr prints string 'rrr' before the number [default=empty]
-suffix sss prints string 'sss' after the number [default=empty]
-scale fff multiplies each number by the factor 'fff';
if this option is used, -digits is ignored and
the floating point format '%g' is used for output.
('fff' can be a floating point number.)
The main application of this program is for use in C shell programming:
foreach fred ( `count 1 20` )
mv wilma.${fred} barney.${fred}
end
The backward quote operator in the foreach statement executes the
count program, captures its output, and puts it on the command line.
The loop body renames each file wilma.0001 to wilma.0020 to barney.0001
to barney.0020. Read the man page for csh to get more information. In
particular, the csh built-in command '@' can be useful.
This page auto-generated on Thu Aug 25 16:49:40 EDT 2005
|
| CreateIcosahedron |
Usage: CreateIcosahedron [-rad r] [-rd recDepth] [-ld linDepth]
[-ctr ctr] [-prefix fout] [-help]
-rad r: size of icosahedron. (optional, default 100)
-rd recDepth: recursive (binary) tesselation depth for icosahedron
(optional, default:3)
(recommended to approximate number of nodes in brain: 6
let rd2 = 2 * recDepth
Nvert = 2 + 10 * 2^rd2
Ntri = 20 * 2^rd2
Nedge = 30 * 2^rd2
-ld linDepth: number of edge divides for linear icosahedron tesselation
(optional, default uses binary tesselation).
Nvert = 2 + 10 * linDepth^2
Ntri = 20 * linDepth^2
Nedge = 30 * linDepth^2
-nums: output the number of nodes (vertices), triangles, edges, total volume and total area then quit
-nums_quiet: same as -nums but less verbose. For the machine in you.
-ctr ctr: coordinates of center of icosahedron.
(optional, default 0,0,0)
-tosphere: project nodes to sphere.
-prefix fout: prefix for output files.
(optional, default CreateIco)
-help: help message
++ SUMA version 2004_12_29
CVS tag:
SUMA_2005_04_29_1733
Compile Date:
Aug 25 2005
Brenna D. Argall LBC/NIMH/NIH bargall@codon.nih.gov
Ziad S. Saad SSC/NIMH/NIH ziad@nih.gov
This page auto-generated on Thu Aug 25 16:49:40 EDT 2005
|
| dicom_hdr |
Usage: dicom_hdr [options] fname [...]
Prints information from the DICOM file 'fname' to stdout.
OPTIONS:
-hex = Include hexadecimal printout for integer values.
-noname = Don't include element names in the printout.
-sexinfo = Dump Siemens EXtra INFO text (0029 1020), if present
(can be VERY lengthy).
-v n = Dump n words of binary data also.
Based on program dcm_dump_file from the RSNA, developed at
the Mallinckrodt Institute of Radiology. See the source
code file mri_dicom_hdr.c for their Copyright and license.
SOME SAMPLE OUTPUT LINES:
0028 0010 2 [1234 ] // IMG Rows// 512
0028 0011 2 [1244 ] // IMG Columns// 512
0028 0030 18 [1254 ] // IMG Pixel Spacing//0.488281\0.488281
0028 0100 2 [1280 ] // IMG Bits Allocated// 16
0028 0101 2 [1290 ] // IMG Bits Stored// 12
0028 0102 2 [1300 ] // IMG High Bit// 11
* The first 2 numbers on each line are the DICOM group and element tags,
in hexadecimal.
* The next number is the number of data bytes, in decimal.
* The next number [in brackets] is the offset in the file of the data,
in decimal. This is where the data bytes start, and does not include
the tag, Value Representation, etc.
* If -noname is NOT given, then the string in the '// ... //' region is
the standard DICOM dictionary name for this data element. If this string
is blank, then this element isn't in the dictionary (e.g., is a private
tag, or an addition to DICOM that I don't know about, ...).
* The value after the last '//' is the value of the data in the element.
* In the example above, we have a 512x512 image with 0.488281 mm pixels,
with 12 bits (stored in 16 bits) per pixel.
* For vastly more detail on DICOM standard, you can start with the
documents at ftp://afni.nimh.nih.gov/dicom/ (1000+ pages of PDF).
This page auto-generated on Thu Aug 25 16:49:40 EDT 2005
|
| dicom_to_raw |
Usage: dicom_to_raw fname ... Reads images from DICOM file 'fname' and writes them to raw file(s) 'fname.raw.0001' etc.This page auto-generated on Thu Aug 25 16:49:40 EDT 2005 |
| Dimon |
Dimon - monitor real-time acquisition of DICOM image files
(or GEMS 5.x I-files, as 'Imon')
This program is intended to be run during a scanning session
on a scanner, to monitor the collection of image files. The
user will be notified of any missing slice or any slice that
is aquired out of order.
When collecting DICOM files, it is recommended to run this
once per run, only because it is easier to specify the input
file pattern for a single run (it may be very difficult to
predict the form of input filenames runs that have not yet
occurred.
This program can also be used off-line (away from the scanner)
to organize the files, run by run. If the DICOM files have
a correct DICOM 'image number' (0x0020 0013), then Dimon can
use the information to organize the sequence of the files,
particularly when the alphabetization of the filenames does
not match the sequencing of the slice positions. This can be
used in conjunction with the '-GERT_Reco' option, which will
write a script that can be used to create AFNI datasets.
See the '-dicom_org' option, under 'other options', below.
If no -quit option is provided, the user should terminate the
program when it is done collecting images according to the
input file pattern.
Dimon can be terminated using <CTRL-C>.
---------------------------------------------------------------
realtime notes for running afni remotely:
- The afni program must be started with the '-rt' option to
invoke the realtime plugin functionality.
- If afni is run remotely, then AFNI_TRUSTHOST will need to be
set on the host running afni. The value of that variable
should be set to the IP address of the host running Dimon.
This may set as an environment variable, or via the .afnirc
startup file.
- The typical default security on a Linux system will prevent
Dimon from communicating with afni on the host running afni.
The iptables firewall service on afni's host will need to be
configured to accept the communication from the host running
Dimon, or it (iptables) will need to be turned off.
---------------------------------------------------------------
usage: Dimon [options] -infile_prefix PREFIX
OR: Dimon [options] -infile_pattern "PATTERN"
---------------------------------------------------------------
examples (no real-time options):
Dimon -infile_pattern 's8912345/i*'
Dimon -infile_prefix s8912345/i
Dimon -help
Dimon -infile_prefix s8912345/i -quit
Dimon -infile_prefix s8912345/i -nt 120 -quit
Dimon -infile_prefix s8912345/i -debug 2
Dimon -infile_prefix s8912345/i -dicom_org -GERT_Reco -quit
examples (with real-time options):
Dimon -infile_prefix s8912345/i -rt
Dimon -infile_pattern 's*/i*' -rt
Dimon -infile_pattern 's*/i*' -rt -nt 120
Dimon -infile_pattern 's*/i*' -rt -quit
** detailed real-time example:
Dimon \
-infile_pattern 's*/i*' \
-rt -nt 120 \
-host some.remote.computer \
-rt_cmd "PREFIX 2005_0513_run3" \
-quit
This example scans data starting from directory 003, expects
160 repetitions (TRs), and invokes the real-time processing,
sending data to a computer called some.remote.computer.name
(where afni is running, and which considers THIS computer to
be trusted - see the AFNI_TRUSTHOST environment variable).
---------------------------------------------------------------
Multiple DRIVE_AFNI commands are passed through '-drive_afni'
options, one requesting to open an axial image window, and
another requesting an axial graph, with 160 data points.
See README.driver for acceptable DRIVE_AFNI commands.
Also, multiple commands specific to the real-time plugin are
passed via '-rt_cmd' options. The PREFIX command sets the
prefix for the datasets output by afni. The GRAPH_XRANGE and
GRAPH_YRANGE commands set the graph dimensions for the 3D
motion correction graph (only). And the GRAPH_EXPR command
is used to replace the 6 default motion correction graphs with
a single graph, according to the given expression, the square
root of the average squared entry of the 3 rotaion parameters,
roll, pitch and yaw, ignoring the 3 shift parameters, dx, dy
and dz.
See README.realtime for acceptable DRIVE_AFNI commands.
Dimon \
-infile_pattern 's*/i*.dcm' \
-nt 160 \
-rt \
-host some.remote.computer.name \
-drive_afni 'OPEN_WINDOW axialimage' \
-drive_afni 'OPEN_WINDOW axialgraph pinnum=160' \
-rt_cmd 'PREFIX eat.more.cheese' \
-rt_cmd 'GRAPH_XRANGE 160' \
-rt_cmd 'GRAPH_YRANGE 1.02' \
-rt_cmd 'GRAPH_EXPR sqrt((d*d+e*e+f*f)/3)'
---------------------------------------------------------------
notes:
- Once started, unless the '-quit' option is used, this
program exits only when a fatal error occurs (single
missing or out of order slices are not considered fatal).
Otherwise, it keeps waiting for new data to arrive.
With the '-quit' option, the program will terminate once
there is a significant (~2 TR) pause in acquisition.
- To terminate this program, use <CTRL-C>.
---------------------------------------------------------------
main options:
For DICOM images, either -infile_pattern or -infile_prefix
is required.
-infile_pattern PATTERN : specify pattern for input files
e.g. -infile_pattern 'run1/i*.dcm'
This option is used to specify a wildcard pattern matching
the names of the input DICOM files. These files should be
sorted in the order that they are to be assembled, i.e.
when the files are sorted alphabetically, they should be
sequential slices in a volume, and the volumes should then
progress over time (as with the 'to3d' program).
The pattern for this option must be within quotes, because
it will be up to the program to search for new files (that
match the pattern), not the shell.
-infile_prefix PREFIX : specify prefix matching input files
e.g. -infile_prefix run1/i
This option is similar to -infile_pattern. By providing
only a prefix, the user need not use wildcard characters
with quotes. Using PREFIX with -infile_prefix is
equivalent to using 'PREFIX*' with -infile_pattern (note
the needed quotes).
Note that it may not be a good idea to use, say 'run1/'
for the prefix, as there might be a readme file under
that directory.
Note also that it is necessary to provide a '/' at the
end, if the prefix is a directory (e.g. use run1/ instead
of simply run1).
---------------------------------------------------------------
real-time options:
-rt : specify to use the real-time facility
With this option, the user tells 'Dimon' to use the real-time
facility, passing each volume of images to an existing
afni process on some machine (as specified by the '-host'
option). Whenever a new volume is aquired, it will be
sent to the afni program for immediate update.
Note that afni must also be started with the '-rt' option
to make use of this.
Note also that the '-host HOSTNAME' option is not required
if afni is running on the same machine.
-drive_afni CMND : send 'drive afni' command, CMND
e.g. -drive_afni 'OPEN_WINDOW axialimage'
This option is used to pass a single DRIVE_AFNI command
to afni. For example, 'OPEN_WINDOW axialimage' will open
such an axial view window on the afni controller.
Note: the command 'CMND' must be given in quotes, so that
the shell will send it as a single parameter.
Note: this option may be used multiple times.
See README.driver for more details.
-host HOSTNAME : specify the host for afni communication
e.g. -host mycomputer.dot.my.network
e.g. -host 127.0.0.127
e.g. -host mycomputer
the default host is 'localhost'
The specified HOSTNAME represents the machine that is
running afni. Images will be sent to afni on this machine
during the execution of 'Dimon'.
Note that the enviroment variable AFNI_TRUSTHOST must be
set on the machine running afni. Set this equal to the
name of the machine running Imon (so that afni knows to
accept the data from the sending machine).
-pause TIME_IN_MS : pause after each new volume
e.g. -pause 200
In some cases, the user may wish to slow down a real-time
process. This option will cause a delay of TIME_IN_MS
milliseconds after each volume is found.
-rev_byte_order : pass the reverse of the BYTEORDER to afni
Reverse the byte order that is given to afni. In case the
detected byte order is not what is desired, this option
can be used to reverse it.
See the (obsolete) '-swap' option for more details.
-rt_cmd COMMAND : send COMMAND(s) to realtime plugin
e.g. -rt_cmd 'GRAPH_XRANGE 120'
e.g. -rt_cmd 'GRAPH_XRANGE 120 \n GRAPH_YRANGE 2.5'
This option is used to pass commands to the realtime
plugin. For example, 'GRAPH_XRANGE 120' will set the
x-scale of the motion graph window to 120 (repetitions).
Note: the command 'COMMAND' must be given in quotes, so
that the shell will send it as a single parameter.
Note: this option may be used multiple times.
See README.realtime for more details.
-swap (obsolete) : swap data bytes before sending to afni
Since afni may be running on a different machine, the byte
order may differ there. This option will force the bytes
to be reversed, before sending the data to afni.
** As of version 3.0, this option should not be necessary.
'Dimon' detects the byte order of the image data, and then
passes that information to afni. The realtime plugin
will (now) decide whether to swap bytes in the viewer.
If for some reason the user wishes to reverse the order
from what is detected, '-rev_byte_order' can be used.
-zorder ORDER : slice order over time
e.g. -zorder alt
e.g. -zorder seq
the default is 'alt'
This options allows the user to alter the slice
acquisition order in real-time mode, simliar to the slice
pattern of the '-sp' option. The main differences are:
o only two choices are presently available
o the syntax is intentionally different (from that
of 'to3d' or the '-sp' option)
ORDER values:
alt : alternating in the Z direction (over time)
seq : sequential in the Z direction (over time)
---------------------------------------------------------------
other options:
-debug LEVEL : show debug information during execution
e.g. -debug 2
the default level is 1, the domain is [0,3]
the '-quiet' option is equivalent to '-debug 0'
-dicom_org : organize files before other processing
e.g. -dicom_org
When this flag is set, the program will attempt to read in
all files subject to -infile_prefix or -infile_pattern,
determine which are DICOM image files, and organize them
into an ordered list of files per run.
This may be necessary since the alphabetized list of files
will not always match the sequential slice and time order
(which means, for instance, that '*.dcm' may not list
files in the correct order.
In this case, if the DICOM files contain a valid 'image
number' field (0x0020 0013), then they will be sorted
before any further processing is done.
Notes:
- This does not work in real-time mode, since the files
must all be organized before processing begins.
- The DICOM images need valid 'image number' fields for
organization to be possible (DICOM field 0x0020 0013).
- This works will in conjunction with '-GERT_Reco', to
create a script to make AFNI datasets. There will be
a single file per run that contains the image filenames
for that run (in order). This is fed to 'to3d'.
-help : show this help information
-hist : display a history of program changes
-nice INCREMENT : adjust the nice value for the process
e.g. -nice 10
the default is 0, and the maximum is 20
a superuser may use down to the minimum of -19
A positive INCREMENT to the nice value of a process will
lower its priority, allowing other processes more CPU
time.
-nt VOLUMES_PER_RUN : set the number of time points per run
e.g. -nt 120
With this option, if a run stalls before the specified
VOLUMES_PER_RUN is reached (notably including the first
run), the user will be notified.
Without this option, Dimon will compute the expected number
of time points per run based on the first run (and will
allow the value to increase based on subsequent runs).
Therefore Dimon would not detect a stalled first run.
-quiet : show only errors and final information
-quit : quit when there is no new data
With this option, the program will terminate once a delay
in new data occurs. This is most appropriate to use when
the image files have already been collected.
-sort_by_num_suffix : sort files according to numerical suffix
e.g. -sort_by_num_suffix
With this option, the program will sort the input files
according to the trailing '.NUMBER' in the filename. This
NUMBER will be evaluated as a positive integer, not via
an alphabetic sort (so numbers need not be zero-padded).
This is intended for use on interleaved files, which are
properly enumerated, but only in the filename suffix.
Consider a set of names for a single, interleaved volume:
im001.1 im002.3 im003.5 im004.7 im005.9 im006.11
im007.2 im008.4 im009.6 im010.8 im011.10
Here the images were named by 'time' of acquisition, and
were interleaved. So an alphabetic sort is not along the
slice position (z-order). However the slice ordering was
encoded in the suffix of the filenames.
NOTE: the suffix numbers must be unique
-start_file S_FILE : have Dimon process starting at S_FILE
e.g. -start_file 043/I.901
With this option, any earlier I-files will be ignored
by Dimon. This is a good way to start processing a later
run, if it desired not to look at the earlier data.
In this example, all files in directories 003 and 023
would be ignored, along with everything in 043 up through
I.900. So 043/I.901 might be the first file in run 2.
-use_imon : revert to Imon functionality
-version : show the version information
---------------------------------------------------------------
GERT_Reco options:
-GERT_Reco : output a GERT_Reco_dicom script
Create a script called 'GERT_Reco_dicom', similar to the
one that Ifile creates. This script may be run to create
the AFNI datasets corresponding to the I-files.
-gert_outdir OUTPUT_DIR : set output directory in GERT_Reco
e.g. -gert_outdir subject_A7
e.g. -od subject_A7
the default is '-gert_outdir .'
This will add '-od OUTPUT_DIR' to the @RenamePanga command
in the GERT_Reco script, creating new datasets in the
OUTPUT_DIR directory, instead of the 'afni' directory.
-sp SLICE_PATTERN : set output slice pattern in GERT_Reco
e.g. -sp alt-z
the default is 'alt+z'
This options allows the user to alter the slice
acquisition pattern in the GERT_Reco script.
See 'to3d -help' for more information.
---------------------------------------------------------------
Author: R. Reynolds - version 2.1 (August 23, 2005)
This page auto-generated on Thu Aug 25 16:49:40 EDT 2005
|
| djpeg |
usage: /var/www/html/pub/dist/bin/linux_gcc32/djpeg [switches] [inputfile] Switches (names may be abbreviated): -colors N Reduce image to no more than N colors -fast Fast, low-quality processing -grayscale Force grayscale output -scale M/N Scale output image by fraction M/N, eg, 1/8 -bmp Select BMP output format (Windows style) -gif Select GIF output format -os2 Select BMP output format (OS/2 style) -pnm Select PBMPLUS (PPM/PGM) output format (default) -targa Select Targa output format Switches for advanced users: -dct int Use integer DCT method (default) -dct fast Use fast integer DCT (less accurate) -dct float Use floating-point DCT method -dither fs Use F-S dithering (default) -dither none Don't use dithering in quantization -dither ordered Use ordered dither (medium speed, quality) -map FILE Map to colors used in named image file -nosmooth Don't use high-quality upsampling -onepass Use 1-pass quantization (fast, low quality) -maxmemory N Maximum memory to use (in kbytes) -outfile name Specify name for output file -verbose or -debug Emit debug outputThis page auto-generated on Thu Aug 25 16:49:40 EDT 2005 |
| DTIStudioFibertoSegments |
Usage: DTIStudioFibertoSegments [options] dataset
Convert a DTIStudio Fiber file to a SUMA segment file
Options:
-output / -prefix = name of the output file (not an AFNI dataset prefix)
the default output name will be rawxyzseg.dat
This page auto-generated on Thu Aug 25 16:49:40 EDT 2005
|
| @DTI_studio_reposition |
@DTI_studio_reposition <DTI_HDR_VOLUME> <AFNI_REFERENCE_VOLUME> This script reslices and repositions an DTI_studio ANALYZE volume to match the original volume used to input data into DTI studio Check realignment with AFNI to be sure all went well. Example: FA35.hdr is a (renamed) volume from DTI_studio that contains fractional anisotropy sample_dti_vol+orig is an AFNI volume of one DWI in the first gradient direction (54 slices). sample_dti_vol+orig was created using: to3d -prefix sample_dti_vol DTIepi2new-000[0-4]?.dcm DTIepi2new-0005[0-4].dcm To create a version of FA35 that is in alignment with sample_dti_vol do: @DTI_studio_reposition FA35.hdr sample_dti_vol+origThis page auto-generated on Thu Aug 25 16:49:40 EDT 2005 |
| ent16 |
Usage: ent16 [-%nn]
Computes an estimate of the entropy of stdin.
If the flag '-%75' is given (e.g.), then the
exit status is 1 only if the input could be
compressed at least 75%, otherwise the exit
status is 0. Legal values of 'nn' are 1..99.
In any case, the entropy and compression estimates
are printed to stdout, even if no '-%nn' flag is.
given.
METHOD: entropy is estimated by building a histogram
of all 16 bit words in the input, then summing
over -p[i]*log2(p[i]), i=0..65535. Compression
estimate seems to work pretty good for gzip -1
in most cases of binary image data.
SAMPLE USAGE (csh syntax):
ent16 -%75 < fred+orig.BRIK
if( $status == 1 ) gzip -1v fred+orig.BRIK
This page auto-generated on Thu Aug 25 16:49:40 EDT 2005
|
| FD2 |
Functional Display (32x32, 64x64, 128x128, 256x256) in X11 window.
EPI images in 256x256 Signa format are accepted too.
It displays EPI time or frequency course window.
Usage: /var/www/html/pub/dist/bin/linux_gcc32/FD2 [options] image1, [image2, ..., image10000]
Where options are:
-d display - X11 display
-geom geometry - initial geometry
-nc #_of_colors - initial number of colors [2-200] (def 64)
-sp #_of_degree - range of color spectrum [0-360] degree (def 240)
-gam gamma - gamma correction (1 for no correction)
-num #_of_images - # of images in time course [2-10000].
-im1 image_# - first image in time course. Previous images will be
filled with this one for proper timing of others.
-ideal ref_file - use ref_file for fim-like calculations
-pcthresh # - use # as threshold for correlation
-extra - files after this are not used in time course
(used instead of -num option)
-fim_colors L thr1 pos1 neg2 ... thrL posL negL
- set up L thresholds and colors for FIM overlay
-gsize x y - set graph window size to x by y pixels
-fmag val - magnify scale of FFT by val
-grid val - initial grid separation
-phase - image has negative values (for FFT)
-cf - center image to the frame
-swap - byte-swap data (default is no)
*** this is a new default!
Events:
Program quit : <Q> or <Q>
Change to colors : <C>
Change to B & W :
Swap colors : <S>
Restore colors : Button_3 at image center
Squeeze colors : #2 or #3 button - right side of image
Expand colors : left side of image
Circ. color bar : #2 or #3 button at the color bar
Color saturation : #2 or #3 button - the top or bottom
Exact image number: press <I>, enter_number, <CR>
First image : 1
Last image : l
Next image : >
Previous image : <
dragging red pointer works too
Scale Plot up : +
Scale Plot down : -
Increase Grid Spacing : G
Decrease Grid Spacing : g
Toggle Grid and Colors: r
Toggle Frame colors : R
Increase matrix size : M
Decrease matrix size : m
Exact matrix size : N #of_size <CR> (1 to 25 only)
Save minigraph in ASCII file : press <P>
[with xxx_yyy.suffix filename] press <W>
Save current image to a file : press <S>
Save averaged image (not norm) : press <X>
Position frame in the image : press Button_1 in the image area,
drag cursor, and release button.
Center frame on desired pixel : press Button_1 over desired minigraph.
Rotate image 90 deg. clockwise : press Button_3 in [Rot] window.
counterclockwise : press Button_1 in [Rot] window.
Change to differential display : press [Diff] window. Set first and
last image for averaged reference.
Average of set of images : press [AvIm] (can be used in Diff mode).
Compute FIM overlay : press [FIM], choose ref file,threshold,
then press [GO]
Last image in time course : L
Toggle autoscale of images : A
Hide FIM overlay : H
Hide frame in image : h
Toggle overlay checkerboard : O
Read image into program : F (for file)
Remove image from program : K (for kill)
Move to image 1..9 : 1,2,...9
Toggle common graph baselines : b
Toggle baseline to zero : x
Add/[subtract] 3600 from pixel : D / [d]
In FT edit mode:
increase value : Arrow Up
decrease value : Arrow Down
Shift or Control Arrow : larger changes
undo last change : u
undo all changes : U
</P>
This page auto-generated on Thu Aug 25 16:49:40 EDT 2005 </S></I></S></Q></Q>
|
| fftest |
Usage: fftest [-q] len num nvecThis page auto-generated on Thu Aug 25 16:49:41 EDT 2005 |
| file_tool |
/var/www/html/pub/dist/bin/linux_gcc32/file_tool - display or modify sections of a file
This program can be used to display or edit data in arbitrary
files. If no '-mod_data' option is provided (with DATA), it
is assumed the user wishes only to display the specified data
(using both '-offset' and '-length', or using '-ge_XXX').
usage: /var/www/html/pub/dist/bin/linux_gcc32/file_tool [options] -infiles file1 file2 ...
examples:
----- help examples -----
1. get detailed help:
/var/www/html/pub/dist/bin/linux_gcc32/file_tool -help
2. get descriptions of GE struct elements:
/var/www/html/pub/dist/bin/linux_gcc32/file_tool -help_ge
----- GEMS 4.x and 5.x display examples -----
3. display GE header and extras info for file I.100:
/var/www/html/pub/dist/bin/linux_gcc32/file_tool -ge_all -infiles I.100
4. display GEMS 4.x series and image headers for file I.100:
/var/www/html/pub/dist/bin/linux_gcc32/file_tool -ge4_all -infiles I.100
5. display run numbers for every 100th I-file in this directory
/var/www/html/pub/dist/bin/linux_gcc32/file_tool -ge_uv17 -infiles I.?42
/var/www/html/pub/dist/bin/linux_gcc32/file_tool -ge_run -infiles I.?42
----- general value display examples -----
6. display the 32 characters located 100 bytes into each file:
/var/www/html/pub/dist/bin/linux_gcc32/file_tool -offset 100 -length 32 -infiles file1 file2
7. display the 8 4-byte reals located 100 bytes into each file:
/var/www/html/pub/dist/bin/linux_gcc32/file_tool -disp_real4 -offset 100 -length 32 -infiles file1 file2
----- character modification examples -----
8. in each file, change the 8 characters at 2515 to 'hi there':
/var/www/html/pub/dist/bin/linux_gcc32/file_tool -mod_data "hi there" -offset 2515 -length 8 -infiles I.*
9. in each file, change the 21 characters at 2515 to all 'x's
(and print out extra debug info)
/var/www/html/pub/dist/bin/linux_gcc32/file_tool -debug 1 -mod_data x -mod_type val -offset 2515 \
-length 21 -infiles I.*
----- raw number modification examples -----
10. in each file, change the 3 short integers starting at position
2508 to '2 -419 17'
/var/www/html/pub/dist/bin/linux_gcc32/file_tool -mod_data '2 -419 17' -mod_type sint2 -offset 2508 \
-length 6 -infiles I.*
11. in each file, change the 3 binary floats starting at position
2508 to '-83.4 2 17' (and set the next 8 bytes to zero by
setting the length to 20, instead of just 12).
/var/www/html/pub/dist/bin/linux_gcc32/file_tool -mod_data '-83.4 2 17' -mod_type float4 -offset 2508 \
-length 20 -infiles I.*
12. in each file, change the 3 binary floats starting at position
2508 to '-83.4 2 17', and apply byte swapping
/var/www/html/pub/dist/bin/linux_gcc32/file_tool -mod_data '-83.4 2 17' -mod_type float4 -offset 2508 \
-length 12 -swap_bytes -infiles I.*
notes:
o Use of '-infiles' is required.
o Use of '-length' or a GE information option is required.
o As of this version, only modification with text is supported.
Editing binary data is coming soon to a workstation near you.
special options:
-help : show this help information
: e.g. -help
-version : show version information
: e.g. -version
-hist : show the program's modification history
-debug LEVEL : print extra info along the way
: e.g. -debug 1
: default is 0, max is 2
required 'options':
-infiles f1 f2 ... : specify input files to print from or modify
: e.g. -infiles file1
: e.g. -infiles I.*
Note that '-infiles' should be the final option. This is
to allow the user an arbitrary number of input files.
GE info options:
-ge_all : display GE header and extras info
-ge_header : display GE header info
-ge_extras : display extra GE image info
-ge_uv17 : display the value of uv17 (the run #)
-ge_run : (same as -ge_uv17)
-ge_off : display file offsets for various fields
GEMS 4.x info options:
-ge4_all : display GEMS 4.x series and image headers
-ge4_image : display GEMS 4.x image header
-ge4_series : display GEMS 4.x series header
-ge4_study : display GEMS 4.x study header
raw ascii options:
-length LENGTH : specify the number of bytes to print/modify
: e.g. -length 17
This includes numbers after the conversion to binary. So
if -mod_data is '2 -63 186', and -mod_type is 'sint2' (or
signed shorts), then 6 bytes will be written (2 bytes for
each of 3 short integers).
** Note that if the -length argument is MORE than what is
needed to write the numbers out, the remaind of the length
bytes will be written with zeros. If '17' is given for
the length, and 3 short integers are given as data, there
will be 11 bytes of 0 written after the 6 bytes of data.
-mod_data DATA : specify a string to change the data to
: e.g. -mod_data hello
: e.g. -mod_data '2 -17.4 649'
: e.g. -mod_data "change to this string"
This is the data that will be writting into the modified
file. If the -mod_type is 'str' or 'char', then the
output data will be those characters. If the -mod_type
is any other (i.e. a binary numerical format), then the
output will be the -mod_data, converted from numerical
text to binary.
** Note that a list of numbers must be contained in quotes,
so that it will be processed as a single parameter.
-mod_type TYPE : specify the data type to write to the file
: e.g. -mod_type string
: e.g. -mod_type sint2
: e.g. -mod_type float4
: default is 'str'
TYPE can be one of:
str : perform a string substitution
char, val : perform a (repeated?) character substitution
uint1 : single byte unsigned int (binary write)
sint1 : single byte signed int (binary write)
uint2 : two byte unsigned int (binary write)
sint2 : two byte signed int (binary write)
uint4 : four byte unsigned int (binary write)
sint4 : four byte signed int (binary write)
float4 : four byte floating point (binary write)
float8 : eight byte floating point (binary write)
If 'str' is used, which is the default action, the data is
replaced by the contents of the string DATA (from the
'-mod_data' option).
If 'char' is used, then LENGTH bytes are replaced by the
first character of DATA, repeated LENGTH times.
For any of the others, the list of numbers found in the
-mod_data option will be written in the supplied binary
format. LENGTH must be large enough to accomodate this
list. And if LENGTH is higher, the output will be padded
with zeros, to fill to the requesed length.
-offset OFFSET : use this offset into each file
: e.g. -offset 100
: default is 0
This is the offset into each file for the data to be
read or modified.
-quiet : do not output header information
numeric options:
-disp_int2 : display 2-byte integers
: e.g. -disp_int2
-disp_int4 : display 4-byte integers
: e.g. -disp_int4
-disp_real4 : display 4-byte real numbers
: e.g. -disp_real4
-swap_bytes : use byte-swapping on numbers
: e.g. -swap_bytes
If this option is used, then byte swapping is done on any
multi-byte numbers read from or written to the file.
- R Reynolds, version: 3.2a (March 22, 2005), compiled: Aug 25 2005
This page auto-generated on Thu Aug 25 16:49:41 EDT 2005
|
| fim2 |
Usage: fim2 [options] image_files ...
where 'image_files ...' is a sequence of MRI filenames,
options are:
-pcnt # correlation coeff. threshold will be 1 - 0.01 * #
-pcthresh # correlation coeff. threshold will be #
-im1 # index of image file to use as first in time series;
default is 1; previous images are filled with this
image to synchronize with the reference time series
-num # number of images to actually use, if more than this
many are specified on the command line; default is
to use all images
-non this option turns off the default normalization of
the output activation image; the user should provide
a scaling factor via '-coef #', or '1' will be used
-coef # the scaling factor used to convert the activation output
from floats to short ints (if -non is also present)
-ort fname fname = filename of a time series to which the image data
will be orthogonalized before correlations are computed;
any number of -ort options (from 0 on up) may be used
-ideal fname fname = filename of a time series to which the image data
is to be correlated; exactly one such time series is
required; if the -ideal option is not used, then the
first filename after all the options will be used
N.B.: This version of fim2 allows the specification of more than
one ideal time series file. Each one is separately correlated
with the image time series and the one most highly correlated
is selected for each pixel. Multiple ideals are specified
using more than one '-ideal fname' option, or by using the
form '-ideal [ fname1 fname2 ... ]' -- this latter method
allows the use of wildcarded ideal filenames.
The '[' character that indicates the start of a group of
ideals can actually be any ONE of these: [{/%
and the ']' that ends the group can be: ]}/%
[Format of ort and ideal time series files:
ASCII; one number per line;
Same number of lines as images in the time series;
Value over 33333 --> don't use this image in the analysis]
-polref # use polynomials of order 0..# as extra 'orts';
[or -polort #] default is 0 (yielding a constant vector).
Use # = -1 to suppress this feature.
-fimfile fname fname = filename to save activation magnitudes in;
if not given, the last name on the command line will
be used
-corr if present, indicates to write correlation output to
image file 'fimfile.CORR' (next option is better)
-corfile fname fname = filename to save correlation image in;
if not present, and -corr is not present, correlation
image is not saved.
-cnrfile fname fname = filename to save contrast-to-noise image in;
if not present, will not be computed or saved;
CNR is scaled by 100 if images are output as shorts
and is written 'as-is' if output as floats (see -flim).
[CNR is defined here to be alpha/sigma, where
alpha = amplitude of normalized ideal in a pixel
sigma = standard deviation of pixel after removal
of orts and ideal
normalized ideal = ideal scaled so that trough-to-peak
height is one.]
-sigfile fname fname = filename to save standard deviation image in;
the standard deviation is of what is left after the
least squares removal of the -orts, -polrefs, and -ideal.
N.B.: This is always output in the -flim format!
-fitfile fname Image files of the least squares fit coefficients of
all the -ort and -polref time series that
are projected out of the data time series before
the -ideal is fit. The actual filenames will
be fname.01 fname.02 ....
Their order is -orts, then -polrefs, and last -ideal.
N.B.: These are always output in the -flim format!
-subort fname A new timeseries of images is written to disk, with
names of the form 'fname.0001', etc. These images
have the orts and polrefs (but not ideals) subtracted out.
N.B.: These are always output in the -flim format!
-flim If present, write outputs in mrilib 'float' format,
rather than scale+convert to integers
[The 'ftosh' program can later convert to short integers]
-clean if present, then output images won't have the +/- 10000
values forced into their corners for scaling purposes.
-clip if present, output correlations, etc., will be set to
zero in regions of low intensity.
-q if present, indicates 'quiet' operation.
-dfspace[:0] Indicates to use the 'dfspace' filter (a la imreg) to
register the images spatially before filtering.
-regbase fname Indicates to read image in file 'fname' as the base
image for registration. If not given, the first image
in the time series that is used in the correlation
computations will be used. This is also the image
that is used to define 'low intensity' for the -clip option.
This page auto-generated on Thu Aug 25 16:49:41 EDT 2005
|
| float_scan |
Usage: float_scan [options] input_filename
Scans the input file of IEEE floating point numbers for
illegal values: infinities and not-a-number (NaN) values.
Options:
-fix = Writes a copy of the input file to stdout (which
should be redirected using '>'), replacing
illegal values with 0. If this option is not
used, the program just prints out a report.
-v = Verbose mode: print out index of each illegal value.
-skip n = Skip the first n floating point locations
(i.e., the first 4*n bytes) in the file
N.B.: This program does NOT work on compressed files, nor does it
work on byte-swapped files (e.g., files transferred between
Sun/SGI/HP and Intel platforms), nor does it work on images
stored in the 'flim' format!
The program 'exit status' is 1 if any illegal values were
found in the input file. If no errors were found, then
the exit status is 0. You can check the exit status by
using the shell variable $status. A C-shell example:
float_scan fff
if ( $status == 1 ) then
float_scan -fix fff > Elvis.Aaron.Presley
rm -f fff
mv Elvis.Aaron.Presley fff
endif
This page auto-generated on Thu Aug 25 16:49:41 EDT 2005
|
| from3d |
Program: from3d
Author: B. Douglas Ward
Initial Release: 30 August 1996
Latest Revision: 15 August 2001
Usage: from3d [options] -input fname -prefix rname
Purpose: Extract 2D image files from a 3D AFNI dataset.
Options:
-v Print out verbose information during the run.
-nsize Adjust size of 2D data file to be NxN, by padding
with zeros, where N is a power of 2.
-raw Write images in 'raw' format (just the data bytes)
N.B.: there will be no header information saying
what the image dimensions are - you'll have
to get that information from the x and y
axis information output by 3dinfo.
-float Write images as floats, no matter what they are in
the dataset itself.
-zfirst num Set 'num' = number of first z slice to be extracted.
(default = 1)
-zlast num Set 'num' = number of last z slice to be extracted.
(default = largest)
-tfirst num Set 'num' = number of first time slice to be extracted.
(default = 1)
-tlast num Set 'num' = number of last time slice to be extracted.
(default = largest)
-input fname Read 3D dataset from file 'fname'.
'fname' may include a sub-brick selector list.
-prefix rname Write 2D images using prefix 'rname'.
(-input and -prefix are non-optional options: they)
(must be present or the program will not execute. )
N.B.: * Image data is extracted directly from the dataset bricks.
If a brick has a floating point scaling factor, it will NOT
be applied.
* Images are extracted parallel to the xy-plane of the dataset
orientation (which can be determined by program 3dinfo).
This is the order in which the images were input to the
dataset originally, via to3d.
* If either of these conditions is unacceptable, you can also
try to use the Save:bkg function from an AFNI image window.
This page auto-generated on Thu Aug 25 16:49:41 EDT 2005
|
| FSread_annot |
Usage:
FSread_annot <-input ANNOTFILE>
[-col_1D annot.1D.col]
[-roi_1D annot.1D.roi]
[-cmap_1D annot.1D.cmap]
[show_FScmap]
[-help]
Reads a FreeSurfer annotaion file and outputs
an equivalent ROI file and/or a colormap file
for use with SUMA.
Required options:
-input ANNOTFILE: Binary formatted FreeSurfer
annotation file.
AND one of the optional options.
Optional options:
-col_1D annot.1D.col: Write a 4-column 1D color file.
The first column is the node
index followed by r g b values.
This color file can be imported
using the 'c' option in SUMA.
If no colormap was found in the
ANNOTFILE then the file has 2 columns
with the second being the annotation
value.
-roi_1D annot.1D.roi: Write a 5-column 1D roi file.
The first column is the node
index, followed by its index in the
colormap, followed by r g b values.
This roi file can be imported
using the 'Load' button in SUMA's
'Draw ROI' controller.
If no colormap was found in the
ANNOTFILE then the file has 2 columns
with the second being the annotation
value.
-cmap_1D annot.1D.cmap: Write a 4-column 1D color map file.
The first column is the color index,
followed by r g b and flag values.
The name of each color is inserted
as a comment because 1D files do not
support text data.
-show_FScmap: Show the info of the colormap in the ANNOT file.
++ SUMA version 2004_12_29
CVS tag:
SUMA_2005_04_29_1733
Compile Date:
Aug 25 2005
Ziad S. Saad SSCC/NIMH/NIH ziad@nih.gov
This page auto-generated on Thu Aug 25 16:49:41 EDT 2005
|
| ftosh |
ftosh: convert float images to shorts, by RW Cox
Usage: ftosh [options] image_files ...
where the image_files are in the same format to3d accepts
and where the options are
-prefix pname: The output files will be named in the format
-suffix sname: 'pname.index.sname' where 'pname' and 'sname'
-start si: are strings given by the first 2 options.
-step ss: 'index' is a number, given by 'si+(i-1)*ss'
for the i-th output file, for i=1,2,...
*** Default pname = 'sh'
*** Default sname = nothing at all
*** Default si = 1
*** Default ss = 1
-nsize: Enforce the 'normal size' option, to make
the output images 64x64, 128x128, or 256x256.
-scale sval: 'sval' and 'bval' are numeric values; if
-base bval: sval is given, then the output images are
-top tval: formed by scaling the inputs by the formula
'output = sval*(input-bval)'.
*** Default sval is determined by finding
V = largest abs(input-bval) in all the input
images and then sval = tval / V.
*** Default tval is 32000; note that tval is only
used if sval is not given on the command line.
*** Default bval is 0.
This page auto-generated on Thu Aug 25 16:49:41 EDT 2005
|
| ge_header |
Usage: ge_header [-verb] file ... Prints out information from the GE image header of each file. Options: -verb: Print out some probably useless extra stuff.This page auto-generated on Thu Aug 25 16:49:41 EDT 2005 |
| @GetAfniOrient |
Usage: @GetAfniOrient <NAME> ..... example: @GetAfniOrient Hello+orig.HEAD returns the orient code of Hello+orig.HEAD Ziad Saad (ziad@nih.gov) SSCC/NIMH/ National Institutes of Health, Bethesda MarylandThis page auto-generated on Thu Aug 25 16:49:41 EDT 2005 |
| @GetAfniPrefix |
Usage: @GetAfniPrefix <NAME> ..... example: @GetAfniPrefix /Data/stuff/Hello+orig.HEAD returns the afni prefix of name (Hello) Wildcards are treated as regular characters: example: @GetAfniPrefix 'AAzst1r*+orig' returns : AAzst1r* Ziad Saad (ziad@nih.gov) LBC/NIMH/ National Institutes of Health, Bethesda MarylandThis page auto-generated on Thu Aug 25 16:49:41 EDT 2005 |
| @GetAfniView |
Usage: @GetAfniView <NAME> ..... example: @GetAfniView /Data/stuff/Hello+orig.HEAD returns the afni view of Name (+orig) Wildcards are treated as regular characters: example: @GetAfniView 'AAzst1r*+orig' returns : +orig Ziad Saad (ziad@nih.gov) LBC/NIMH/ National Institutes of Health, Bethesda MarylandThis page auto-generated on Thu Aug 25 16:49:41 EDT 2005 |
| Ifile |
Usage: Ifile [Options] <FILE List> [-nt]: Do not use time stamp to identify complete scans. Complete scans are identified from 'User Variable 17' in the image header. [-sp Pattern]: Slice acquisition pattern. Sets the slice acquisition pattern. The default option is alt+z. See to3d -help for acceptable options. [-od Output_Directory]: Set the output directory in @RenamePanga. The default is afni . <FILE List>: Strings of wildcards defining series of GE-Real Time (GERT) images to be assembled as an afni brick. Example: Ifile '*/I.*' or Ifile '083/I.*' '103/I.*' '123/I.*' '143/I.*' The program attempts to identify complete scans from the list of images supplied on command line and generates the commands necessary to turn them into AFNI bricks using the script @RenamePanga. If at least one complete scan is identified, a script file named GERT_Reco is created and executing it creates the afni bricks placed in the afni directory. How does it work? With the -nt option: Ifile uses the variable 'User Variable 17' in the I file's header. This option appears to be augmented each time a new scan is started. (Thanks to S. Marrett for discovering the elusive variable.) Without -nt option: Ifile first examines the modification time for each image and infers from that which images form a single scan. Consecutive images that are less than T seconds apart belong to the same scan. T is set based on the mean time delay difference between successive images. The threshold currently used works for the test data that we have. If it fails for your data, let us know and supply us with the data. Once a set of images is grouped into a scan the sequence of slice location is analysed and duplicate, missing slices, and incomplete volumes are detected. Sets of images that do not pass these tests are ignored. Preserving Time Info: (not necessary with -nt option but does not hurt to preserve anyway) It is important to preserve the file modification time info as you copy or untar the data. If you neglect to do so and fail to write down where each scan ends and/or begins, you might have a hell of a time reconstructing your data. When copying image directories, use [1m cp -rp ???/* [0m and when untaring the archive, use [1m tar --atime-preserve -xf Archive.tar [0m on linux. On Sun and SGI, tar -xf Archive.tar preserves the time info. Future Improvements: Out of justifiable laziness, and for other less convincing reasons, I have left Ifile and @RenamePanga separate. They can be combined into one program but it's usage would become more complicated. At any rate, the user should not notice any difference since all they have to do is run the script GERT_reco that is created by Ifile. Dec. 12/01 (Last modified July 24/02) SSCC/NIMH Robert W. Cox(rwcox@nih.gov) and Ziad S. Saad (ziad@nih.gov)This page auto-generated on Thu Aug 25 16:49:41 EDT 2005 |
| im2niml |
Usage: im2niml imagefile [imagefile ...] Converts the input image(s) to a text-based NIML element and writes the result to stdout. Sample usage: aiv -p 4444 & im2niml zork.jpg | nicat tcp:localhost:4444 -- Author: RW Cox.This page auto-generated on Thu Aug 25 16:49:41 EDT 2005 |
| imand |
Usage: imand [-thresh #] input_images ... output_image * Only pixels nonzero in all input images * (and above the threshold, if given) will be output.This page auto-generated on Thu Aug 25 16:49:41 EDT 2005 |
| imaver |
Usage: imaver out_ave out_sig input_images ...
(use - to skip output of out_ave and/or out_sig)
* Computes the mean and standard deviation, pixel-by-pixel,
of a whole bunch of images.
* Write output images in 'short int' format if inputs are
short ints, otherwise output images are floating point.
This page auto-generated on Thu Aug 25 16:49:41 EDT 2005
|
| imcalc |
Do arithmetic on 2D images, pixel-by-pixel.
Usage: imcalc options
where the options are:
-datum type = Coerce the output data to be stored as the given type,
which may be byte, short, or float.
[default = datum of first input image]
-a dname = Read image 'dname' and call the voxel values 'a'
in the expression. 'a' may be any letter from 'a' to 'z'.
** If some letter name is used in the expression, but not
present in one of the image options here, then that
variable is set to 0.
-expr "expression"
Apply the expression within quotes to the input images,
one voxel at a time, to produce the output image.
("sqrt(a*b)" to compute the geometric mean, for example)
-output name = Use 'name' for the output image filename.
[default='imcalc.out']
See the output of '3dcalc -help' for details on what kinds of expressions
are possible. Note that complex-valued images cannot be processed (byte,
short, and float are OK).
This page auto-generated on Thu Aug 25 16:49:41 EDT 2005
|
| imcutup |
Usage: imcutup [options] nx ny fname1
Breaks up larger images into smaller image files of size
nx by ny pixels. Intended as an aid to using image files
which have been catenated to make one big 2D image.
OPTIONS:
-prefix ppp = Prefix the output files with string 'ppp'
-xynum = Number the output images in x-first, then y [default]
-yxnum = Number the output images in y-first, then x
-x.ynum = 2D numbering, x.y format
-y.xnum = 2D numbering, y.x format
For example:
imcutup -prefix Fred 64 64 3D:-1:0:256:128:1:zork.im
will break up the big 256 by 128 image in file zork.im
into 8 images, each 64 by 64. The output filenames would be
-xynum => Fred.001 Fred.002 Fred.003 Fred.004
Fred.005 Fred.006 Fred.007 Fred.008
-yxnum => Fred.001 Fred.003 Fred.005 Fred.007
Fred.002 Fred.004 Fred.006 Fred.008
-x.ynum => Fred.001.001 Fred.002.001 Fred.003.001 Fred.004.001
Fred.001.002 Fred.002.002 Fred.003.002 Fred.004.002
-y.xnum => Fred.001.001 Fred.001.002 Fred.001.003 Fred.001.004
Fred.002.001 Fred.002.002 Fred.002.003 Fred.002.004
You may want to look at the input image file with
afni -im fname [then open the Sagittal image window]
before deciding on what to do with the image file.
N.B.: the file specification 'fname' must result in a single
input 2D image - multiple images can't be cut up in one
call to this program.
This page auto-generated on Thu Aug 25 16:49:41 EDT 2005
|
| imdump |
Usage: imdump input_image * Prints out nonzero pixels in an image; * Results to stdout; redirect (with >) to save to a file; * Format: x-index y-index value, one pixel per line.This page auto-generated on Thu Aug 25 16:49:41 EDT 2005 |
| immask |
Usage: immask [-thresh #] [-mask mask_image] [-pos] input_image output_image * Masks the input_image and produces the output_image; * Use of -thresh # means all pixels with absolute value below # in input_image will be set to zero in the output_image * Use of -mask mask_image means that only locations that are nonzero in the mask_image will be nonzero in the output_image * Use of -pos means only positive pixels from input_image will be used * At least one of -thresh, -mask, -pos must be used; more than one is OK.This page auto-generated on Thu Aug 25 16:49:41 EDT 2005 |
| Imon |
Imon - monitor real-time acquisition of I-files
This program is intended to be run during a scanning session
on a GE scanner, to monitor the collection of I-files. The
user will be notified of any missing slice or any slice that
is aquired out of order.
It is recommended that the user runs 'Imon' just after the
scanner is first prepped, and then watches for error messages
during the scanning session. The user should terminate the
program whey they are done with all runs.
Note that 'Imon' can also be run separate from scanning, either
to verify the integrity of I-files, or to create a GERT_Reco2
script, which is used to create AFNI datasets.
At the present time, the user must use <CTRL-C> to terminate
the program.
---------------------------------------------------------------
usage: Imon [options] -start_dir DIR
---------------------------------------------------------------
examples (no real-time options):
Imon -start_dir 003
Imon -help
Imon -start_dir 003 -GERT_reco2 -quit
Imon -start_dir 003 -nt 120 -start_file 043/I.901
Imon -debug 2 -nice 10 -start_dir 003
examples (with real-time options):
Imon -start_dir 003 -rt
Imon -start_dir 003 -rt -host pickle
Imon -start_dir 003 -nt 120 -rt -host pickle
** detailed real-time example:
This example scans data starting from directory 003, expects
160 repetitions (TRs), and invokes the real-time processing,
sending data to a computer called some.remote.computer.name
(where afni is running, and which considers THIS computer to
be trusted - see the AFNI_TRUSTHOST environment variable).
Multiple DRIVE_AFNI commands are passed through '-drive_afni'
options, one requesting to open an axial image window, and
another requesting an axial graph, with 160 data points.
See README.driver for acceptable DRIVE_AFNI commands.
Also, multiple commands specific to the real-time plugin are
passed via the '-rt_cmd' options. The 'REFIX command sets the
prefix for the datasets output by afni. The GRAPH_XRANGE and
GRAPH_YRANGE commands set the graph dimensions for the 3D
motion correction graph (only). And the GRAPH_EXPR command
is used to replace the 6 default motion correction graphs with
a single graph, according to the given expression, the square
root of the average squared entry of the 3 rotaion parameters,
roll, pitch and yaw, ignoring the 3 shift parameters, dx, dy
and dz.
See README.realtime for acceptable DRIVE_AFNI commands.
Imon \
-start_dir 003 \
-nt 160 \
-rt \
-host some.remote.computer.name \
-drive_afni 'OPEN_WINDOW axialimage' \
-drive_afni 'OPEN_WINDOW axialgraph pinnum=160' \
-rt_cmd 'PREFIX eat.more.cheese' \
-rt_cmd 'GRAPH_XRANGE 160' \
-rt_cmd 'GRAPH_YRANGE 1.02' \
-rt_cmd 'GRAPH_EXPR sqrt((d*d+e*e+f*f)/3)'
---------------------------------------------------------------
notes:
- Once started, this program exits only when a fatal error
occurs (single missing or out of order slices are not
considered fatal).
** This has been modified. The '-quit' option tells Imon
to terminate once it runs out of new data to use.
- To terminate this program, use <CTRL-C>.
---------------------------------------------------------------
main option:
-start_dir DIR : (REQUIRED) specify starting directory
e.g. -start_dir 003
The starting directory, DIR, must be of the form 00n,
where n is a digit. The program then monitors all
directories of the form ??n, created by the GE scanner.
For instance, with the option '-start_dir 003', this
program watches for new directories 003, 023, 043, etc.
---------------------------------------------------------------
real-time options:
-rt : specify to use the real-time facility
With this option, the user tells 'Imon' to use the real-time
facility, passing each volume of images to an existing
afni process on some machine (as specified by the '-host'
option). Whenever a new volume is aquired, it will be
sent to the afni program for immediate update.
Note that afni must also be started with the '-rt' option
to make use of this.
Note also that the '-host HOSTNAME' option is not required
if afni is running on the same machine.
-drive_afni CMND : send 'drive afni' command, CMND
e.g. -drive_afni 'OPEN_WINDOW axialimage'
This option is used to pass a single DRIVE_AFNI command
to afni. For example, 'OPEN_WINDOW axialimage' will open
such an axial view window on the afni controller.
Note: the command 'CMND' must be given in quotes, so that
the shell will send it as a single parameter.
Note: this option may be used multiple times.
See README.driver for more details.
-host HOSTNAME : specify the host for afni communication
e.g. -host mycomputer.dot.my.network
e.g. -host 127.0.0.127
e.g. -host mycomputer
the default host is 'localhost'
The specified HOSTNAME represents the machine that is
running afni. Images will be sent to afni on this machine
during the execution of 'Imon'.
Note that the enviroment variable AFNI_TRUSTHOST must be
set on the machine running afni. Set this equal to the
name of the machine running Imon (so that afni knows to
accept the data from the sending machine).
-rev_byte_order : pass the reverse of the BYTEORDER to afni
Reverse the byte order that is given to afni. In case the
detected byte order is not what is desired, this option
can be used to reverse it.
See the (obsolete) '-swap' option for more details.
-rt_cmd COMMAND : send COMMAND(s) to realtime plugin
e.g. -rt_cmd 'GRAPH_XRANGE 120'
e.g. -rt_cmd 'GRAPH_XRANGE 120 \n GRAPH_YRANGE 2.5'
This option is used to pass commands to the realtime
plugin. For example, 'GRAPH_XRANGE 120' will set the
x-scale of the motion graph window to 120 (repetitions).
Note: the command 'COMMAND' must be given in quotes, so
that the shell will send it as a single parameter.
Note: this option may be used multiple times.
See README.realtime for more details.
-swap (obsolete) : swap data bytes before sending to afni
Since afni may be running on a different machine, the byte
order may differ there. This option will force the bytes
to be reversed, before sending the data to afni.
** As of version 3.0, this option should not be necessary.
'Imon' detects the byte order of the image data, and then
passes that information to afni. The realtime plugin
will (now) decide whether to swap bytes in the viewer.
If for some reason the user wishes to reverse the order
from what is detected, '-rev_byte_order' can be used.
-zorder ORDER : slice order over time
e.g. -zorder alt
e.g. -zorder seq
the default is 'alt'
This options allows the user to alter the slice
acquisition order in real-time mode, simliar to the slice
pattern of the '-sp' option. The main differences are:
o only two choices are presently available
o the syntax is intentionally different (from that
of 'to3d' or the '-sp' option)
ORDER values:
alt : alternating in the Z direction (over time)
seq : sequential in the Z direction (over time)
---------------------------------------------------------------
other options:
-debug LEVEL : show debug information during execution
e.g. -debug 2
the default level is 1, the domain is [0,3]
the '-quiet' option is equivalent to '-debug 0'
-help : show this help information
-hist : display a history of program changes
-nice INCREMENT : adjust the nice value for the process
e.g. -nice 10
the default is 0, and the maximum is 20
a superuser may use down to the minimum of -19
A positive INCREMENT to the nice value of a process will
lower its priority, allowing other processes more CPU
time.
-nt VOLUMES_PER_RUN : set the number of time points per run
e.g. -nt 120
With this option, if a run stalls before the specified
VOLUMES_PER_RUN is reached (notably including the first
run), the user will be notified.
Without this option, Imon will compute the expected number
of time points per run based on the first run (and will
allow the value to increase based on subsequent runs).
Therefore Imon would not detect a stalled first run.
-quiet : show only errors and final information
-quit : quit when there is no new data
With this option, the program will terminate once a delay
in new data occurs. This is most appropriate to use when
the image files have already been collected.
-start_file S_FILE : have Imon process starting at S_FILE
e.g. -start_file 043/I.901
With this option, any earlier I-files will be ignored
by Imon. This is a good way to start processing a later
run, if it desired not to look at the earlier data.
In this example, all files in directories 003 and 023
would be ignored, along with everything in 043 up through
I.900. So 043/I.901 might be the first file in run 2.
-version : show the version information
---------------------------------------------------------------
GERT_Reco2 options:
-GERT_Reco2 : output a GERT_Reco2 script
Create a script called 'GERT_Reco2', similar to the one
that Ifile creates. This script may be run to create the
AFNI datasets corresponding to the I-files.
-gert_outdir OUTPUT_DIR : set output directory in GERT_Reco2
e.g. -gert_outdir subject_A7
e.g. -od subject_A7
the default is '-gert_outdir afni'
This will add '-od OUTPUT_DIR' to the @RenamePanga command
in the GERT_Reco2 script, creating new datasets in the
OUTPUT_DIR directory, instead of the 'afni' directory.
-sp SLICE_PATTERN : set output slice pattern in GERT_Reco2
e.g. -sp alt-z
the default is 'alt+z'
This options allows the user to alter the slice
acquisition pattern in the GERT_Reco2 script.
See 'to3d -help' for more information.
---------------------------------------------------------------
Author: R. Reynolds - version 3.3a (March 22, 2005)
(many thanks to R. Birn)
This page auto-generated on Thu Aug 25 16:49:41 EDT 2005
|
| imreg |
Usage: imreg [options] base_image image_sequence ...
* Registers each 2D image in 'image_sequence' to 'base_image'.
* If 'base_image' = '+AVER', will compute the base image as
the average of the images in 'image_sequence'.
* If 'base_image' = '+count', will use the count-th image in the
sequence as the base image. Here, count is 1,2,3, ....
OUTPUT OPTIONS:
-nowrite Don't write outputs, just print progress reports.
-prefix pname The output files will be named in the format
-suffix sname 'pname.index.sname' where 'pname' and 'sname'
-start si are strings given by the first 2 options.
-step ss 'index' is a number, given by 'si+(i-1)*ss'
for the i-th output file, for i=1,2,...
*** Default pname = 'reg.'
*** Default sname = nothing at all
*** Default si = 1
*** Default ss = 1
-flim Write output in mrilib floating point format
(which can be converted to shorts using program ftosh).
*** Default is to write images in format of first
input file in the image_sequence.
-quiet Don't write progress report messages.
-debug Write lots of debugging output!
-dprefix dname Write files 'dname'.dx, 'dname'.dy, 'dname'.phi
for use in time series analysis.
ALIGNMENT ALGORITHMS:
-bilinear Uses bilinear interpolation during the iterative
adjustment procedure, rather than the default
bicubic interpolation. NOT RECOMMENDED!
-modes c f r Uses interpolation modes 'c', 'f', and 'r' during
the coarse, fine, and registration phases of the
algorithm, respectively. The modes can be selected
from 'bilinear', 'bicubic', and 'Fourier'. The
default is '-modes bicubic bicubic bicubic'.
-mlcF Equivalent to '-modes bilinear bicubic Fourier'.
-wtim filename Uses the image in 'filename' as a weighting factor
for each voxel (the larger the value the more
importance is given to that voxel).
-dfspace[:0] Uses the 'iterated diffential spatial' method to
align the images. The optional :0 indicates to
skip the iteration of the method, and to use the
simpler linear differential spatial alignment method.
ACCURACY: displacments of at most a few pixels.
*** This is the default method (without the :0).
-cmass Initialize the translation estimate by aligning
the centers of mass of the images.
N.B.: The reported shifts from the registration algorithm
do NOT include the shifts due to this initial step.
The new two options are used to play with the -dfspace algorithm,
which has a 'coarse' fit phase and a 'fine' fit phase:
-fine blur dxy dphi Set the 3 'fine' fit parameters:
blur = FWHM of image blur prior to registration,
in pixels [must be > 0];
dxy = convergence tolerance for translations,
in pixels;
dphi = convergence tolerance for rotations,
in degrees.
-nofine Turn off the 'fine' fit algorithm. By default, the
algorithm is on, with parameters 1.0, 0.07, 0.21.
This page auto-generated on Thu Aug 25 16:49:41 EDT 2005
|
| imrotate |
Usage: imrotate [-linear | -Fourier] dx dy phi input_image output_image Shifts and rotates an image: dx pixels rightwards (not necessarily an integer) dy pixels downwards phi degrees clockwise -linear means to use bilinear interpolation (default is bicubic) -Fourier means to use Fourier interpolaion Values outside the input_image are taken to be zero.This page auto-generated on Thu Aug 25 16:49:41 EDT 2005 |
| imstack |
Usage: imstack [options] image_filenames ...
Stacks up a set of 2D images into one big file (a la MGH).
Options:
-datum type Converts the output data file to be 'type',
which is either 'short' or 'float'.
The default type is the type of the first image.
-prefix name Names the output files to be 'name'.b'type' and 'name'.hdr.
The default name is 'obi-wan-kenobi'.
This page auto-generated on Thu Aug 25 16:49:41 EDT 2005
|
| imstat |
Calculation of statistics of one or more images.
Usage: imstat [-nolabel] [-pixstat prefix] [-quiet] image_file ...
-nolabel = don't write labels on each file's summary line
-quiet = don't print statistics for each file
-pixstat prefix = if more than one image file is given, then
'prefix.mean' and 'prefix.sdev' will be written
as the pixel-wise statistics images of the whole
collection. These images will be in the 'flim'
floating point format. [This option only works
on 2D images!]
This page auto-generated on Thu Aug 25 16:49:41 EDT 2005
|
| imupsam |
Usage: imupsam [-A] n input_image output_image
* Upsamples the input 2D image by a factor of n and
writes result into output_image; n must be an
integer in the range 2..30.
* 7th order polynomial interpolation is used in each
direction.
* Inputs can be complex, float, short, PGM, PPM, or JPG.
* If input_image is in color (PPM or JPG), output will
be PPM unless output_image ends in '.jpg'.
* If output_image is '-', the result will be written
to stdout (so you could pipe it into something else).
* The '-A' option means to write the result in ASCII
format: all the numbers for the file are output,
and nothing else (no header info).
* Author: RW Cox -- 16 April 1999.
This page auto-generated on Thu Aug 25 16:49:41 EDT 2005
|
| inspec |
Usage: inspec <-spec specfile> [-detail d] [-h/-help]
Outputs information found from specfile.
-spec specfile: specfile to be read
-detail d: level of output detail default is 1.
Available levels are 1, 2 and 3.
-h or -help: This message here.
++ SUMA version 2004_12_29
CVS tag:
SUMA_2005_04_29_1733
Compile Date:
Aug 25 2005
Ziad S. Saad SSCC/NIMH/NIH ziad@nih.gov
Dec 2 03
This page auto-generated on Thu Aug 25 16:49:41 EDT 2005
|
| IsoSurface |
Usage: A program to perform isosurface extraction from a volume.
Based on code by Thomas Lewiner (see below).
IsoSurface < -input VOL | -shape S GR >
< -isoval V | -isorange V0 V1 | -isocmask MASK_COM >
[< -o_TYPE PREFIX>]
[< -debug DBG >]
Mandatory parameters:
You must use one of the following two options:
-input VOL: Input volume.
-shape S GR: Built in shape.
where S is the shape number,
between 0 and 9 (see below).
and GR is the grid size (like 64).
If you use -debug 1 with this option
a .1D volume called mc_shape*.1D is
written to disk. Watch the debug output
for a command suggesting how to turn
this 1D file into a BRIK volume for viewing
in AFNI.
You must use one of the following iso* options:
-isoval V: Create isosurface where volume = V
-isorange V0 V1: Create isosurface where V0 <= volume < V1
-isocmask MASK_COM: Create isosurface where MASK_COM != 0
For example: -isocmask '-a VOL+orig -expr (1-bool(a-V))'
is equivalent to using -isoval V.
NOTE: -isorange and -isocmask are only allowed with -xform mask
See -xform below for details.
Optional Parameters:
-xform XFORM: Transform to apply to volume values
before searching for sign change
boundary. XFORM can be one of:
mask: values that meet the iso* conditions
are set to 1. All other values are set
to -1. This is the default XFORM.
shift: subtract V from the dataset and then
search for 0 isosurface. This has the
effect of constructing the V isosurface
if your dataset has a continuum of values.
This option can only be used with -isoval V.
none: apply no transforms. This assumes that
your volume has a continuum of values
from negative to positive and that you
are seeking to 0 isosurface.
This option can only be used with -isoval 0.
-o_TYPE PREFIX: prefix of output surface.
where TYPE specifies the format of the surface
and PREFIX is, well, the prefix.
TYPE is one of: fs, 1d (or vec), sf, ply.
Default is: -o_ply
Specifying output surfaces using -o_TYPE options:
-o_TYPE outSurf specifies the output surface,
TYPE is one of the following:
fs: FreeSurfer ascii surface.
fsp: FeeSurfer ascii patch surface.
In addition to outSurf, you need to specify
the name of the parent surface for the patch.
using the -ipar_TYPE option.
This option is only for ConvertSurface
sf: SureFit surface.
For most programs, you are expected to specify prefix:
i.e. -o_sf brain. In some programs, you are allowed to
specify both .coord and .topo file names:
i.e. -o_sf XYZ.coord TRI.topo
The program will determine your choice by examining
the first character of the second parameter following
-o_sf. If that character is a '-' then you have supplied
a prefix and the program will generate the coord and topo names.
vec (or 1D): Simple ascii matrix format.
For most programs, you are expected to specify prefix:
i.e. -o_1D brain. In some programs, you are allowed to
specify both coord and topo file names:
i.e. -o_1D brain.1D.coord brain.1D.topo
coord contains 3 floats per line, representing
X Y Z vertex coordinates.
topo contains 3 ints per line, representing
v1 v2 v3 triangle vertices.
ply: PLY format, ascii or binary.
-debug DBG: debug levels of 0 (default), 1, 2, 3.
This is no Rick Reynolds debug, which is oft nicer
than the results, but it will do.
Built In Shapes:
0: Cushin
1: Sphere
2: Plane
3: Cassini
4: Blooby
5: Chair
6: Cyclide
7: 2 Torus
8: mc case
9: Drip
NOTE:
The code for the heart of this program is a translation of:
Thomas Lewiner's C++ implementation of the algorithm in:
Efficient Implementation of Marching Cubes´ Cases with Topological Guarantees
by Thomas Lewiner, Hélio Lopes, Antônio Wilson Vieira and Geovan Tavares
in Journal of Graphics Tools.
http://www-sop.inria.fr/prisme/personnel/Thomas.Lewiner/JGT.pdf
Common Debugging Options:
[-trace]: Turns on In/Out debug and Memory tracing.
For speeding up the tracing log, I recommend
you redirect stdout to a file when using this option.
For example, if you were running suma you would use:
suma -spec lh.spec -sv ... > TraceFile
This option replaces the old -iodbg and -memdbg.
[-TRACE]: Turns on extreme tracing.
[-nomall]: Turn off memory tracing.
[-yesmall]: Turn on memory tracing (default).
[-novolreg]: Ignore any Volreg or Tagalign transformations
present in the Surface Volume.
NOTE: For programs that output results to stdout
(that is to your shell/screen), the debugging info
might get mixed up with your results.
++ SUMA version 2004_12_29
CVS tag:
SUMA_2005_04_29_1733
Compile Date:
Aug 25 2005
Ziad S. Saad SSCC/NIMH/NIH ziad@nih.gov
This page auto-generated on Thu Aug 25 16:49:41 EDT 2005
|
| MakeColorMap |
Usage1:
MakeColorMap <-fn Fiducials_Ncol> [-pos] [-ah prefix] [-h/-help]
Creates a colormap of N colors that contains the fiducial colors.
-fn Fiducials_Ncol: Fiducial colors and their indices in the color
map are listed in file Fiducials_Ncol.
Each row contains 4 tab delimited values:
R G B i
R G B values are between 0 and 1 and represent the
i-th color in the colormap. i should be between 0 and
N-1, N being the total number of colors in the colormap.
Usage2:
MakeColorMap <-f Fiducials> <-nc N> [-sl] [-ah prefix] [-h/-help]
Creates a colormap of N colors that contains the fiducial colors.
-f Fiducials: Fiducial colors are listed in an ascii file Fiducials.
Each row contains 3 tab delimited R G B values between 0 and 1.
-nc N: Total number of colors in the color map.
-sl: (optional, default is NO) if used, the last color in the Fiducial
list is omitted. This is useful in creating cyclical color maps.
Usage3:
MakeColorMap <-std MapName>
Returns one of SUMA's standard colormaps. Choose from:
rgybr20, ngray20, gray20, bw20, bgyr19,
matlab_default_byr64, roi128, roi256, roi64
Common options to all usages:
-ah prefix: (optional, Afni Hex format.
default is RGB values in decimal form)
use this option if you want a color map formatted to fit
in AFNI's .afnirc file. The colormap is written out as
prefix_01 = #xxxxxxx
prefix_02 = #xxxxxxx
etc...
-h or -help: displays this help message.
Example Usage 1: Creating a colormap of 20 colors that goes from
Red to Green to Blue to Yellow to Red.
The file FidCol_Nind contains the following:
1 0 0 0
0 1 0 5
0 0 1 10
1 1 0 15
1 0 0 19
The following command will generate the RGB colormap in decimal form:
MakeColorMap -fn FidCol_Nind
The following command will generate the colormap and write it as
an AFNI color palette file:
MakeColorMap -fn FidCol_Nind -ah TestPalette > TestPalette.pal
Example Usage 2: Creating a cyclical version of the colormap in usage 1:
The file FidCol contains the following:
1 0 0
0 1 0
0 0 1
1 1 0
1 0 0
The following command will generate the RGB colormap in decimal form:
MakeColorMap -f FidCol -sl -nc 20
Example Usage 3: MakeColorMap -std ngray20
To read in a new colormap into AFNI, either paste the contents of
TestPalette.pal in your .afnirc file or read the .pal file using
AFNI as follows:
1- run afni
2- Define Function --> right click on Inten (over colorbar)
--> Read in palette (choose TestPalette.pal)
3- set the #colors chooser (below colorbar) to 20 (the number of colors in
TestPalette.pal).
Common Debugging Options:
[-trace]: Turns on In/Out debug and Memory tracing.
For speeding up the tracing log, I recommend
you redirect stdout to a file when using this option.
For example, if you were running suma you would use:
suma -spec lh.spec -sv ... > TraceFile
This option replaces the old -iodbg and -memdbg.
[-TRACE]: Turns on extreme tracing.
[-nomall]: Turn off memory tracing.
[-yesmall]: Turn on memory tracing (default).
[-novolreg]: Ignore any Volreg or Tagalign transformations
present in the Surface Volume.
NOTE: For programs that output results to stdout
(that is to your shell/screen), the debugging info
might get mixed up with your results.
++ SUMA version 2004_12_29
CVS tag:
SUMA_2005_04_29_1733
Compile Date:
Aug 25 2005
Ziad S. Saad & Rick R. Reynolds SSCC/NIMH/NIH ziad@nih.gov Tue Apr 23 14:14:48 EDT 2002
This page auto-generated on Thu Aug 25 16:49:41 EDT 2005
|
| @make_stim_file |
@make_stim_file - create a time series file, suitable for 3dDeconvolve
This script reads in column headers and stimulus times for
each header (integers), and computes a 'binary' file (all
0s and 1s) with column headers, suitable for use as input to
3dDeconvolve.
The user must specify an output file on the command line (using
-outfile), and may specify a maximum repetition number for rows
of output (using -maxreps).
------------------------------
Usage: @make_stim_file [options] -outfile OUTFILE
examples:
@make_stim_file -outfile green_n_gold
@make_stim_file -outfile green_n_gold < my_input_file
@make_stim_file -maxreps 200 -outfile green_n_gold -headers
@make_stim_file -help
@make_stim_file -maxreps 200 -outfile green_n_gold -debug 1
------------------------------
options:
-help : show this help information
-debug LEVEL : print debug information along the way
e.g. -debug 1
the default is 0, max is 2
-outfile OUTFILE : (required) results are sent to this output file
e.g. -outfile green.n.gold.out
-maxreps REPS : use REPS as the maximum repeptition time
e.g. -maxreps 200
the default is to use the maximum rep time from the input
This option basically pads the output columns with 0s,
so that each column has REPS rows (of 1s and 0s).
-no_headers : do not include headers in output file
e.g. -no_headers
the default is print column headers (# commented out)
------------------------------
Notes:
1. It is probably easiest to use redirection from an input file
for execution of the program. That way, mistakes can be more
easily fixed and retried. See 'Sample execution 2'.
2. Since most people start off with stimulus data in colums, and
since this program requires input in rows for each header, it
may be easiest to go through a few initial steps:
- make sure all data is in integer form
- make sure all blank spaces are filled with 0
- save the file to an ascii data file (without headers)
- use AFNI program '1dtranspose' to convert column data
to row format
- add the column headers back to the top of the ascii file
3. The -maxreps option is recommended when using redirection, so
that the user does not have to add the value to the bottom of
the file.
------------------------------
Sample execution 1: (typing input on command line)
a. executing the following command:
@make_stim_file -outfile red_blue_out
b. and providing input data as follows:
headers -> red blue
'red' -> 2 4
'blue' -> 2 3 5
maxreps -> 6
c. will produce 'red_blue_out', containing:
red blue
0 0
1 1
0 1
1 0
0 1
0 0
------------------------------
Sample execution 2: (using redirection)
a. given input file 'my_input_file': (a text file with input data)
red blue
2 4
2 3 5
6
b. run the script using redirection with -maxreps option
@make_stim_file -maxreps 6 -outfile red_blue_out < my_input_file
c. now there exists output file 'red_blue_out':
red blue
0 0
1 1
0 1
1 0
0 1
0 0
------------------------------
R. Reynolds
------------------------------
This page auto-generated on Thu Aug 25 16:49:41 EDT 2005
|
| MapIcosahedron |
Usage: MapIcosahedron <-spec specFile>
[-rd recDepth] [-ld linDepth]
[-morph morphSurf]
[-it numIt] [-prefix fout]
[-verb] [-help]
Creates new versions of the original-mesh surfaces using the mesh
of an icosahedron.
-spec specFile: spec file containing original-mesh surfaces
including the spherical and warped spherical surfaces.
-rd recDepth: recursive (binary) tesselation depth for icosahedron.
(optional, default:3) See CreateIcosahedron for more info.
-ld linDepth: number of edge divides for linear icosahedron tesselation
(optional, default uses binary tesselation).
See CreateIcosahedron -help for more info.
*Note: Enter -1 for recDepth or linDepth to let program
choose a depth that best approximates the number of nodes in
original-mesh surfaces.
-morph morphSurf: surface state to which icosahedron is inflated
accectable inputs are 'sphere.reg' and 'sphere'
(optional, default uses sphere.reg over sphere).
-it numIt: number of smoothing interations
(optional, default none).
-prefix fout: prefix for output files.
(optional, default MapIco)
NOTE: See program SurfQual -help for more info on the following 2 options.
[-sph_check]: Run tests for checking the spherical surface (sphere.asc)
The program exits after the checks.
This option is for debugging FreeSurfer surfaces only.
[-sphreg_check]: Run tests for checking the spherical surface (sphere.reg.asc)
The program exits after the checks.
This option is for debugging FreeSurfer surfaces only.
-sph_check and -sphreg_check are mutually exclusive.
-verb: When specified, includes original-mesh surfaces
and icosahedron in output spec file.
(optional, default does not include original-mesh surfaces)
NOTE 1: The algorithm used by this program is applicable
to any surfaces warped to a spherical coordinate
system. However for the moment, the interface for
this algorithm only deals with FreeSurfer surfaces.
This is only due to user demand and available test
data. If you want to apply this algorithm using surfaces
created by other programs such as SureFit and Caret,
Send ziad@nih.gov a note and some test data.
NOTE 2: At times, the standard-mesh surfaces are visibly
distorted in some locations from the original surfaces.
So far, this has only occurred when original spherical
surfaces had topological errors in them.
See SurfQual -help and SUMA's online documentation
for more detail.
++ SUMA version 2004_12_29
CVS tag:
SUMA_2005_04_29_1733
Compile Date:
Aug 25 2005
Brenna D. Argall LBC/NIMH/NIH brenna.argall@nih.gov
Ziad S. Saad SSC/NIMH/NIH ziad@nih.gov
Fri Sept 20 2002
This page auto-generated on Thu Aug 25 16:49:41 EDT 2005
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| mayo_analyze |
Usage: mayo_analyze file.hdr ... Prints out info from the Mayo Analyze 7.5 header file(s)This page auto-generated on Thu Aug 25 16:49:41 EDT 2005 |
| mpeg_encode |
Error: Cannot open parameter file: -help Usage: mpeg_encode [options] param_file Options: -stat stat_file: append stats to stat_file -quiet n: don't report remaining time for at least n seconds -realquiet: output nothing at all if successful -no_frame_summary: suppress frame summary lines -float_dct: use more accurate floating point DCT -gop gop_num: encode only the numbered GOP -combine_gops: combine GOP files instead of encode -frames first_frame last_frame: encode only the specified frames -combine_frames: combine frame files instead of encode -nice: run slave processes nicely -max_machines num_machines: use at most num_machines machines -snr: print signal-to-noise ratio -bit_rate_info rate_file: put bit rate in specified file -mv_histogram: show histograms of motion vectorsThis page auto-generated on Thu Aug 25 16:49:41 EDT 2005 |
| mpegtoppm |
Usage: mpegtoppm [-prefix ppp] file.mpg Writes files named 'ppp'000001.ppm, etc.This page auto-generated on Thu Aug 25 16:49:41 EDT 2005 |
| mritopgm |
Converts an image to raw pgm format.
Results go to stdout and should be redirected.
Usage: mritopgm [-pp] input_image
Example: mritopgm fred.001 | ppmtogif > fred.001.gif
The '-pp' option expresses a clipping percentage.
That is, if this option is given, the pp%-brightest
pixel is mapped to white; all above it are also white,
and all below are mapped linearly down to black.
The default is that pp=100; that is, the brightest
pixel is white. A useful operation for many MR images is
mritopgm -99 fred.001 | ppmtogif > fred.001.gif
This will clip off the top 1% of voxels, which are often
super-bright due to arterial inflow effects, etc.
This page auto-generated on Thu Aug 25 16:49:41 EDT 2005
|
| nifti1_test |
Usage: nifti1_test [-n2|-n1|-na|-a2] infile [prefix] If prefix is given, then the options mean: -a2 ==> write an ANALYZE 7.5 file pair: prefix.hdr/prefix.img -n2 ==> write a NIFTI-1 file pair: prefix.hdr/prefix.img -n1 ==> write a NIFTI-1 single file: prefix.nii -na ==> write a NIFTI-1 ASCII+binary file: prefix.nia -za2 ==> write an ANALYZE 7.5 file pair: prefix.hdr.gz/prefix.img.gz -zn2 ==> write a NIFTI-1 file pair: prefix.hdr.gz/prefix.img.gz -zn1 ==> write a NIFTI-1 single file: prefix.nii.gz -zna ==> write a NIFTI-1 ASCII+binary file: prefix.nia.gz The default is '-n1'. If prefix is not given, then the header info from infile file is printed to stdout. Please note that the '.nia' format is NOT part of the NIFTI-1 specification, but is provided mostly for ease of visualization (e.g., you can edit a .nia file and change some header fields, then rewrite it as .nii) sizeof(nifti_1_header)=348This page auto-generated on Thu Aug 25 16:49:41 EDT 2005 |
| nifti_stats |
Demo program for computing NIfTI statistical functions. Usage: nifti_stats [-q|-d|-1|-z] val CODE [p1 p2 p3] val can be a single number or in the form bot:top:step. default ==> output p = Prob(statistic < val). -q ==> output is 1-p. -d ==> output is density. -1 ==> output is x such that Prob(statistic < x) = val. -z ==> output is z such that Normal cdf(z) = p(val). -h ==> output is z such that 1/2-Normal cdf(z) = p(val). Allowable CODEs: CORREL TTEST FTEST ZSCORE CHISQ BETA BINOM GAMMA POISSON NORMAL FTEST_NONC CHISQ_NONC LOGISTIC LAPLACE UNIFORM TTEST_NONC WEIBULL CHI INVGAUSS EXTVAL PVAL LOGPVAL LOG10PVAL Following CODE are distributional parameters, as needed. Results are written to stdout, 1 number per output line. Example (piping output into AFNI program 1dplot): nifti_stats -d 0:4:.001 INVGAUSS 1 3 | 1dplot -dx 0.001 -stdin Author - RW Cox - SSCC/NIMH/NIH/DHHS/USA/EARTH - March 2004This page auto-generated on Thu Aug 25 16:49:41 EDT 2005 |
| nifti_tool |
nifti_tool
- display, modify or compare nifti structures in datasets
- copy a dataset by selecting a list of volumes from the original
- copy a dataset, collapsing any dimensions, each to a single index
- display a time series for a voxel, or more generally, the data
from any collapsed image, in ASCII text
This program can be used to display information from nifti datasets,
to modify information in nifti datasets, to look for differences
between two nifti datasets (like the UNIX 'diff' command), and to copy
a dataset to a new one, either by restricting any dimensions, or by
copying a list of volumes (the time dimension) from a dataset.
Only one action type is allowed, e.g. one cannot modify a dataset
and then take a 'diff'.
one can display - any or all fields in the nifti_1_header structure
- any or all fields in the nifti_image structure
- the extensions in the nifti_image structure
- the time series from a 4-D dataset, given i,j,k
- the data from any collapsed image, given dims. list
one can modify - any or all fields in the nifti_1_header structure
- any or all fields in the nifti_image structure
add/rm - any or all extensions in the nifti_image structure
remove - all extensions and descriptions from the datasets
one can compare - any or all field pairs of nifti_1_header structures
- any or all field pairs of nifti_image structures
one can copy - an arbitrary list of dataset volumes (time points)
- a dataset, collapsing across arbitrary dimensions
(restricting those dimensions to the given indices)
Note: to learn about which fields exist in either of the structures,
or to learn a field's type, size of each element, or the number
of elements in the field, use either the '-help_hdr' option, or
the '-help_nim' option. No further options are required.
------------------------------
usage styles:
nifti_tool -help : show this help
nifti_tool -help_hdr : show nifti_1_header field info
nifti_tool -help_nim : show nifti_image field info
nifti_tool -ver : show the current version
nifti_tool -hist : show the modification history
nifti_tool -nifti_ver : show the nifti library version
nifti_tool -nifti_hist : show the nifti library history
nifti_tool -copy_brick_list -infiles f1'[indices...]'
nifti_tool -copy_collapsed_image I J K T U V W -infiles f1
nifti_tool -disp_hdr [-field FIELDNAME] [...] -infiles f1 ...
nifti_tool -disp_nim [-field FIELDNAME] [...] -infiles f1 ...
nifti_tool -disp_exts -infiles f1 ...
nifti_tool -disp_ts I J K [-dci_lines] -infiles f1 ...
nifti_tool -disp_ci I J K T U V W [-dci_lines] -infiles f1 ...
nifti_tool -mod_hdr [-mod_field FIELDNAME NEW_VAL] [...] -infiles f1 ...
nifti_tool -mod_nim [-mod_field FIELDNAME NEW_VAL] [...] -infiles f1 ...
nifti_tool -add_afni_ext 'extension in quotes' [...] -infiles f1 ...
nifti_tool -add_comment_ext 'extension in quotes' [...] -infiles f1 ...
nifti_tool -rm_ext INDEX [...] -infiles f1 ...
nifti_tool -strip_extras -infiles f1 ...
nifti_tool -diff_hdr [-field FIELDNAME] [...] -infiles f1 f2
nifti_tool -diff_nim [-field FIELDNAME] [...] -infiles f1 f2
------------------------------
options for copy actions:
-copy_brick_list : copy a list of volumes to a new dataset
-cbl : (a shorter, alternative form)
This action allows the user to copy a list of volumes (over time)
from one dataset to another. The listed volumes can be in any
order and contain repeats, but are of course restricted to
the set of values {1, 2, ..., nt-1}, from dimension 4.
This option is a flag. The index list is specified with the input
dataset, contained in square brackets. Note that square brackets
are special to most UNIX shells, so they should be contained
within single quotes. Syntax of an index list:
notes:
- indices start at zero
- indices end at nt-1, which has the special symbol '$'
- single indices should be separated with commas, ','
e.g. -infiles dset0.nii'[0,3,8,5,2,2,2]'
- ranges may be specified using '..' or '-'
e.g. -infiles dset0.nii'[2..95]'
e.g. -infiles dset0.nii'[2..$]'
- ranges may have step values, specified in ()
example: 2 through 95 with a step of 3, i.e. {2,5,8,11,...,95}
e.g. -infiles dset0.nii'[2..95(3)]'
This functionality applies only to 4-dimensional datasets.
e.g. to copy sub-bricks 0 and 7:
nifti_tool -cbl -prefix new_07.nii -infiles dset0.nii'[0,7]'
e.g. to copy an entire dataset:
nifti_tool -cbl -prefix new_all.nii -infiles dset0.nii'[0..$]'
e.g. to copy ever other time point, skipping the first three:
nifti_tool -cbl -prefix new_partial.nii -infiles dset0.nii'[3..$(2)]'
-copy_collapsed_image ... : copy a list of volumes to a new dataset
-cci I J K T U V W : (a shorter, alternative form)
This action allows the user to copy a collapsed dataset, where
some dimensions are collapsed to a given index. For instance, the
X dimension could be collapsed to i=42, and the time dimensions
could be collapsed to t=17. To collapse a dimension, set Di to
the desired index, where i is in {0..ni-1}. Any dimension that
should not be collapsed must be listed as -1.
Any number (of valid) dimensions can be collapsed, even down to a
a single value, by specifying enough valid indices. The resulting
dataset will then have a reduced number of non-trivial dimensions.
Assume dset0.nii has nim->dim[8] = { 4, 64, 64, 21, 80, 1, 1, 1 }.
Note that this is a 4-dimensional dataset.
e.g. copy the time series for voxel i,j,k = 5,4,17
nifti_tool -cci 5 4 17 -1 -1 -1 -1 -prefix new_5_4_17.nii
e.g. read the single volume at time point 26
nifti_tool -cci -1 -1 -1 26 -1 -1 -1 -prefix new_t26.nii
Assume dset1.nii has nim->dim[8] = { 6, 64, 64, 21, 80, 4, 3, 1 }.
Note that this is a 6-dimensional dataset.
e.g. copy all time series for voxel i,j,k = 5,0,17, with v=2
(and add the command to the history)
nifti_tool -cci 5 0 17 -1 -1 2 -1 -keep_hist -prefix new_5_0_17_2.nii
e.g. copy all data where i=3, j=19 and v=2
(I do not claim a good reason to do this)
nifti_tool -cci 3 19 -1 -1 -1 2 -1 -prefix new_mess.nii
See '-disp_ci' for more information (which displays/prints the
data, instead of copying it to a new dataset).
------------------------------
options for display actions:
-disp_hdr : display nifti_1_header fields for datasets
This flag means the user wishes to see some of the nifti_1_header
fields in one or more nifti datasets. The user may want to specify
mutliple '-field' options along with this. This option requires
one or more files input, via '-infiles'.
If no '-field' option is present, all fields will be displayed.
e.g. to display the contents of all fields:
nifti_tool -disp_hdr -infiles dset0.nii
nifti_tool -disp_hdr -infiles dset0.nii dset1.nii dset2.nii
e.g. to display the contents of select fields:
nifti_tool -disp_hdr -field dim -infiles dset0.nii
nifti_tool -disp_hdr -field dim -field descrip -infiles dset0.nii
-disp_nim : display nifti_image fields for datasets
This flag option works the same way as the '-disp_hdr' option,
except that the fields in question are from the nifti_image
structure.
-disp_exts : display all AFNI-type extensions
This flag option is used to display all nifti_1_extension data,
for only those extensions of type AFNI (code = 4). The only
other option used will be '-infiles'.
e.g. to display the extensions in datasets:
nifti_tool -disp_exts -infiles dset0.nii
nifti_tool -disp_exts -infiles dset0.nii dset1.nii dset2.nii
-disp_ts I J K : display ASCII time series at i,j,k = I,J,K
This option is used to display the time series data for the voxel
at i,j,k indices I,J,K. The data is displayed in text, either all
on one line (the default), or as one number per line (via the
'-dci_lines' option).
Notes:
o This function applies only to 4-dimensional datasets.
o The '-quiet' option can be used to suppress the text header,
leaving only the data.
o This option is short for using '-disp_ci' (display collapsed
image), restricted to 4-dimensional datasets. i.e. :
-disp_ci I J K -1 -1 -1 -1
e.g. to display the time series at voxel 23, 0, 172:
nifti_tool -disp_ts 23 0 172 -infiles dset1_time.nii
nifti_tool -disp_ts 23 0 172 -dci_lines -infiles dset1_time.nii
nifti_tool -disp_ts 23 0 172 -quiet -infiles dset1_time.nii
-disp_collapsed_image : display ASCII values for collapsed dataset
-disp_ci I J K T U V W : (a shorter, alternative form)
This option is used to display all of the data from a collapsed
image, given the dimension list. The data is displayed in text,
either all on one line (the default), or as one number per line
(by using the '-dci_lines' flag).
The '-quiet' option can be used to suppress the text header.
e.g. to display the time series at voxel 23, 0, 172:
nifti_tool -disp_ci 23 0 172 -1 0 0 0 -infiles dset1_time.nii
e.g. to display z-slice 14, at time t=68:
nifti_tool -disp_ci -1 -1 14 68 0 0 0 -infiles dset1_time.nii
See '-ccd' for more information, which copies such data to a new
dataset, instead of printing it to the terminal window.
------------------------------
options for modification actions:
-mod_hdr : modify nifti_1_header fields for datasets
This action is used to modify some of the nifti_1_header fields in
one or more datasets. The user must specify a list of fields to
modify via one or more '-mod_field' options, which include field
names, along with the new (set of) values.
The user can modify a dataset in place, or use '-prefix' to
produce a new dataset, to which the changes have been applied.
It is recommended to normally use the '-prefix' option, so as not
to ruin a dataset.
Note that some fields have a length greater than 1, meaning that
the field is an array of numbers, or a string of characters. In
order to modify an array of numbers, the user must provide the
correct number of values, and contain those values in quotes, so
that they are seen as a single option.
To modify a string field, put the string in quotes.
The '-mod_field' option takes a field_name and a list of values.
e.g. to modify the contents of various fields:
nifti_tool -mod_hdr -prefix dnew -infiles dset0.nii \
-mod_field qoffset_x -17.325
nifti_tool -mod_hdr -prefix dnew -infiles dset0.nii \
-mod_field dim '4 64 64 20 30 1 1 1 1'
nifti_tool -mod_hdr -prefix dnew -infiles dset0.nii \
-mod_field descrip 'beer, brats and cheese, mmmmm...'
e.g. to modify the contents of multiple fields:
nifti_tool -mod_hdr -prefix dnew -infiles dset0.nii \
-mod_field qoffset_x -17.325 -mod_field slice_start 1
e.g. to modify the contents of multiple files (must overwrite):
nifti_tool -mod_hdr -overwrite -mod_field qoffset_x -17.325 \
-infiles dset0.nii dset1.nii
-mod_nim : modify nifti_image fields for datasets
This action option is used the same way that '-mod_hdr' is used,
except that the fields in question are from the nifti_image
structure.
-strip_extras : remove extensions and descriptions from datasets
This action is used to attempt to 'clean' a dataset of general
text, in order to make it more anonymous. Extensions and the
nifti_image descrip field are cleared by this action.
e.g. to strip all *.nii datasets in this directory:
nifti_tool -strip -overwrite -infiles *.nii
------------------------------
options for adding/removing extensions:
-add_afni_ext EXT : add an AFNI extension to the dataset
This option is used to add AFNI-type extensions to one or more
datasets. This option may be used more than once to add more than
one extension.
The '-prefix' option is recommended, to create a new dataset.
In such a case, only a single file may be taken as input. Using
'-overwrite' allows the user to overwrite the current file, or
to add the extension(s) to multiple files, overwriting them.
e.g. to add a generic AFNI extension:
nifti_tool -add_afni_ext 'wow, my first extension :)' -prefix dnew \
-infiles dset0.nii
e.g. to add multiple AFNI extensions:
nifti_tool -add_afni_ext 'wow, my first extension :)' \
-add_afni_ext 'look, my second...' \
-prefix dnew -infiles dset0.nii
e.g. to add an extension, and overwrite the dataset:
nifti_tool -add_afni_ext 'some AFNI extension' -overwrite \
-infiles dset0.nii dset1.nii
-add_comment_ext EXT : add a COMMENT extension to the dataset
This option is used to add COMMENT-type extensions to one or more
datasets. This option may be used more than once to add more than
one extension. This option may also be used with '-add_afni_ext'.
The '-prefix' option is recommended, to create a new dataset.
In such a case, only a single file may be taken as input. Using
'-overwrite' allows the user to overwrite the current file, or
to add the extension(s) to multiple files, overwriting them.
e.g. to add a comment about the dataset:
nifti_tool -add_comment 'converted from MY_AFNI_DSET+orig' \
-prefix dnew \
-infiles dset0.nii
e.g. to add multiple extensions:
nifti_tool -add_comment 'add a comment extension' \
-add_afni_ext 'and an AFNI XML style extension' \
-add_comment 'dataset copied from dset0.nii' \
-prefix dnew -infiles dset0.nii
-rm_ext INDEX : remove the extension given by INDEX
This option is used to remove any single extension from the
dataset. Multiple extensions require multiple options.
notes - extension indices begin with 0 (zero)
- to view the current extensions, see '-disp_exts'
- all exensions can be removed using ALL or -1 for INDEX
e.g. to remove the extension #0:
nifti_tool -rm_ext 0 -overwrite -infiles dset0.nii
e.g. to remove ALL extensions:
nifti_tool -rm_ext ALL -prefix dset1 -infiles dset0.nii
nifti_tool -rm_ext -1 -prefix dset1 -infiles dset0.nii
e.g. to remove the extensions #2, #3 and #5:
nifti_tool -rm_ext 2 -rm_ext 3 -rm_ext 5 -overwrite -infiles dset0.nii
------------------------------
options for showing differences:
-diff_hdr : display header field diffs between two datasets
This option is used to find differences between two datasets.
If any fields are different, the contents of those fields is
displayed (unless the '-quiet' option is used).
A list of fields can be specified by using multiple '-field'
options. If no '-field' option is given, all fields will be
checked.
Exactly two dataset names must be provided via '-infiles'.
e.g. to display all nifti_1_header field differences:
nifti_tool -diff_hdr -infiles dset0.nii dset1.nii
e.g. to display selected nifti_1_header field differences:
nifti_tool -diff_hdr -field dim -field intent_code \
-infiles dset0.nii dset1.nii
-diff_nim : display nifti_image field diffs between datasets
This option works the same as '-diff_hdr', except that the fields
in question are from the nifti_image structure.
------------------------------
miscellaneous options:
-debug LEVEL : set the debugging level
Level 0 will attempt to operate with no screen output, but errors.
Level 1 is the default.
Levels 2 and 3 give progressively more infomation.
e.g. -debug 2
-field FIELDNAME : provide a field to work with
This option is used to provide a field to display, modify or
compare. This option can be used along with one of the action
options presented above.
See '-disp_hdr', above, for complete examples.
e.g. nifti_tool -field descrip
e.g. nifti_tool -field descrip -field dim
-infiles file0... : provide a list of files to work with
This parameter is required for any of the actions, in order to
provide a list of files to process. If input filenames do not
have an extension, the directory we be searched for any
appropriate files (such as .nii or .hdr).
See '-mod_hdr', above, for complete examples.
e.g. nifti_tool -infiles file0.nii
e.g. nifti_tool -infiles file1.nii file2 file3.hdr
-mod_field NAME 'VALUE_LIST' : provide new values for a field
This parameter is required for any the modification actions.
If the user wants to modify any fields of a dataset, this is
where the fields and values are specified.
NAME is a field name (in either the nifti_1_header structure or
the nifti_image structure). If the action option is '-mod_hdr',
then NAME must be the name of a nifti_1_header field. If the
action is '-mod_nim', NAME must be from a nifti_image structure.
VALUE_LIST must be one or more values, as many as are required
for the field, contained in quotes if more than one is provided.
Use 'nifti_tool -help_hdr' to get a list of nifti_1_header fields
Use 'nifti_tool -help_nim' to get a list of nifti_image fields
See '-mod_hdr', above, for complete examples.
e.g. modifying nifti_1_header fields:
-mod_field descrip 'toga, toga, toga'
-mod_field qoffset_x 19.4 -mod_field qoffset_z -11
-mod_field pixdim '1 0.9375 0.9375 1.2 1 1 1 1'
-keep_hist : add the command as COMMENT (to the 'history')
When this option is used, the current command will be added
as a NIFTI_ECODE_COMMENT type extension. This provides the
ability to keep a history of commands affecting a dataset.
e.g. -keep_hist
-overwrite : any modifications will be made to input files
This option is used so that all field modifications, including
extension additions or deletions, will be made to the files that
are input.
In general, the user is recommended to use the '-prefix' option
to create new files. But if overwriting the contents of the
input files is prefered, this is how to do it.
See '-mod_hdr' or '-add_afni_ext', above, for complete examples.
e.g. -overwrite
-prefix : specify an output file to write change into
This option is used to specify an output file to write, after
modifications have been made. If modifications are being made,
then either '-prefix' or '-overwrite' is required.
If no extension is given, the output extension will be '.nii'.
e.g. -prefix new_dset
e.g. -prefix new_dset.nii
e.g. -prefix new_dset.hdr
-quiet : report only errors or requested information
This option is equivalent to '-debug 0'.
------------------------------
basic help options:
-help : show this help
e.g. nifti_tool -help
-help_hdr : show nifti_1_header field info
e.g. nifti_tool -help_hdr
-help_nim : show nifti_image field info
e.g. nifti_tool -help_nim
-ver : show the program version number
e.g. nifti_tool -ver
-hist : show the program modification history
e.g. nifti_tool -hist
-nifti_ver : show the nifti library version number
e.g. nifti_tool -nifti_ver
-nifti_hist : show the nifti library modification history
e.g. nifti_tool -nifti_hist
------------------------------
R. Reynolds
compiled: Aug 25 2005
version 1.8 (April 19, 2005)
This page auto-generated on Thu Aug 25 16:49:41 EDT 2005
|
| @NoExt |
Usage: @NoExt <NAME> <EXT1> <EXT2> ..... example: @NoExt Hello.HEAD HEAD BRIK returns Hello @NoExt Hello.BRIK HEAD BRIK returns Hello @NoExt Hello.Jon HEAD BRIK returns Hello.Jon \012Ziad Saad (ziad@nih.gov)\012LBC/NIMH/ National Institutes of Health, Bethesda Maryland\012This page auto-generated on Thu Aug 25 16:49:41 EDT 2005 |
| nsize |
Usage: nsize image_in image_out Zero pads 'image_in' to NxN, N=64,128,256,512, or 1024, whichever is the closest size larger than 'image_in'. [Works only for byte and short images.]This page auto-generated on Thu Aug 25 16:49:42 EDT 2005 |
| p2t |
*** NOTE: This program has been superseded by program 'cdf' ***
Usage #1: p2t p dof
where p = double sided tail probability for t-distribution
dof = number of degrees of freedom to use
OUTPUT = t value that matches the input p
Usage #2: p2t p N L M
where p = double sided tail probability of beta distribution
N = number of measured data points
L = number of nuisance parameters (orts)
M = number of fit parameters
OUTPUT = threshold for correlation coefficient
Usage #3: p2t p
where p = one sided tail probability of Gaussian distribution
OUTPUT = z value for which P(x>z) = p
Usage #4: p2t p dof N
where p = double sided tail probability for distribution of
the mean of N iid zero-mean t-variables
dof = number of degrees of freedom of each t-variable
N = number of t variables averaged
OUTPUT = threshold for the t average statistic
N.B.: The method used for this calculation is the Cornish-
Fisher expansion in N, and is only an approximation.
This also requires dof > 6, and the results will be
less accurate as dof approaches 6 from above!
This page auto-generated on Thu Aug 25 16:49:42 EDT 2005
|
| @parse_afni_name |
Usage 1: A script to parse an AFNI name @parse_afni_name <NAME> Outputs the path, prefix, view and sub-brick selection string.This page auto-generated on Thu Aug 25 16:49:42 EDT 2005 |
| plugout_drive |
Usage: plugout_drive [-host name] [-v]
This program connects to AFNI and sends commands
that the user specifies interactively or on command line
over to AFNI to be executed.
Options:
-host name Means to connect to AFNI running on the
computer 'name' using TCP/IP. The default is to
connect on the current host using shared memory.
-v Verbose mode.
-port pp Use TCP/IP port number 'pp'. The default is
8099, but if two plugouts are running on the
same computer, they must use different ports.
-name sss Use the string 'sss' for the name that AFNI assigns
to this plugout. The default is something stupid.
-com 'ACTION DATA' Execute the following command. For example:
-com 'SET_FUNCTION SomeFunction'
will switch AFNI's function (overlay) to
dataset with prefix SomeFunction.
Make sure ACTION and DATA are together enclosed
in one pair of single quotes.
There are numerous actions listed in AFNI's
README.driver file.
You can use the option -com repeatedly.
-quit Quit after you are done with all the -com commands.
The default is for the program to wait for more
commands to be typed at the terminal's prompt.
NOTE:
You will need to turn plugouts on in AFNI using one of the
following methods:
1. Including '-yesplugouts' as an option on AFNI's command line
2. From AFNI: Define Datamode->Misc->Start Plugouts
3. Set environment variable AFNI_YESPLUGOUTS to YES in .afnirc
Otherwise, AFNI won't be listening for a plugout connection.
This page auto-generated on Thu Aug 25 16:49:42 EDT 2005
|
| plugout_ijk |
Usage: plugout_ijk [-host name] [-v]
This program connects to AFNI and send (i,j,k)
dataset indices to control the viewpoint.
Options:
-host name Means to connect to AFNI running on the
computer 'name' using TCP/IP. The default is to
connect on the current host using shared memory.
-v Verbose mode.
-port pp Use TCP/IP port number 'pp'. The default is
8009, but if two plugouts are running on the
same computer, they must use different ports.
-name sss Use the string 'sss' for the name that AFNI assigns
to this plugout. The default is something stupid.
This page auto-generated on Thu Aug 25 16:49:42 EDT 2005
|
| plugout_tt |
Usage: plugout_tt [-host name] [-v]
This program connects to AFNI and receives notification
whenever the user changes Talairach coordinates.
Options:
-host name Means to connect to AFNI running on the
computer 'name' using TCP/IP. The default is to
connect on the current host using shared memory.
-ijk Means to get voxel indices from AFNI, rather
than Talairach coordinates.
-v Verbose mode: prints out lots of stuff.
-port pp Use TCP/IP port number 'pp'. The default is
8001, but if two copies of this are running on
the same computer, they must use different ports.
-name sss Use the string 'sss' for the name that AFNI assigns
to this plugout. The default is something stupid.
This page auto-generated on Thu Aug 25 16:49:42 EDT 2005
|
| @Purify_1D |
Usage: @Purify_1D [<-sub SUB_STRING>] dset1 dset2 ...
Purifies a series of 1D files for faster I/O into matlab.
-sub SUB_STRING: You can use the sub-brick selection
mode, a la AFNI, to output a select
number of columns. See Example below.
-suf STRING: STRING is attached to the output prefix
which is formed from the input names
Example:
@Purify_1D -sub '[0,3]' somedataset.1D.dset
Ziad S. Saad SSCC/NIMH/NIH ziad@nih.gov
This page auto-generated on Thu Aug 25 16:49:42 EDT 2005
|
| quickspec |
Usage: quickspec
<-tn TYPE NAME> ...
<-tsn TYPE STATE NAME> ...
[<-spec specfile>] [-h/-help]
Use this spec file for quick and dirty way of
loading a surface into SUMA or the command line programs.
Options:
-tn TYPE NAME: specify surface type and name.
See below for help on the parameters.
-tsn TYPE STATE NAME: specify surface type state and name.
TYPE: Choose from the following (case sensitive):
1D: 1D format
FS: FreeSurfer ascii format
PLY: ply format
SF: Caret/SureFit format
BV: BrainVoyager format
NAME: Name of surface file.
For SF and 1D formats, NAME is composed of two names
the coord file followed by the topo file
STATE: State of the surface.
Default is S1, S2.... for each surface.
-spec specfile: Name of spec file output.
Default is quick.spec
The program will only overwrite
quick.spec (the default) spec file.
-h or -help: This message here.
You can use any combinaton of -tn and -tsn options.
Fields in the spec file that are (or cannot) be specified
by this program are set to default values.
This program was written to ward off righteous whiners and is
not meant to replace the venerable @SUMA_Make_Spec_XX scripts.
++ SUMA version 2004_12_29
CVS tag:
SUMA_2005_04_29_1733
Compile Date:
Aug 25 2005
Ziad S. Saad SSCC/NIMH/NIH ziad@nih.gov
Tue Dec 30
This page auto-generated on Thu Aug 25 16:49:42 EDT 2005
|
| @RenamePanga |
Usage: @RenamePanga <DIR #> <FIRST # Image> <# slices> <# reps> <OUTPUT Root>
[-kp] [-i] [-oc] [-sp Pattern] [-od Output Directory]
Creates AFNI bricks from RealTime GE EPI series.
This script is designed to run from the directory where the famed RT image directories are copied to.
If the data were copied from fim3T-adw using @RTcp, this directory should be something like:
/mnt/arena/03/users/sdc-nfs/Data/RTime/2005.08.25/<PID>/<EXAM #>/
<DIR #> : (eg: 3) The directory number where the first image of the series is stored.
<FIRST # Image> : (eg: 19) The number of the first image in the series.
<# slices> : (eg: 18) The number of slices making up the imaged volume.
<# reps> : (eg: 160) The number of samples in your time series.
<OUTPUT Root> : (eg: PolcCw) The prefix for the output brick.
Bricks are automatically saved into the output directory
Unless you use -kp option, bricks are automatically named
<OUTPUT Root>_r# where # is generated each time you
run the script and successfully create a new brick.
Optional Parameters:
-i : Launches to3d in interactive mode. This allows you to double check the automated settings.
-kp: Forces @RenamePanga to use the prefix you designate without modification.
-oc: Performs outliers check. This is useful to do but it slows to3d down and
maybe annoying when checking your data while scanning. If you choose -oc, the
outliers are written to a .1D file and placed in the output directory.
-sp Pattern: Sets the slice acquisition pattern. The default option is alt+z.
see to3d -help for various acceptable options.
-od <OUTPUT Directory>: Directory where the output (bricks and 1D files) will
be stored. The default directory is ./afni
A log file (MAPLOG_Panga) is created in the current directory.
Panga: A state of revenge.
***********
Dec 4 2001 Changes:
- No longer requires the program pad_str.
- Uses to3d to read geometric slice information.
- Allows for bypassing the default naming convention.
- You need to be running AFNI built after Dec 3 2001 to use this script.
- Swapping needs are now determined by to3d.
If to3d complains about not being able to determine swapping needs, check the data manually
- Geom parent option (-gp) has been removed.
- TR is no longer set from command line, it is obtained from the image headers.
Thanks to Jill W., Mike B. and Shruti J. for reporting bugs and testing the scripts.
***********
Usage: @RenamePanga <DIR #> <FIRST # Image> <# slices> <# reps> <OUTPUT Root>
[-kp] [-i] [-oc] [-sp Pattern] [-od Output Directory]
Version 3.2 (09/02/03) Ziad Saad (ziad@nih.gov) Dec 5 2001 SSCC/LBC/NIMH.
</DIR></DIR></DIR>
This page auto-generated on Thu Aug 25 16:49:42 EDT 2005
|
| rmz |
Usage: rmz [-q] [-#] filename ... -- Zeros out files before removing themThis page auto-generated on Thu Aug 25 16:49:42 EDT 2005 |
| ROI2dataset |
Usage:
ROI2dataset <-prefix dsetname> [...] <-input ROI1 ROI2 ...>
[<-of ni_bi|ni_as|1D>]
[<-dom_par_id idcode>]
This program transforms a series of ROI files
to a node dataset. This data set will contain
the node indices in the first column and their
ROI values in the second column.
Duplicate node entries (nodes that are part of
multiple ROIs) will get ignored. You will be
notified when this occurs.
Mandatory parameters:
-prefix dsetname: Prefix of output dataset.
Program will not overwrite existing
datasets.
-input ROI1 ROI2....: ROI files to turn into a
data set. This parameter MUST
be the last one on command line.
Optional parameters:
(all optional parameters must be specified before the
-input parameters.)
-h | -help: This help message
-of FORMAT: Output format of dataset. FORMAT is one of:
ni_bi: NIML binary
ni_as: NIML ascii (default)
1D : 1D AFNI format.
-dom_par_id id: Idcode of domain parent.
When specified, only ROIs have the same
domain parent are included in the output.
If id is not specified then the first
domain parent encountered in the ROI list
is adopted as dom_par_id.
1D roi files do not have domain parent
information. They will be added to the
output data under the chosen dom_par_id.
-pad_to_node max_index: Output a full dset from node 0
to node max_index (a total of
max_index + 1 nodes). Nodes that
are not part of any ROI will get
a default label of 0 unless you
specify your own padding label.
-pad_val padding_label: Use padding_label (an integer) to
label nodes that do not belong
to any ROI. Default is 0.
++ SUMA version 2004_12_29
CVS tag:
SUMA_2005_04_29_1733
Compile Date:
Aug 25 2005
Ziad S. Saad SSCC/NIMH/NIH ziad@nih.gov
This page auto-generated on Thu Aug 25 16:49:42 EDT 2005
|
| rotcom |
Usage: rotcom '-rotate aaI bbR ccA -ashift ddS eeL ffP' [dataset]
Prints to stdout the 4x3 transformation matrix+vector that would be
applied by 3drotate to the given dataset.
The -rotate and -ashift options combined must be input inside single
quotes (i.e., as one long command string):
* These options follow the same form as specified by '3drotate -help'.
* That is, if you include the '-rotate' component, it must be followed
by 3 angles.
* If you include the '-ashift' component, it must be followed by 3 shifts;
* For example, if you only want to shift in the 'I' direction, you could use
'-ashift 10I 0 0'.
* If you only want to rotate about the 'I' direction, you could use
'-rotate 10I 0R 0A'.
Note that the coordinate order for the matrix and vector is that of
the dataset, which can be determined from program 3dinfo. This is the
only function of the 'dataset' command line argument.
If no dataset is given, the coordinate order is 'RAI', which means:
-x = Right [and so +x = Left ]
-y = Anterior [ so +y = Posterior]
-z = Inferior [ so +z = Superior ]
For example, the output of command
rotcom '-rotate 10I 0R 0A'
is the 3 lines below:
0.984808 -0.173648 0.000000 0.000
0.173648 0.984808 0.000000 0.000
0.000000 0.000000 1.000000 0.000
-- RWCox - Nov 2002
This page auto-generated on Thu Aug 25 16:49:42 EDT 2005
|
| RSFgen |
Program: RSFgen
Author: B. Douglas Ward
Initial Release: 06 July 1999
Latest Revision: 13 March 2003
Sample program to generate random stimulus functions.
Usage:
RSFgen
-nt n n = length of time series
-num_stimts p p = number of input stimuli (experimental conditions)
[-nblock i k] k = block length for stimulus i (1<=i<=p)
(default: k = 1)
[-seed s] s = random number seed
[-quiet] flag to suppress screen output
[-one_file] place stimulus functions into a single .1D file
[-one_col] write stimulus functions as a single column of decimal
integers (default: multiple columns of binary nos.)
[-prefix pname] pname = prefix for p output .1D stimulus functions
e.g., pname1.1D, pname2.1D, ..., pnamep.1D
The following Random Permutation, Markov Chain, and Input Table options
are mutually exclusive.
Random Permutation options:
-nreps i r r = number of repetitions for stimulus i (1<=i<=p)
[-pseed s] s = stim label permutation random number seed
p
Note: Require n >= Sum (r[i] * k[i])
i=1
Markov Chain options:
-markov mfile mfile = file containing the transition prob. matrix
[-pzero z] probability of a zero (i.e., null) state
(default: z = 0)
Input Table row permutation options:
[-table dfile] dfile = filename of column or table of numbers
Note: dfile may have a column selector attached
Note: With this option, all other input options,
except -seed and -prefix, are ignored
Warning: This program will overwrite pre-existing .1D files
This page auto-generated on Thu Aug 25 16:49:42 EDT 2005
|
| rtfeedme |
Usage: rtfeedme [options] dataset [dataset ...]
Test the real-time plugin by sending all the bricks in 'dataset' to AFNI.
* 'dataset' may include a sub-brick selector list.
* If more than one dataset is given, multiple channel acquisition
will be simulated. Each dataset must then have the same datum
and dimensions.
* If you put the flag '-break' between datasets, then the datasets
in each group will be transmitted in parallel, but the groups
will be transmitted serially (one group, then another, etc.).
+ For example:
rtfeedme A+orig B+orig -break C+orig -break D+orig
will send the A and B datasets in parallel, then send
the C dataset separately, then send the D dataset separately.
(That is, there will be 3 groups of datasets.)
+ There is a 1 second delay between the end transmission for
a group and the start transmission for the next group.
+ You can extend the inter-group delay by using a break option
of the form '-break_20' to indicate a 20 second delay.
+ Within a group, each dataset must have the same datum and
same x,y,z,t dimensions. (Different groups don't need to
be conformant to each other.)
+ All the options below apply to each group of datasets;
i.e., they will all get the same notes, drive commands, ....
Options:
-host sname = Send data, via TCP/IP, to AFNI running on the
computer system 'sname'. By default, uses the
current system, and transfers data using shared
memory. To send on the current system using
TCP/IP, use the system 'localhost'.
-dt ms = Tries to maintain an inter-transmit interval of
'ms' milliseconds. The default is to send data
as fast as possible.
-3D = Sends data in 3D bricks. By default, sends in
2D slices.
-buf m = When using shared memory, sets the interprocess
communications buffer to 'm' megabytes. Has no
effect if using TCP/IP. Default is m=1.
If you use m=0, then a 50 Kbyte buffer is used.
-verbose = Be talkative about actions.
-swap2 = Swap byte pairs before sending data.
-nzfake nz = Send 'nz' as the value of nzz (for debugging).
-drive cmd = Send 'cmd' as a DRIVE_AFNI command; e.g.,
-drive 'OPEN_WINDOW A.axialimage'
If cmd contains blanks, it must be in 'quotes'.
Multiple -drive options may be used.
-note sss = Send 'sss' as a NOTE to the realtime plugin.
Multiple -note options may be used.
-gyr v = Send value 'v' as the y-range for realtime motion
estimation graphing.
This page auto-generated on Thu Aug 25 16:49:42 EDT 2005
|
| SampBias |
Usage:
SampBias -spec SPECFILE -surf SURFNAME -plimit limit -dlimit limit -out FILE
Mandatory parameters:
-spec SpecFile: Spec file containing input surfaces.
-surf SURFNAME: Name of input surface
-plimit limit: maximum length of path along surface in mm.
default is 50 mm
-dlimit limit: maximum length of euclidean distance in mm.
default is 1000 mm
-out FILE: output dataset
Common Debugging Options:
[-trace]: Turns on In/Out debug and Memory tracing.
For speeding up the tracing log, I recommend
you redirect stdout to a file when using this option.
For example, if you were running suma you would use:
suma -spec lh.spec -sv ... > TraceFile
This option replaces the old -iodbg and -memdbg.
[-TRACE]: Turns on extreme tracing.
[-nomall]: Turn off memory tracing.
[-yesmall]: Turn on memory tracing (default).
[-novolreg]: Ignore any Volreg or Tagalign transformations
present in the Surface Volume.
NOTE: For programs that output results to stdout
(that is to your shell/screen), the debugging info
might get mixed up with your results.
++ SUMA version 2004_12_29
CVS tag:
SUMA_2005_04_29_1733
Compile Date:
Aug 25 2005
blame Ziad S. Saad SSCC/NIMH/NIH ziad@nih.gov
This page auto-generated on Thu Aug 25 16:49:42 EDT 2005
|
| ScaleToMap |
Usage: ScaleToMap <-input IntFile icol vcol>
[-cmap MapType] [-cmapfile Mapfile] [-cmapdb Palfile] [-frf]
[-clp/-perc_clp clp0 clp1] [-apr/-anr range]
[-interp/-nointerp/-direct] [-msk msk0 msk1] [-nomsk_col]
[-msk_col R G B] [-br BrightFact]
[-h/-help] [-verb] [-showmap] [-showdb]
-input IntFile icol vcol: input data.
Infile: 1D formatted ascii file containing node values
icol: index of node index column
(-1 if the node index is implicit)
vcol: index of node value column.
Example: -input ValOnly.1D -1 0
for a 1D file containing node values
in the first column and no node indices.
Example: -input NodeVal.1D 1 3
for a 1D file containing node indices in
the SECOND column and node values in the
FOURTH column (index counting begins at 0)
-v and -iv options are now obsolete.
Use -input option instead.
-cmap MapName: (optional, default RGYBR20)
choose one of the standard colormaps available with SUMA:
RGYBR20, BGYR19, BW20, GRAY20, MATLAB_DEF_BYR64,
ROI64, ROI128
You can also use AFNI's default paned color maps:
The maps are labeled according to the number of
panes and their sign. Example: afni_p10
uses the positive 10-pane afni colormap.
afni_n10 is the negative counterpart.
These maps are meant to be used with
the options -apr and -anr listed below.
You can also load non-default AFNI colormaps
from .pal files (AFNI's colormap format); see option
-cmapdb below.
-cmapdb Palfile: read color maps from AFNI .pal file
In addition to the default paned AFNI colormaps, you
can load colormaps from a .pal file.
To access maps in the Palfile you must use the -cmap option
with the label formed by the name of the palette, its sign
and the number of panes. For example, to following palette:
***PALETTES deco [13]
should be accessed with -cmap deco_n13
***PALETTES deco [13+]
should be accessed with -cmap deco_p13
-cmapfile Mapfile: read color map from Mapfile.
Mapfile:1D formatted ascii file containing colormap.
each row defines a color in one of two ways:
R G B or
R G B f
where R, G, B specify the red, green and blue values,
between 0 and 1 and f specifies the fraction of the range
reached at this color. THINK values of right of AFNI colorbar.
The use of fractions (it is optional) would allow you to create
non-linear color maps where colors cover differing fractions of
the data range.
Sample colormap with positive range only (a la AFNI):
0 0 1 1.0
0 1 0 0.8
1 0 0 0.6
1 1 0 0.4
0 1 1 0.2
Note the order in which the colors and fractions are specified.
The bottom color of the +ve colormap should be at the bottom of the
file and have the lowest +ve fraction. The fractions here define a
a linear map so they are not necessary but they illustrate the format
of the colormaps.
Comparable colormap with negative range included:
0 0 1 1.0
0 1 0 0.6
1 0 0 0.2
1 1 0 -0.2
0 1 1 -0.6
The bottom color of the -ve colormap should have the
lowest -ve fraction.
You can use -1 -1 -1 for a color to indicate a no color
(like the 'none' color in AFNI). Values mapped to this
'no color' will be masked as with the -msk option.
If your 1D color file has more than three or 4 columns,
you can use the [] convention adopted by AFNI programs
to select the columns you need.
-frf: (optional) first row in file is the first color.
As explained in the -cmapfile option above, the first
or bottom (indexed 0 )color of the colormap should be
at the bottom of the file. If the opposite is true, use
the -frf option to signal that.
This option is only useful with -cmapfile.
-clp/-perc_clp clp0 clp1: (optional, default no clipping)
clips values in IntVect. if -clp is used then values in vcol
< clp0 are clipped to clp0 and > clp1 are clipped to clp1
if -perc_clp is used them vcol is clipped to the values
corresponding to clp0 and clp1 percentile.
The -clp/-prec_clp options are mutually exclusive with -apr/-anr.
-apr range: (optional) clips the values in IntVect to [0 range].
This option allows range of colormap to be set as in AFNI,
with Positive colorbar (Pos selected).
This option is mutually exclusive with -clp/-perc_clp).
set range = 0 for autoranging.
If you use -apr and your colormap contains fractions, you
must use a positive range colormap.
-anr range: (optional) clips the values in IntVect to [-range range].
This option allows range of colormap to be set as in AFNI,
with Negative colorbar (Pos NOT selected).
This option is mutually exclusive with -clp/-perc_clp).
set range = 0 for autoranging.
If you use -anr and your colormap contains fractions, you
must use a negative range colormap.
-interp: (default) use color interpolation between colors in colormap
If a value is assigned between two colors on the colorbar,
it receives a color that is an interpolation between those two colors.
This is the default behaviour in SUMA and AFNI when using the continuous
colorscale. Mutually exclusive with -nointerp and -direct options.
-nointerp: (optional) turns off color interpolation within the colormap
Color assigniment is done a la AFNI when the paned colormaps are used.
Mutually exclusive with -interp and -direct options.
-direct: (optional) values (typecast to integers) are mapped directly
to index of color in color maps. Example: value 4 is assigned
to the 5th (index 4) color in the color map (same for values
4.2 and 4.7). This mapping scheme is useful for ROI indexed type
data. Negative data values are set to 0 and values >= N_col
(the number of colors in the colormap) are set to N_col -1
-msk_zero: (optional) values that are 0 will get masked no matter
what colormaps or mapping schemes you are using.
AFNI masks all zero values by default.
-msk msk0 msk1: (optinal, default is no masking)
Values in vcol (BEFORE clipping is performed)
between [msk0 msk1] are masked by the masking color.
-msk_col R G B: (optional, default is 0.3 0.3 0.3)
Sets the color of masked voxels.
-nomsk_col: do not output nodes that got masked.
It does not make sense to use this option with
-msk_col.
-br BrightFact: (optional, default is 1)
Applies a brightness factor to the colors
of the colormap and the mask color.
-h or -help: displays this help message.
The following options are for debugging and sanity checks.
-verb: (optional) verbose mode.
-showmap: (optional) print the colormap to the screen and quit.
This option is for debugging and sanity checks.
-showdb: (optional) print the colors and colormaps of AFNI
along with any loaded from the file Palfile.
Common Debugging Options:
[-trace]: Turns on In/Out debug and Memory tracing.
For speeding up the tracing log, I recommend
you redirect stdout to a file when using this option.
For example, if you were running suma you would use:
suma -spec lh.spec -sv ... > TraceFile
This option replaces the old -iodbg and -memdbg.
[-TRACE]: Turns on extreme tracing.
[-nomall]: Turn off memory tracing.
[-yesmall]: Turn on memory tracing (default).
[-novolreg]: Ignore any Volreg or Tagalign transformations
present in the Surface Volume.
NOTE: For programs that output results to stdout
(that is to your shell/screen), the debugging info
might get mixed up with your results.
++ SUMA version 2004_12_29
CVS tag:
SUMA_2005_04_29_1733
Compile Date:
Aug 25 2005
Ziad S. Saad SSCC/NIMH/NIH ziad@nih.gov
July 31/02
This page auto-generated on Thu Aug 25 16:49:42 EDT 2005
|
| serial_helper |
------------------------------------------------------------
/var/www/html/pub/dist/bin/linux_gcc32/serial_helper - pass motion parameters from socket to serial port
This program is meant to receive registration (motion?)
correction parameters from afni's realtime plugin, and to
pass that data on to a serial port.
The program is meant to run as a tcp server. It listens
for a connection, then processes data until a termination
flag is received (sending data from the tcp socket to the
serial port), closes the new connection, and goes back
to a listening state.
The basic outline is:
open tcp server socket
repeat forever:
wait for a tcp client connection
open a serial port
while the client sends new data
write that data to the serial port
close the serial port and client socket
The expected client is the realtime plugin to afni,
plug_realtime.so. If the afni user has their environment
variable AFNI_REALTIME_MP_HOST_PORT set as HOST:PORT,
then for EACH RUN, the realtime plugin will open a tcp
connection to the given HOST and PORT, pass the magic hello
data (0xabcdefab), pass the 6 motion parameters for each
time point, and signal a closure by passing the magic bye
data (0xdeaddead).
On this server end, the 'repeat forever' loop will do the
following. First it will establish the connection by
checking for the magic hello data. If that data is found,
the serial port will be opened.
Then it will repeatedly check the incoming data for the
magic bye data. As long as that check fails, the data is
assumed to be valid motion parameters. And so 6 floats at a
time are read from the incoming socket and passed to the
serial port.
usage: /var/www/html/pub/dist/bin/linux_gcc32/serial_helper [options] -serial_port FILENAME
------------------------------------------------------------
examples:
1. display this help :
/var/www/html/pub/dist/bin/linux_gcc32/serial_helper -help
2. display the module history :
/var/www/html/pub/dist/bin/linux_gcc32/serial_helper -hist
3. display the current version number :
/var/www/html/pub/dist/bin/linux_gcc32/serial_helper -ver
* 4. run normally, using the serial port file /dev/ttyS0 :
/var/www/html/pub/dist/bin/linux_gcc32/serial_helper -serial_port /dev/ttyS0
* 5. same as 4, but specify socket number 53214 :
/var/www/html/pub/dist/bin/linux_gcc32/serial_helper -serial_port /dev/ttyS0 -sock_num 53214
6. same as 5, but specify minmum and maximum bounds on
the values :
/var/www/html/pub/dist/bin/linux_gcc32/serial_helper \
-serial_port /dev/ttyS0 \
-sock_num 53214 \
-mp_min -12.7 \
-mp_max 12.7
7. run the program in socket test mode, without serial
communication, and printing all the incoming data
/var/www/html/pub/dist/bin/linux_gcc32/serial_helper -no_serial -debug 3
8. same as 4, but use debug level 3 to see the parameters
that will be passed on, and duplicate all output to the
file, helper.output
note: this command is for the t-shell, and will not work
under bash (for bash do the 2>&1 thingy...)
/var/www/html/pub/dist/bin/linux_gcc32/serial_helper -serial_port /dev/ttyS0 -debug 3 |& tee helper.out
------------------------------------------------------------
program setup:
1. Start '/var/www/html/pub/dist/bin/linux_gcc32/serial_helper' on the computer with the serial port that
the motion parameters should be written to. Example 3
is the most likely case, though it might be useful to
use example 8.
2. On the computer which will be used to run 'afni -rt',
set the environment variable AFNI_REALTIME_MP_HOST_PORT
to the appropriate host:port pair. See the '-sock_num'
option below for more details.
This variable can also be set in the ~/.cshrc file, or
as part of the AFNI environment via the ~/.afnirc file.
3. Start 'afni -rt'. Be sure to request 'realtime' graphing
of the '3D: realtime' Registration parameters.
4. Start receiving data (sending it to the realtime plugin).
Note that for testing purposes, I may work well to get a
set of I-files (say, in directories 003, 023, etc.), and
to use Imon to send not-so-real-time data to afni. An
example of Imon for this purpose might be:
Imon -start_dir 003 -quit -rt -host localhost
See 'Imon -help' for more information.
------------------------------------------------------------
'required' parameter:
-serial_port FILENAME : specify output serial port
: -serial_port /dev/ttyS0
If the user is not using any of the 'special' options,
below, then this parameter is required.
The FILENAME is the device file for the serial port
which will be used for output.
------------------------------
special options (for information or testing):
-help : show this help information
-hist : show the module history
-debug LEVEL : set the debugging level to LEVEL
: e.g. -debug 2
: default is 0, max is 3
-no_serial : turn of serial port output
This option is used for testing the incoming data,
when output to a serial port is not desired. The
program will otherwise operate normally.
-version : show the current version number
------------------------------
'normal' options:
-mp_max MAX_VAL : limit the maximum value of the MP data
: e.g. -mp_max 12.7
: default is 12.7
If any incoming data is greater than this value, it will
be set to this value. The default of 12.7 is used to
scale incoming floats to signed bytes.
-mp_min MIN_VAL : limit the minimum value of the MP data
: e.g. -mp_min -12.7
: default is -12.7
If any incoming data is less than this value, it will
be set to this value. The default of -12.7 is used to
scale incoming floats to signed bytes.
-sock_num SOCK : specify socket number to serve
: e.g. -sock_num 53214
: default is 53214
This is the socket the program will use to listen for
new connections. This is the socket number that should
be provided to the realtime plugin via the environment
variable, AFNI_REALTIME_MP_HOST_PORT.
On the machine the user run afni from, that environment
variable should have the form HOST:PORT, where a basic
example might be localhost:53214.
------------------------------------------------------------
Authors: R. Reynolds, T. Ross (March, 2004)
------------------------------------------------------------
This page auto-generated on Thu Aug 25 16:49:42 EDT 2005
|
| sfim |
MCW SFIM: Stepwise Functional IMages, by RW Cox
Usage: sfim [options] image_files ...
+ image_files are in the same format AFNI accepts
+ options are from the following:
-sfint iname: 'iname' is the name of a file which has
the interval definitions; an example is
3*# 5*rest 4*A 5*rest 4*B 5*rest 4*A 5*rest
which says:
- ignore the 1st 3 images
- take the next 5 as being in task state 'rest'
- take the next 4 as being in task state 'A'
and so on;
task names that start with a nonalphabetic character
are like the '#' above and mean 'ignore'.
*** the default 'iname' is 'sfint'
-base bname: 'bname' is the task state name to use as the
baseline; other task states will have the mean
baseline state subtracted; if there are no task
states from 'iname' that match 'bname', this
subtraction will not occur.
*** the default 'bname' is 'rest'
-localbase: if this option is present, then each non-base
task state interval has the mean of the two
nearest base intervals subtracted instead of the
grand mean of all the base task intervals.
-prefix pname: 'pname' is the prefix for output image filenames for
all states: the i'th interval with task state name
'fred' will be writen to file 'pname.fred.i'.
*** the default 'pname' is 'sfim'
Output files are the base-mean-removed averages for each non-base
task interval, and simply the mean for each base task interval.
Output images are in the 'flim' (floating pt. image) format, and
may be converted to 16 bit shorts using the program 'ftosh'.
This page auto-generated on Thu Aug 25 16:49:42 EDT 2005
|
| siemens_vision |
Usage: siemens_vision [options] filename ... Prints out information from the Siemens .ima file header(s). The only option is to rename the file according to the TextImageNumber field stored in the header. The option is: -rename ppp which will rename each file to the form 'ppp.nnnn.ima', where 'nnnn' is the image number expressed with 4 digits. When '-rename' is used, the header info from the input files will not be printed.This page auto-generated on Thu Aug 25 16:49:42 EDT 2005 |
| sqwave |
Usage: /var/www/html/pub/dist/bin/linux_gcc32/sqwave [-on #] [-off #] [-length #] [-cycles #]
[-init #] [-onkill #] [-offkill #] [-initkill #] [-name name]
FatalError
This page auto-generated on Thu Aug 25 16:49:42 EDT 2005
|
| strblast |
Usage: strblast [options] TARGETSTRING filename ...
Finds exact copies of the target string in each of
the input files, and replaces all characters with
some junk string.
options:
-help : show this help
-new_char CHAR : replace TARGETSTRING with CHAR (repeated)
This option is used to specify what TARGETSTRING is
replaced with. In this case, replace it with repeated
copies of the character CHAR.
-new_string STRING : replace TARGETSTRING with STRING
This option is used to specify what TARGETSTRING is
replaced with. In this case, replace it with the string
STRING. If STRING is not long enough, then CHAR from the
-new_char option will be used to complete the overwrite
(or the character 'x', by default).
-unescape : parse TARGETSTRING for escaped characters
(includes '\t', '\n', '\r')
If this option is given, strblast will parse TARGETSTRING
replacing any escaped characters with their encoded ASCII
values.
Examples:
strings I.001 | more # see if Subject Name is present
strblast 'Subject Name' I.*
strblast -unescape "END OF LINE\n" infile.txt
strblast -new_char " " "BAD STRING" infile.txt
strblast -new_string "GOOD" "BAD STRING" infile.txt
Notes and Warnings:
* strblast will modify the input files irreversibly!
You might want to test if they are still usable.
* strblast reads files into memory to operate on them.
If the file is too big to fit in memory, strblast
will fail.
* strblast will do internal wildcard expansion, so
if there are too many input files for your shell to
handle, you can do something like
strblast 'Subject Name' 'I.*'
and strblast will expand the 'I.*' wildcard for you.
This page auto-generated on Thu Aug 25 16:49:42 EDT 2005
|
| suma |
Usage:
Mode 1: Using a spec file to specify surfaces
suma -spec <SPEC file>
[-sv <SURFVOL>] [-ah AfniHost]
-spec <SPEC file>: File containing surface specification.
This file is typically generated by
@SUMA_Make_Spec_FS (for FreeSurfer surfaces) or
@SUMA_Make_Spec_SF (for SureFit surfaces).
The Spec file should be located in the directory
containing the surfaces.
[-sv <SURFVOL>]: Anatomical volume used in creating the surface
and registerd to the current experiment's anatomical
volume (using @SUMA_AlignToExperiment).
This parameter is optional, but linking to AFNI is
not possible without it.If you find the need for it
(as some have), you can specify the SurfVol in the
specfile. You can do so by adding the field
SurfaceVolume to each surface in the spec file.
In this manner, you can have different surfaces using
different surface volumes.
[-ah <AFNIHOST>]: Name (or IP address) of the computer running AFNI. This
parameter is optional, the default is localhost.
When both AFNI and SUMA are on the same computer,
communication is through shared memory. You can turn that
off by explicitly setting AfniHost to 127.0.0.1
[-niml]: Start listening for NIML-formatted elements.
[-dev]: Allow access to options that are not well polished for consuption.
Mode 2: Using -t_TYPE or -t* options to specify surfaces on command line.
-sv, -ah, -niml and -dev are still applicable here. This mode
is meant to simplify the quick viewing of a surface model.
suma [-i_TYPE surface] [-t* surface]
Surfaces specified on command line are place in a group
called 'DefGroup'.
If you specify nothing on command line, you will have a random
surface created for you. Some of these surfaces are generated
using Thomas Lewiner's sample volumes for creating isosurfaces.
See suma -sources for a complete reference.
Specifying input surfaces using -i_TYPE options:
-i_TYPE inSurf specifies the input surface,
TYPE is one of the following:
fs: FreeSurfer surface.
If surface name has .asc it is assumed to be
in ASCII format. Otherwise it is assumed to be
in BINARY_BE (Big Endian) format.
Patches in Binary format cannot be read at the moment.
sf: SureFit surface.
You must specify the .coord followed by the .topo file.
vec (or 1D): Simple ascii matrix format.
You must specify the coord (NodeList) file followed by
the topo (FaceSetList) file.
coord contains 3 floats per line, representing
X Y Z vertex coordinates.
topo contains 3 ints per line, representing
v1 v2 v3 triangle vertices.
ply: PLY format, ascii or binary.
Only vertex and triangulation info is preserved.
bv: BrainVoyager format.
Only vertex and triangulation info is preserved.
dx: OpenDX ascii mesh format.
Only vertex and triangulation info is preserved.
Requires presence of 3 objects, the one of class
'field' should contain 2 components 'positions'
and 'connections' that point to the two objects
containing node coordinates and topology, respectively.
Specifying surfaces using -t* options:
-tn TYPE NAME: specify surface type and name.
See below for help on the parameters.
-tsn TYPE STATE NAME: specify surface type state and name.
TYPE: Choose from the following (case sensitive):
1D: 1D format
FS: FreeSurfer ascii format
PLY: ply format
SF: Caret/SureFit format
BV: BrainVoyager format
NAME: Name of surface file.
For SF and 1D formats, NAME is composed of two names
the coord file followed by the topo file
STATE: State of the surface.
Default is S1, S2.... for each surface.
Modes 1 & 2: You can mix the two modes for loading surfaces but the -sv
option may not be properly applied.
If you mix these modes, you will have two groups of
surfaces loaded into SUMA. You can switch between them
using the 'Switch Group' button in the viewer controller.
Common Debugging Options:
[-trace]: Turns on In/Out debug and Memory tracing.
For speeding up the tracing log, I recommend
you redirect stdout to a file when using this option.
For example, if you were running suma you would use:
suma -spec lh.spec -sv ... > TraceFile
This option replaces the old -iodbg and -memdbg.
[-TRACE]: Turns on extreme tracing.
[-nomall]: Turn off memory tracing.
[-yesmall]: Turn on memory tracing (default).
[-novolreg]: Ignore any Volreg or Tagalign transformations
present in the Surface Volume.
NOTE: For programs that output results to stdout
(that is to your shell/screen), the debugging info
might get mixed up with your results.
[-visuals] Shows the available glxvisuals and exits.
[-version] Shows the current version number.
[-latest_news] Shows the latest news for the current
version of the entire SUMA package.
[-all_latest_news] Shows the history of latest news.
[-progs] Lists all the programs in the SUMA package.
[-sources] Lists code sources used in parts of SUMA.
For help on interacting with SUMA, press 'ctrl+h' with the mouse
pointer inside SUMA's window.
For more help: http://afni.nimh.nih.gov/ssc/ziad/SUMA/SUMA_doc.htm
If you can't get help here, please get help somewhere.
++ SUMA version 2004_12_29
New Programs:
+ SurfClust: Program to find clusters of activation
on the surface.
+ IsoSurface: Program to create isosurfaces from AFNI volumes.
+ ConvexHull: Program to create the convex hull of a set of
points.
+ 3dSkullStrip: Program to remove the skull from anatomical
volumes.
+ 3dCRUISEtoAFNI: Program to convert CRUISE volumes to AFNI
+ 3dBRAIN_VOYAGERtoAFNI: Program to convert BrainVoyager .vmr
volumes to AFNI
+ SurfMesh: Program to increase or decrease a mesh's density.
+ SurfMask: Program to find the volume enclosed by a surface.
+ SurfToSurf: Program to interpolate between non-isotopic surfaces.
Modifications:
+ SUMA:
o Slight modification to threshold scale.
o Added environment variable SUMA_ThresholdScalePower.
o Fixed a few kinks in the surface controller.
o Fixed ROI drawing trace on OSX.
o Added geodesic distance measurements in ROI drawing
controller.
o Suma can read surfaces specified on command line.
o Fixed bug reading AFNI generated niml files.
o Useful axis displayed with F2 key.
o Fixed bug with recursive function used to fill ROIs.
o Support for reading CRUISE surfaces in OpenDX format
o Support for reading BrainVoyager surfaces (.srf) format
o Mouse motion effect is modulated with Zoom level
o F8 toggles between orthographic and perspective viewing
+ ConvertSurface:
o Option -make_consistent added to make the winding
of the mesh consistent.
+ SurfQual:
o Checks and warns about mesh's winding inconsistency.
+ SurfSmooth:
o Added NN_geom, nearest neighbor interpolation option.
o Combined with -match_vol or -match_area, this geometry
smoothing mode can be used to inflate surfaces.
+ SurfaceMetrics:
o Option -vol calculates the volume of the closed surface.
+ SurfPatch:
o Option -vol to calculate the volume between two isotopic
surface patches.
+ ROI2dataset:
o Option -pad_to_node and -pad_label to output datasets
containing full node listings.
+ ConvertDset:
o Option -o_1dp was added to write 1D file data only,
without additional comments.
CVS tag:
SUMA_2005_04_29_1733
Compile Date:
Aug 25 2005
Ziad S. Saad SSCC/NIMH/NIH ziad@nih.gov
This page auto-generated on Thu Aug 25 16:49:42 EDT 2005
|
|
@SUMA_Align ToExperiment |
Usage: @SUMA_AlignToExperiment <EXPERIMENT Anatomy> <SURFACE Anatomy>
[dxyz] [-wd] [-prefix PREFIX] [-EA_clip_below CLP]
creates a version of Surface Anatomy that is registered to Experiment Anatomy.
Mandatory parameters:
<EXPERIMENT Anatomy>: Name of high resolution anatomical data set in register
with experimental data.
<SURFACE Anatomy> Path and Name of high resolution antomical data set used to
create the surface.
Optional parameters:
[DXYZ|-dxyz DXYZ]: This optional parameter indicates that the anatomical
volumes must be downsampled to dxyz mm voxel resolution before
registration. That is only necessary if 3dvolreg runs out of memory.
You MUST have 3dvolreg that comes with afni distributions newer than
version 2.45l. It contains an option for reducing memory usage and
thus allow the registration of large data sets.
[-wd]: Use 3dWarpDrive's general affine transform (12 param) instead of
3dvolreg's 6 parameters.
If the anatomical coverage differs markedly between 'Experiment
Anatomy' and 'Surface Anatomy', you might need to use -EA_clip_below
option or you could end up with a very distorted brain.
[-EA_clip_below CLP]: Set slices below CLPmm in 'Experiment Anatomy' to zero.
Use this if the coverage of 'Experiment Anatomy' dataset
extends far below the data in 'Surface Anatomy' dataset.
To get the value of CLP, use AFNI to locate the slice
below which you want to clip and set CLP to the z coordinate
from AFNI's top left corner. Coordinate must be in RAI, DICOM.
[-prefix PREFIX]: Use PREFIX for the output volume. Default is the prefix
of the 'Surface Anatomy' suffixed by _AlndExp.
NOTE: You must run the script from the directory where Experiment Anatomy resides.
Example 1: For datasets with no relative distortion and comparable coverage.
Using 6 param. rigid body transform.
@SUMA_AlignToExperiment DemoSubj_spgrsa+orig. \
../FreeSurfer/SUMA/DemoSubj_SurfVol+orig.
Example 2: For datasets with some distortion and different coverage.
Using 12 param. transform and clipping of areas below cerebellum:
@SUMA_AlignToExperiment ABanat+orig. DemoSubj_SurfVol+orig. \
-wd -prefix DemoSubj_SurfVol_WD_AlndExp \
-EA_clip_below -30
More help may be found at http://afni.nimh.nih.gov/ssc/ziad/SUMA/SUMA_doc.htm
Ziad Saad (ziad@nih.gov)
SSCC/NIMH/ National Institutes of Health, Bethesda Maryland
This page auto-generated on Thu Aug 25 16:49:42 EDT 2005
|
| suma_change_spec |
Unknown option: help suma_change_spec: This program changes SUMA's surface specification (Spec) files. At minimum, the flags input and state are required. Available flags: input: Which is the SUMA Spec file you want to change. state: The state within the Spec file you want to change. domainparent: The new Domain Parent for the state within the Spec file you want to change. output: The name to which your new Spec file will be temporarily written to. (this flag is optional, if omitted the new Spec file will be temporarily written to 'input_file.change'). remove: This flag will remove the automatically created backup. anatomical: This will add 'Anatomical = Y' to the selected SurfaceState. Usage: This program will take the user given flags and create a spec file, named from the output flag or <INPUT>.change. It will then take this new spec file and overwrite the original input file. If the -remove flag is not used the original input file can be found at <INPUTFILE>.bkp. If the -remove is used the .bkp file will be automatically deleted. ex. suma_change_spec -input <FILE> -state <STATENAME> -domainparent <NEW_PARENT> -anatomicalThis page auto-generated on Thu Aug 25 16:49:43 EDT 2005 |
| @SUMA_Make_Spec_FS |
@SUMA_Make_Spec_FS - prepare for surface viewing in SUMA
This script goes through the following steps:
- verify existence of necessary programs
(afni, to3d, suma, mris_convert)
- determine the location of surface and COR files
- creation of ascii surface files via 'mris_convert'
- creation of left and right hemisphere SUMA spec files
- creation of an AFNI dataset from the COR files via 'to3d'
- all created files are stored in a new SUMA directory
Usage: @SUMA_Make_Spec_FS [options] -sid SUBJECT_ID
examples:
@SUMA_Make_Spec_FS -sid subject1
@SUMA_Make_Spec_FS -help
@SUMA_Make_Spec_FS -fspath subject1/surface_stuff -sid subject1
@SUMA_Make_Spec_FS -neuro -sid 3.14159265 -debug 1
options:
-help : show this help information
-debug LEVEL : print debug information along the way
e.g. -debug 1
the default level is 0, max is 2
-fspath PATH : path to 'surf' and 'orig' directories
e.g. -fspath subject1/surface_info
the default PATH value is './', the current directory
This is generally the location of the 'surf' directory,
though having PATH end in surf is OK. The mri/orig
directory should also be located here.
Note: when this option is provided, all file/path
messages will be with respect to this directory.
-neuro : use neurological orientation
e.g. -neuro
the default is radiological orientation
In the default radiological orientation, the subject's
right is on the left side of the image. In the
neurological orientation, left is really left.
-sid SUBJECT_ID : required subject ID for file naming
notes:
0. More help may be found at http://afni.nimh.nih.gov/ssc/ziad/SUMA/SUMA_doc.htm
1. Surface file names should look like 'lh.smoothwm'.
2. Patches of surfaces need the word patch in their name, in
order to use the correct option for 'mris_convert'.
3. Flat surfaces must have .flat in their name.
4. You can tailor the script to your needs. Just make sure you rename it or risk
having your modifications overwritten with the next SUMA version you install.
R. Reynolds (rickr@codon.nih.gov), Z. Saad (ziad@nih.gov)
This page auto-generated on Thu Aug 25 16:49:43 EDT 2005
|
| @SUMA_Make_Spec_SF |
@SUMA_Make_Spec_SF - prepare for surface viewing in SUMA
This script goes through the following steps:
- determine the location of surfaces and
then AFNI volume data sets used to create them.
- creation of left and right hemisphere SUMA spec files
- all created files are stored in SURFACES directory
Usage: @SUMA_Make_Spec_SF [options] -sid SUBJECT_ID
examples:
@SUMA_Make_Spec_SF -sid subject1
@SUMA_Make_Spec_SF -help
@SUMA_Make_Spec_SF -sfpath subject1/surface_stuff -sid subject1
options:
-help : show this help information
-debug LEVEL : print debug information along the way
e.g. -debug 1
the default level is 0, max is 2
-sfpath PATH : path to directory containing 'SURFACES'
and AFNI volume used in creating the surfaces.
e.g. -sfpath subject1/surface_models
the default PATH value is './', the current directory
This is generally the location of the 'SURFACES' directory,
though having PATH end in SURFACES is OK.
Note: when this option is provided, all file/path
messages will be with respect to this directory.
-sid SUBJECT_ID : required subject ID for file naming
notes:
0. More help may be found at http://afni.nimh.nih.gov/ssc/ziad/SUMA/SUMA_doc.htm
1. Surface file names should look like the standard names used by SureFit:
rw_1mmLPI.L.full.segment_vent_corr.fiducial.58064.coord
Otherwise the script cannot detect them. You will need to decide which
surface is the most recent (the best) and the script helps you by listing
the available surfaces with the most recent one first.
This sorting ususally works except when the time stamps on the surface files
are messed up. In such a case you just need to know which one to use.
Once the fiducial surface is chosen, it's complimentary surfaces are selected
using the node number in the file name.
3. You can tailor the script to your needs. Just make sure you rename it or risk
having your modifications overwritten with the next SUMA version you install.
R. Reynolds (rickr@codon.nih.gov), Z. Saad (ziad@nih.gov)
This page auto-generated on Thu Aug 25 16:49:43 EDT 2005
|
| SurfaceMetrics |
Error Main_SUMA_SurfaceMetrics (SUMA_Load_Surface_Object.c:3246):
Too few parameters
Usage: SurfaceMetrics <-Metric1> [[-Metric2] ...]
<-spec SpecFile> <-surf_A insurf>
[<-sv SurfaceVolume [VolParam for sf surfaces]>]
[-tlrc] [<-prefix prefix>]
Outputs information about a surface's mesh
-Metric1: Replace -Metric1 with the following:
-vol: calculates the volume of a surface.
Volume unit is the cube of your surface's
coordinates unit, obviously.
Volume's sign depends on the orientation
of the surface's mesh.
Make sure your surface is a closed one
and that winding is consistent.
Use SurfQual to check the surface.
If your surface's mesh has problems,
the result is incorrect.
Volume is calculated using Gauss's theorem,
see [Hughes, S.W. et al. 'Application of a new
discreet form of Gauss's theorem for measuring
volume' in Phys. Med. Biol. 1996].
-conv: output surface convexity at each node.
Output file is prefix.conv. Results in two columns:
Col.0: Node Index
Col.1: Convexity
This is the measure used to shade sulci and gyri in SUMA.
C[i] = Sum(dj/dij) over all neighbors j of i
dj is the distance of neighboring node j to the tangent plane at i
dij is the length of the segment ij
-area: output area of each triangle.
Output file is prefix.area. Results in two columns:
Col.0: Triangle Index
Col.1: Triangle Area
-curv: output curvature at each node.
Output file is prefix.curv. Results in nine columns:
Col.0: Node Index
Col.1-3: vector of 1st principal direction of surface
Col.4-6: vector of 2nd principal direction of surface
Col.7: Curvature along T1
Col.8: Curvature along T2
Curvature algorithm by G. Taubin from:
'Estimating the tensor of curvature of surface
from a polyhedral approximation.'
-edges: outputs info on each edge.
Output file is prefix.edges. Results in five columns:
Col.0: Edge Index (into a SUMA structure).
Col.1: Index of the first node forming the edge
Col.2: Index of the second node forming the edge
Col.3: Number of triangles containing edge
Col.4: Length of edge.
-node_normals: Outputs segments along node normals.
Segments begin at node and have a default
magnitude of 1. See option 'Alt+Ctrl+s' in
SUMA for visualization.
-face_normals: Outputs segments along triangle normals.
Segments begin at centroid of triangles and
have a default magnitude of 1. See option
'Alt+Ctrl+s' in SUMA for visualization.
-normals_scale SCALE: Scale the normals by SCALE (1.0 default)
For use with options -node_normals and -face_normals
-coords: Output coords of each node after any transformation
that is normally carried out by SUMA on such a surface.
Col. 0: Node Index
Col. 1: X
Col. 2: Y
Col. 3: Z
-sph_coords: Output spherical coords of each node.
-sph_coords_center x y z: Shift each node by x y z
before calculating spherical
coordinates. Default is the
center of the surface.
Both sph_coords options output the following:
Col. 0: Node Index
Col. 1: R (radius)
Col. 2: T (azimuth)
Col. 3: P (elevation)
You can use any or all of these metrics simultaneously.
-spec SpecFile: Name of specfile containing surface of interest.
If the surface does not have a spec file, use the
program quickspec to create one.
-surf_A insurf: Name of surface of interest.
NOTE: i_TYPE inSurf option is now obsolete.
-sv SurfaceVolume [VolParam for sf surfaces]: Specify a surface volume
for surface alignment. See ConvertSurface -help for more info.
-tlrc: Apply Talairach transform to surface.
See ConvertSurface -help for more info.
-prefix prefix: Use prefix for output files. (default is prefix of inSurf)
Common Debugging Options:
[-trace]: Turns on In/Out debug and Memory tracing.
For speeding up the tracing log, I recommend
you redirect stdout to a file when using this option.
For example, if you were running suma you would use:
suma -spec lh.spec -sv ... > TraceFile
This option replaces the old -iodbg and -memdbg.
[-TRACE]: Turns on extreme tracing.
[-nomall]: Turn off memory tracing.
[-yesmall]: Turn on memory tracing (default).
[-novolreg]: Ignore any Volreg or Tagalign transformations
present in the Surface Volume.
NOTE: For programs that output results to stdout
(that is to your shell/screen), the debugging info
might get mixed up with your results.
++ SUMA version 2004_12_29
CVS tag:
SUMA_2005_04_29_1733
Compile Date:
Aug 25 2005
Ziad S. Saad SSCC/NIMH/NIH ziad@nih.gov
Mon May 19 15:41:12 EDT 2003
This page auto-generated on Thu Aug 25 16:49:43 EDT 2005
|
| SurfClust |
Usage: A program to perform clustering analysis surfaces.
SurfClust <-spec SpecFile>
<-surf_A insurf>
<-input inData.1D dcol_index>
<-rmm rad>
[-amm2 minarea]
[-prefix OUTPREF]
[-out_clusterdset] [-out_roidset]
[-out_fulllist]
[-sort_none | -sort_n_nodes | -sort_area]
The program can outputs a table of the clusters on the surface,
a mask dataset formed by the different clusters and a clustered
version of the input dataset.
Mandatory parameters:
-spec SpecFile: The surface spec file.
-surf_A insurf: The input surface name.
-input inData.1D dcol_index: The input 1D dataset
and the index of the
datacolumn to use
(index 0 for 1st column).
Values of 0 indicate
inactive nodes.
-rmm rad: Maximum distance between an activated node
and the cluster to which it belongs.
Distance is measured on the surface's graph (mesh).
Optional Parameters:
-thresh_col tcolind: Index of thresholding column.
Default is column 0.
-thresh tval: Apply thresholding prior to clustering.
A node n is considered if thresh_col[n] > tval.
-athresh tval: Apply absolute thresholding prior to clustering.
A node n is considered if | thresh_col[n] | > tval.
-amm2 minarea: Do not output resutls for clusters having
an area less than minarea.
-prefix OUTPREF: Prefix for output.
Default is the prefix of
the input dataset.
If this option is used, the
cluster table is written to a file called
OUTPREF_ClstTable_rXX_aXX.1D. Otherwise the
table is written to stdout.
-out_clusterdset: Output a clustered version of inData.1D
preserving only the values of nodes that
belong to clusters that passed the rmm and amm2
conditions above.
The clustered dset's prefix has
_Clustered_rXX_aXX affixed to the OUTPREF
-out_roidset: Output an ROI dataset with the value
at each node being the rank of its
cluster. The ROI dataset's prefix has
_ClstMsk_rXX_aXX affixed to the OUTPREF
where XX represent the values for the
the -rmm and -amm2 options respectively.
The program will not overwrite pre-existing
dsets.
-out_fulllist: Output a value for all nodes of insurf.
This option must be used in conjuction with
-out_roidset and/or out_clusterdset.
With this option, the output files might
be mostly 0, if you have small clusters.
However, you should use it if you are to
maintain the same row-to-node correspondence
across multiple datasets.
-sort_none: No sorting of ROI clusters.
-sort_n_nodes: Sorting based on number of nodes
in cluster.
-sort_area: Sorting based on area of clusters
(default).
-update perc: Pacify me when perc of the data have been
processed. perc is between 1% and 50%.
Default is no update.
-no_cent: Do not find the central nodes.
Finding the central node is a
relatively slow operation. Use
this option to skip it.
The cluster table output:
A table where ach row shows results from one cluster.
Each row contains 13 columns:
Col. 0 Rank of cluster (sorting order).
Col. 1 Number of nodes in cluster.
Col. 2 Total area of cluster. Units are the
the surface coordinates' units^2.
Col. 3 Mean data value in cluster.
Col. 4 Mean of absolute data value in cluster.
Col. 5 Central node of cluster (see below).
Col. 6 Weighted central node (see below).
Col. 7 Minimum value in cluster.
Col. 8 Node where minimum value occurred.
Col. 9 Maximum value in cluster.
Col. 10 Node where maximum value occurred.
Col. 11 Variance of values in cluster.
Col. 12 Standard error of the mean ( sqrt(variance / number of nodes) ).
The CenterNode n is such that:
( sum (Uia * dia * wi) ) - ( Uca * dca * sum (wi) ) is minimal
where i is a node in the cluster
a is an anchor node on the surface
sum is carried over all nodes i in a cluster
w. is the weight of a node
= 1.0 for central node
= value at node for the weighted central node
U.. is the unit vector between two nodes
d.. is the distance between two nodes on the graph
(an approximation of the geodesic distance)
If -no_cent is used, CenterNode columns are set to 0.
Common Debugging Options:
[-trace]: Turns on In/Out debug and Memory tracing.
For speeding up the tracing log, I recommend
you redirect stdout to a file when using this option.
For example, if you were running suma you would use:
suma -spec lh.spec -sv ... > TraceFile
This option replaces the old -iodbg and -memdbg.
[-TRACE]: Turns on extreme tracing.
[-nomall]: Turn off memory tracing.
[-yesmall]: Turn on memory tracing (default).
[-novolreg]: Ignore any Volreg or Tagalign transformations
present in the Surface Volume.
NOTE: For programs that output results to stdout
(that is to your shell/screen), the debugging info
might get mixed up with your results.
++ SUMA version 2004_12_29
CVS tag:
SUMA_2005_04_29_1733
Compile Date:
Aug 25 2005
Ziad S. Saad SSCC/NIMH/NIH ziad@nih.gov
This page auto-generated on Thu Aug 25 16:49:43 EDT 2005
|
| SurfMeasures |
SurfMeasures - compute measures from the surface dataset(s)
usage: SurfMeasures [options] -spec SPEC_FILE -out_1D OUTFILE.1D
This program is meant to read in a surface or surface pair,
and to output and user-requested measures over the surfaces.
The surfaces must be specified in the SPEC_FILE.
** Use the 'inspec' command for getting information about the
surfaces in a spec file.
The output will be a 1D format text file, with one column
(or possibly 3) per user-specified measure function. Some
functions require only 1 surface, some require 2.
Current functions (applied with '-func') include:
ang_norms : angular difference between normals
ang_ns_A : angular diff between segment and first norm
ang_ns_B : angular diff between segment and second norm
coord_A : xyz coordinates of node on first surface
coord_B : xyz coordinates of node on second surface
n_area_A : associated node area on first surface
n_area_B : associated node area on second surface
n_avearea_A : for each node, average area of triangles (surf A)
n_avearea_B : for each node, average area of triangles (surf B)
n_ntri : for each node, number of associated triangles
node_vol : associated node volume between surfaces
nodes : node number
norm_A : vector of normal at node on first surface
norm_B : vector of normal at node on second surface
thick : distance between surfaces along segment
------------------------------------------------------------
examples:
1. For each node on the surface smoothwm in the spec file,
fred.spec, output the node number (the default action),
the xyz coordinates, and the area associated with the
node (1/3 of the total area of triangles having that node
as a vertex).
SurfMeasures \
-spec fred1.spec \
-sv fred_anat+orig \
-surf_A smoothwm \
-func coord_A \
-func n_area_A \
-out_1D fred1_areas.1D
2. For each node of the surface pair smoothwm and pial,
display the:
o node index
o node's area from the first surface
o node's area from the second surface
o node's (approximate) resulting volume
o thickness at that node (segment distance)
o coordinates of the first segment node
o coordinates of the second segment node
Additionally, display total surface areas, minimum and
maximum thicknesses, and the total volume for the
cortical ribbon (the sum of node volumes).
SurfMeasures \
-spec fred2.spec \
-sv fred_anat+orig \
-surf_A smoothwm \
-surf_B pial \
-func n_area_A \
-func n_area_B \
-func node_vol \
-func thick \
-func coord_A \
-func coord_B \
-info_area \
-info_thick \
-info_vol \
-out_1D fred2_vol.1D
3. For each node of the surface pair, display the:
o node index
o angular diff between the first and second norms
o angular diff between the segment and first norm
o angular diff between the segment and second norm
o the normal vectors for the first surface nodes
o the normal vectors for the second surface nodes
o angular diff between the segment and second norm
SurfMeasures \
-spec fred2.spec \
-surf_A smoothwm \
-surf_B pial \
-func ang_norms \
-func ang_ns_A \
-func ang_ns_B \
-func norm_A \
-func norm_B \
-out_1D fred2_norm_angles.1D
4. Similar to #3, but output extra debug info, and in
particular, info regarding node 5000.
SurfMeasures \
-spec fred2.spec \
-sv fred_anat+orig \
-surf_A smoothwm \
-surf_B pial \
-func ang_norms \
-func ang_ns_A \
-func ang_ns_B \
-debug 2 \
-dnode 5000 \
-out_1D fred2_norm_angles.1D
5. For each node, output the volume, thickness and areas,
but restrict the nodes to the list contained in column 0
of file sdata.1D. Furthermore, restrict those nodes to
the mask inferred by the given '-cmask' option.
SurfMeasures \
-spec fred2.spec \
-sv fred_anat+orig \
-surf_A smoothwm \
-surf_B pial \
-func node_vol \
-func thick \
-func n_area_A \
-func n_area_B \
-nodes_1D 'sdata.1D[0]' \
-cmask '-a sdata.1D[2] -expr step(a-1000)' \
-out_1D fred2_masked.1D
------------------------------------------------------------
REQUIRED COMMAND ARGUMENTS:
-spec SPEC_FILE : SUMA spec file
e.g. -spec fred2.spec
The surface specification file contains a list of
related surfaces. In order for a surface to be
processed by this program, it must exist in the spec
file.
-surf_A SURF_NAME : surface name (in spec file)
-surf_B SURF_NAME : surface name (in spec file)
e.g. -surf_A smoothwm
e.g. -surf_A lh.smoothwm
e.g. -surf_B lh.pial
This is used to specify which surface(s) will be used
by the program. The 'A' and 'B' correspond to other
program options (e.g. the 'A' in n_area_A).
The '-surf_B' parameter is required only when the user
wishes to input two surfaces.
Any surface name provided must be unique in the spec
file, and must match the name of the surface data file
(e.g. lh.smoothwm.asc).
-out_1D OUT_FILE.1D : 1D output filename
e.g. -out_1D pickle_norm_info.1D
This option is used to specify the name of the output
file. The output file will be in the 1D ascii format,
with 2 rows of comments for column headers, and 1 row
for each node index.
There will be 1 or 3 columns per '-func' option, with
a default of 1 for "nodes".
------------------------------------------------------------
ALPHABETICAL LISTING OF OPTIONS:
-cmask COMMAND : restrict nodes with a mask
e.g. -cmask '-a sdata.1D[2] -expr step(a-1000)'
This option will produce a mask to be applied to the
list of surface nodes. The total mask size, including
zero entries, must match the number of nodes. If a
specific node list is provided via the '-nodes_1D'
option, then the mask size should match the length of
the provided node list.
Consider the provided example using the file sdata.1D.
If a surface has 100000 nodes (and no '-nodes_1D' option
is used), then there must be 100000 values in column 2
of the file sdata.1D.
Alternately, if the '-nodes_1D' option is used, giving
a list of 42 nodes, then the mask length should also be
42 (regardless of 0 entries).
See '-nodes_1D' for more information.
-debug LEVEL : display extra run-time info
e.g. -debug 2
default: -debug 0
Valid debug levels are from 0 to 5.
-dnode NODE : display extra info for node NODE
e.g. -dnode 5000
This option can be used to display extra information
about node NODE during surface evaluation.
-func FUNCTION : request output for FUNCTION
e.g. -func thick
This option is used to request output for the given
FUNCTION (measure). Some measures produce one column
of output (e.g. thick or ang_norms), and some produce
three (e.g. coord_A). These options, in the order they
are given, determine the structure of the output file.
Current functions include:
ang_norms : angular difference between normals
ang_ns_A : angular diff between segment and first norm
ang_ns_B : angular diff between segment and second norm
coord_A : xyz coordinates of node on first surface
coord_B : xyz coordinates of node on second surface
n_area_A : associated node area on first surface
n_area_B : associated node area on second surface
n_avearea_A : for each node, average area of triangles (surf A)
n_avearea_B : for each node, average area of triangles (surf B)
n_ntri : for each node, number of associated triangles
node_vol : associated node volume between surfaces
nodes : node number
norm_A : vector of normal at node on first surface
norm_B : vector of normal at node on second surface
thick : distance between surfaces along segment
Note that the node volumes are approximations. Places
where either normal points in the 'wrong' direction
will be incorrect, as will be the parts of the surface
that 'encompass' this region. Maybe we could refer
to this as a mushroom effect...
Basically, expect the total volume to be around 10%
too large.
** for more accuracy, try 'SurfPatch -vol' **
-help : show this help menu
-hist : display program revision history
This option is used to provide a history of changes
to the program, along with version numbers.
NOTE: the following '-info_XXXX' options are used to display
pieces of 'aggregate' information about the surface(s).
-info_all : display all final info
This is a short-cut to get all '-info_XXXX' options.
-info_area : display info on surface area(s)
Display the total area of each triangulated surface.
-info_norms : display info about the normals
For 1 or 2 surfaces, this will give (if possible) the
average angular difference between:
o the normals of the surfaces
o the connecting segment and the first normal
o the connecting segment and the second normal
-info_thick : display min and max thickness
For 2 surfaces, this is used to display the minimum and
maximum distances between the surfaces, along each of
the connecting segments.
-info_vol : display info about the volume
For 2 surfaces, display the total computed volume.
Note that this node-wise volume computation is an
approximation, and tends to run ~10 % high.
** for more accuracy, try 'SurfPatch -vol' **
-nodes_1D NODELIST.1D : request output for only these nodes
e.g. -nodes_1D node_index_list.1D
e.g. -nodes_1D sdata.1D'[0]'
The NODELIST file should contain a list of node indices.
Output from the program would then be restricted to the
nodes in the list.
For instance, suppose that the file BA_04.1D contains
a list of surface nodes that are located in Broadman's
Area 4. To get output from the nodes in that area, use:
-nodes_1D BA_04.1D
For another example, suppose that the file sdata.1D has
node indices in column 0, and Broadman's Area indices in
column 3. To restrict output to the nodes in Broadman's
area 4, use the pair of options:
-nodes_1D 'sdata.1D[0]' \
-cmask '-a sdata.1D[3] -expr (1-bool(a-4))'
-sv SURF_VOLUME : specify an associated AFNI volume
e.g. -sv fred_anat+orig
If there is any need to know the orientation of the
surface, a surface volume dataset may be provided.
-ver : show version information
Show version and compile date.
------------------------------------------------------------
Author: R. Reynolds - version 1.11 (October 6, 2004)
This page auto-generated on Thu Aug 25 16:49:43 EDT 2005
|
| SurfMesh |
Usage:
SurfMesh <-i_TYPE SURFACE> <-o_TYPE OUTPUT> <-edges FRAC>
[-sv SURF_VOL]
Example:
SurfMesh -i_ply surf1.ply -o_ply surf1_half -edges 0.5
Mandatory parameters:
-i_TYPE SURFACE: Input surface. See below for details.
You can also use the -t* method or
the -spec SPECFILE -surf SURFACE method.
-o_TYPE OUTPUT: Output surface, see below.
-edges FRAC: surface will be simplified to number of
edges times FRAC (fraction). Default is .5
refines surface if edges > 1
Specifying input surfaces using -i_TYPE options:
-i_TYPE inSurf specifies the input surface,
TYPE is one of the following:
fs: FreeSurfer surface.
If surface name has .asc it is assumed to be
in ASCII format. Otherwise it is assumed to be
in BINARY_BE (Big Endian) format.
Patches in Binary format cannot be read at the moment.
sf: SureFit surface.
You must specify the .coord followed by the .topo file.
vec (or 1D): Simple ascii matrix format.
You must specify the coord (NodeList) file followed by
the topo (FaceSetList) file.
coord contains 3 floats per line, representing
X Y Z vertex coordinates.
topo contains 3 ints per line, representing
v1 v2 v3 triangle vertices.
ply: PLY format, ascii or binary.
Only vertex and triangulation info is preserved.
bv: BrainVoyager format.
Only vertex and triangulation info is preserved.
dx: OpenDX ascii mesh format.
Only vertex and triangulation info is preserved.
Requires presence of 3 objects, the one of class
'field' should contain 2 components 'positions'
and 'connections' that point to the two objects
containing node coordinates and topology, respectively.
Specifying surfaces using -t* options:
-tn TYPE NAME: specify surface type and name.
See below for help on the parameters.
-tsn TYPE STATE NAME: specify surface type state and name.
TYPE: Choose from the following (case sensitive):
1D: 1D format
FS: FreeSurfer ascii format
PLY: ply format
SF: Caret/SureFit format
BV: BrainVoyager format
NAME: Name of surface file.
For SF and 1D formats, NAME is composed of two names
the coord file followed by the topo file
STATE: State of the surface.
Default is S1, S2.... for each surface.
Specifying a Surface Volume:
-sv SurfaceVolume [VolParam for sf surfaces]
If you supply a surface volume, the coordinates of the input surface.
are modified to SUMA's convention and aligned with SurfaceVolume.
You must also specify a VolParam file for SureFit surfaces.
Specifying a surface specification (spec) file:
-spec SPEC: specify the name of the SPEC file.
Specifying a surface using -surf_? method:
-surf_A SURFACE: specify the name of the first
surface to load. If the program requires
or allows multiple surfaces, use -surf_B
... -surf_Z .
You need not use _A if only one surface is
expected.
SURFACE is the name of the surface as specified
in the SPEC file. The use of -surf_ option
requires the use of -spec option.
Specifying output surfaces using -o_TYPE options:
-o_TYPE outSurf specifies the output surface,
TYPE is one of the following:
fs: FreeSurfer ascii surface.
fsp: FeeSurfer ascii patch surface.
In addition to outSurf, you need to specify
the name of the parent surface for the patch.
using the -ipar_TYPE option.
This option is only for ConvertSurface
sf: SureFit surface.
For most programs, you are expected to specify prefix:
i.e. -o_sf brain. In some programs, you are allowed to
specify both .coord and .topo file names:
i.e. -o_sf XYZ.coord TRI.topo
The program will determine your choice by examining
the first character of the second parameter following
-o_sf. If that character is a '-' then you have supplied
a prefix and the program will generate the coord and topo names.
vec (or 1D): Simple ascii matrix format.
For most programs, you are expected to specify prefix:
i.e. -o_1D brain. In some programs, you are allowed to
specify both coord and topo file names:
i.e. -o_1D brain.1D.coord brain.1D.topo
coord contains 3 floats per line, representing
X Y Z vertex coordinates.
topo contains 3 ints per line, representing
v1 v2 v3 triangle vertices.
ply: PLY format, ascii or binary.
Common Debugging Options:
[-trace]: Turns on In/Out debug and Memory tracing.
For speeding up the tracing log, I recommend
you redirect stdout to a file when using this option.
For example, if you were running suma you would use:
suma -spec lh.spec -sv ... > TraceFile
This option replaces the old -iodbg and -memdbg.
[-TRACE]: Turns on extreme tracing.
[-nomall]: Turn off memory tracing.
[-yesmall]: Turn on memory tracing (default).
[-novolreg]: Ignore any Volreg or Tagalign transformations
present in the Surface Volume.
NOTE: For programs that output results to stdout
(that is to your shell/screen), the debugging info
might get mixed up with your results.
++ SUMA version 2004_12_29
CVS tag:
SUMA_2005_04_29_1733
Compile Date:
Aug 25 2005
Originally written by Jakub Otwinowski.
Now maintained by Ziad S. Saad SSCC/NIMH/NIH ziad@nih.gov
This program uses the GTS library gts.sf.net
for fun read "Fast and memory efficient polygonal simplification" (1998)
and "Evaluation of memoryless simplification" (1999) by Lindstrom and Turk.
This page auto-generated on Thu Aug 25 16:49:43 EDT 2005
|
| SurfPatch |
Usage:
SurfPatch <-spec SpecFile> <-surf_A insurf> <-surf_B insurf> ...
<-input nodefile inode ilabel> <-prefix outpref>
[-hits min_hits] [-masklabel msk] [-vol]
Usage 1:
The program creates a patch of surface formed by nodes
in nodefile.
Mandatory parameters:
-spec SpecFile: Spec file containing input surfaces.
-surf_X: Name of input surface X where X is a character
from A to Z. If surfaces are specified using two
files, use the name of the node coordinate file.
-input nodefile inode ilabel:
nodefile is the file containing nodes defining the patch.
inode is the index of the column containing the nodes
ilabel is the index of the column containing labels of
the nodes in column inode. If you want to use
all the nodes in column indode, then set this
parameter to -1 (default).
If ilabel is not equal to 0 then the corresponding
node is used in creating the patch.
See -masklabel option for one more variant.
-prefix outpref: Prefix of output patch. If more than one surface
are entered, then the prefix will have _X added
to it, where X is a character from A to Z.
Output format depends on the input surface's.
With that setting, checking on pre-existing files
is only done before writing the new patch, which is
annoying. You can set the output type ahead of time
using -out_type option. This way checking for pre-existing
output files can be done at the outset.
Optional parameters:
-out_type TYPE: Type of all output patches, regardless of input surface type.
Choose from: FreeSurfer, SureFit, 1D and Ply.
-hits min_hits: Minimum number of nodes specified for a triangle
to be made a part of the patch (1 <= min_hits <= 3)
default is 2.
-masklabel msk: If specified, then only nodes that are labeled with
with msk are considered for the patch.
This option is useful if you have an ROI dataset file
and whish to create a patch from one out of many ROIs
in that file. This option must be used with ilabel
specified (not = -1)
Usage 2:
The program can also be used to calculate the volume between the same patch
on two isotopic surfaces. See -vol option below.
-vol: Calculate the volume formed by the patch on surf_A and
and surf_B. For this option, you must specify two and
only two surfaces with surf_A and surf_B options.
-vol_only: Only calculate the volume, don't write out patches.
Common Debugging Options:
[-trace]: Turns on In/Out debug and Memory tracing.
For speeding up the tracing log, I recommend
you redirect stdout to a file when using this option.
For example, if you were running suma you would use:
suma -spec lh.spec -sv ... > TraceFile
This option replaces the old -iodbg and -memdbg.
[-TRACE]: Turns on extreme tracing.
[-nomall]: Turn off memory tracing.
[-yesmall]: Turn on memory tracing (default).
[-novolreg]: Ignore any Volreg or Tagalign transformations
present in the Surface Volume.
NOTE: For programs that output results to stdout
(that is to your shell/screen), the debugging info
might get mixed up with your results.
++ SUMA version 2004_12_29
CVS tag:
SUMA_2005_04_29_1733
Compile Date:
Aug 25 2005
Ziad S. Saad SSCC/NIMH/NIH ziad@nih.gov
This page auto-generated on Thu Aug 25 16:49:43 EDT 2005
|
| SurfQual |
Usage: A program to check the quality of surfaces.
SurfQual <-spec SpecFile> <-surf_A insurf> <-surf_B insurf> ...
<-sphere> [-self_intersect] [-prefix OUTPREF]
Mandatory parameters:
-spec SpecFile: Spec file containing input surfaces.
-surf_X: Name of input surface X where X is a character
from A to Z. If surfaces are specified using two
files, use the name of the node coordinate file.
Mesh winding consistency and 2-manifold checks are performed
on all surfaces.
Optional parameters:
-self_intersect: Check if surface is self intersecting.
This option is rather slow, so be patient.
In the presence of intersections, the output file
OUTPREF_IntersNodes.1D.dset will contain the indices
of nodes forming segments that intersect the surface.
Most other checks are specific to spherical surfaces (see option below).
-sphere: Indicates that surfaces read are spherical.
With this option you get the following output.
- Absolute deviation between the distance (d) of each
node from the surface's center and the estimated
radius(r). The distances, abs (d - r), are
and written to the file OUTPREF_Dist.1D.dset .
The first column represents node index and the
second is the absolute distance. A colorized
version of the distances is written to the file
OUTPREF_Dist.1D.col (node index followed
by r g b values). A list of the 10 largest absolute
distances is also output to the screen.
- Also computed is the cosine of the angle between
the normal at a node and the direction vector formed
formed by the center and that node. Since both vectors
are normalized, the cosine of the angle is the dot product.
On a sphere, the abs(dot product) should be 1 or pretty
close. Nodes where abs(dot product) < 0.9 are flagged as
bad and written out to the file OUTPREF_BadNodes.1D.dset .
The file OUTPREF_dotprod.1D.dset contains the dot product
values for all the nodes. The files with colorized results
are OUTPREF_BadNodes.1D.col and OUTPREF_dotprod.1D.col .
A list of the bad nodes is also output to the screen for
convenience. You can use the 'j' option in SUMA to have
the cross-hair go to a particular node. Use 'Alt+l' to
have the surface rotate and place the cross-hair at the
center of your screen.
NOTE: For detecting topological problems with spherical
surfaces, I find the dot product method to work best.
Optional parameters:
-prefix OUTPREF: Prefix of output files. If more than one surface
are entered, then the prefix will have _X added
to it, where X is a character from A to Z.
THIS PROGRAM WILL OVERWRITE EXISTING FILES.
Default prefix is the surface's label.
Comments:
- The colorized (.col) files can be loaded into SUMA (with the 'c'
option. By focusing on the bright spots, you can find trouble spots
which would otherwise be very difficult to locate.
- You should also pay attention to the messages output when the
surfaces are being loaded, particularly to edges (segments that
join 2 nodes) are shared by more than 2 triangles. For a proper
closed surface, every segment should be shared by 2 triangles.
For cut surfaces, segments belonging to 1 triangle only form
the edge of that surface.
- There are no utilities within SUMA to correct these defects.
It is best to fix these problems with the surface creation
software you are using.
- Some warnings may be redundant. That should not hurt you.
Common Debugging Options:
[-trace]: Turns on In/Out debug and Memory tracing.
For speeding up the tracing log, I recommend
you redirect stdout to a file when using this option.
For example, if you were running suma you would use:
suma -spec lh.spec -sv ... > TraceFile
This option replaces the old -iodbg and -memdbg.
[-TRACE]: Turns on extreme tracing.
[-nomall]: Turn off memory tracing.
[-yesmall]: Turn on memory tracing (default).
[-novolreg]: Ignore any Volreg or Tagalign transformations
present in the Surface Volume.
NOTE: For programs that output results to stdout
(that is to your shell/screen), the debugging info
might get mixed up with your results.
++ SUMA version 2004_12_29
CVS tag:
SUMA_2005_04_29_1733
Compile Date:
Aug 25 2005
Ziad S. Saad SSCC/NIMH/NIH ziad@nih.gov
This page auto-generated on Thu Aug 25 16:49:43 EDT 2005
|
| SurfSmooth |
Usage: SurfSmooth <-spec SpecFile> <-surf_A insurf> <-met method>
Some methods require additional options detailed below.
I recommend using the -talk_suma option to watch the
progression of the smoothing in real-time in suma.
Method specific options:
LB_FEM: <-input inData.1D> <-fwhm f>
This method is used to filter data
on the surface.
LM: [-kpb k] [-lm l m] [-surf_out surfname]
This method is used to filter the surface's
geometry (node coordinates).
NN_geom: smooth by averaging coordinates of
nearest neighbors.
This method causes shrinkage of surface
and is meant for test purposes only.
Common options:
[-Niter N] [-output out.1D] [-h/-help]
[-add_index] [-ni_text|-ni_binary] [-talk_suma]
Detailed usage:
-spec SpecFile: Name of specfile containing surface of interest.
If the surface does not have a spec file, use the
program quickspec to create one.
-surf_A insurf: Name of surface of interest.
NOTE: i_TYPE inSurf option is now obsolete.
-met method: name of smoothing method to use. Choose from:
LB_FEM: The method by Chung et al. 03.
This method is used for filtering
data on the surface not for smoothing the
surface's geometry per se. See References below.
LM: The smoothing method proposed by G. Taubin 2000
This method is used for smoothing
a surface's geometry. See References below.
NN_geom: A simple nearest neighbor coordinate smoothing.
This interpolation method causes surface shrinkage
that might need to be corrected with the -match_*
options below.
Options for LB_FEM:
-input inData.1D: file containing data (in 1D format)
Each column in inData.1D is processed separately.
The number of rows must equal the number of
nodes in the surface. You can select certain
columns using the [] notation adopted by AFNI's
programs.
-fwhm f: Full Width at Half Maximum in surface coordinate units (usuallly mm)
of an equivalent Gaussian filter had the surface been flat.
With curved surfaces, the equation used to estimate FWHM is
an approximation.
Blurring on the surface depends on the geodesic instead
of the Euclidean disntaces. See Ref #1 for more details
on this parameter.
Options for LM:
-kpb k: Band pass frequency (default is 0.1).
values should be in the range 0 < k < 10
-lm and -kpb options are mutually exclusive.
-lm l m: Lambda and Mu parameters. Sample values are:
0.6307 and -.6732
NOTE: -lm and -kpb options are mutually exclusive.
-surf_out surfname: Writes the surface with smoothed coordinates
to disk. For SureFit and 1D formats, only the
coord file is written out.
NOTE: -surf_out and -output are mutually exclusive.
Options for NN_geom:
-match_size r: Adjust node coordinates of smoothed surface to
approximates the original's size.
Node i on the filtered surface is repositioned such
that |c i| = 1/N sum(|cr j|) where
c and cr are the centers of the smoothed and original
surfaces, respectively.
N is the number of nodes that are within r [surface
coordinate units] along the surface (geodesic) from node i.
j is one of the nodes neighboring i.
-match_vol tol: Adjust node coordinates of smoothed surface to
approximates the original's volume.
Nodes on the filtered surface are repositioned such
that the volume of the filtered surface equals,
within tolerance tol, that of the original surface.
See option -vol in SurfaceMetrics for information about
and calculation of the volume of a closed surface.
-match_area tol: Adjust node coordinates of smoothed surface to
approximates the original's surface.
Nodes on the filtered surface are repositioned such
that the surface of the filtered surface equals,
within tolerance tol, that of the original surface.
-match_sphere rad: Project nodes of smoothed surface to a sphere
of radius rad. Projection is carried out along the
direction formed by the surface's center and the node.
Common options:
-Niter N: Number of smoothing iterations (default is 100)
For practical reasons, this number must be a multiple of 2
NOTE: For LB_FEM method, the number of iterations controls the
iteration steps (dt in Ref #1).
dt = fwhm*fwhm / (16*Niter*log(2));
dt must satisfy conditions that depend on the internodal
distance and the spatial derivatives of the signals being
filtered on the surface.
As a rule of thumb, if increasing Niter does not alter
the results then your choice is fine (smoothing has converged).
For an example of the artifact caused by small Niter see:
http://afni.nimh.nih.gov/sscc/staff/ziad/SUMA/SuSmArt/DSart.html
-output out.1D: Name of output file.
The default is inData_sm.1D with LB_FEM method
and NodeList_sm.1D with LM method.
-add_index : Output the node index in the first column.
This is not done by default.
SUMA communication options:
-talk_suma: Send progress with each iteration to SUMA.
-refresh_rate rps: Maximum number of updates to SUMA per second.
The default is the maximum speed.
-send_kth kth: Send the kth element to SUMA (default is 1).
This allows you to cut down on the number of elements
being sent to SUMA.
-sh <SUMAHOST>: Name (or IP address) of the computer running SUMA.
This parameter is optional, the default is 127.0.0.1
-ni_text: Use NI_TEXT_MODE for data transmission.
-ni_binary: Use NI_BINARY_MODE for data transmission.
(default is ni_binary).
-feed_afni: Send updates to AFNI via SUMA's talk.
Common Debugging Options:
[-trace]: Turns on In/Out debug and Memory tracing.
For speeding up the tracing log, I recommend
you redirect stdout to a file when using this option.
For example, if you were running suma you would use:
suma -spec lh.spec -sv ... > TraceFile
This option replaces the old -iodbg and -memdbg.
[-TRACE]: Turns on extreme tracing.
[-nomall]: Turn off memory tracing.
[-yesmall]: Turn on memory tracing (default).
[-novolreg]: Ignore any Volreg or Tagalign transformations
present in the Surface Volume.
NOTE: For programs that output results to stdout
(that is to your shell/screen), the debugging info
might get mixed up with your results.
Sample commands lines for data smoothing:
SurfSmooth -spec quick.spec -surf_A NodeList.1D -met LB_FEM \
-input in.1D -Niter 100 -fwhm 8 -add_index \
-output in_sm8.1D
This command filters (on the surface) the data in in.1D
and puts the output in in_sm8.1D with the first column
containing the node index and the second containing the
filtered version of in.1D.
The surface used in this example had no spec file, so
a quick.spec was created using:
quickspec -tn 1D NodeList.1D FaceSetList.1D
You can colorize the input and output data using ScaleToMap:
ScaleToMap -input in.1D 0 1 -cmap BGYR19 \
-clp MIN MAX > in.1D.col \
ScaleToMap -input in_sm8.1D 0 1 -cmap BGYR19 \
-clp MIN MAX > in_sm8.1D.col \
For help on using ScaleToMap see ScaleToMap -help
Note that the MIN MAX represent the minimum and maximum
values in in.1D. You should keep them constant in both
commands in order to be able to compare the resultant colorfiles.
You can import the .col files with the 'c' command in SUMA.
You can send the data to SUMA with each iteration.
To do so, start SUMA with these options:
suma -spec quick.spec -niml &
and add these options to SurfSmooth's command line above:
-talk_suma -refresh_rate 5
Sample commands lines for surface smoothing:
SurfSmooth -spec quick.spec -surf_A NodeList.1D -met LM \
-output NodeList_sm100.1D -Niter 100 -kpb 0.1
This command smoothes the surface's geometry. The smoothed
node coordinates are written out to NodeList_sm100.1D.
Sample command for considerable surface smoothing and inflation
back to original volume:
SurfSmooth -spec quick.spec -surf_A NodeList.1D -met NN_geom \
-output NodeList_inflated_mvol.1D -Niter 1500 \
-match_vol 0.01
Sample command for considerable surface smoothing and inflation
back to original area:
SurfSmooth -spec quick.spec -surf_A NodeList.1D -met NN_geom \
-output NodeList_inflated_marea.1D -Niter 1500 \
-match_area 0.01
References:
(1) M.K. Chung et al. Deformation-based surface morphometry
applied to gray matter deformation.
Neuroimage 18 (2003) 198-213
M.K. Chung Statistical morphometry in computational
neuroanatomy. Ph.D. thesis, McGill Univ.,
Montreal, Canada
(2) G. Taubin. Mesh Signal Processing.
Eurographics 2000.
See Also:
ScaleToMap to colorize the output, however it is better
to load surface datasets directly into SUMA and colorize
them interactively.
++ SUMA version 2004_12_29
CVS tag:
SUMA_2005_04_29_1733
Compile Date:
Aug 25 2005
Ziad S. Saad SSCC/NIMH/NIH ziad@nih.gov
This page auto-generated on Thu Aug 25 16:49:43 EDT 2005
|
| SurfToSurf |
Usage: SurfToSurf <-i_TYPE S1> [<-sv SV1>]
<-i_TYPE S2> [<-sv SV1>]
[<-prefix PREFIX>]
[<-output_params PARAM_LIST>]
[<-node_indices NODE_INDICES>]
[<-proj_dir PROJ_DIR>]
[<-data DATA>]
[<-node_debug NODE>]
[<-debug DBG_LEVEL>]
[-make_consistent]
This program is used to interpolate data from one surface (S2)
to another (S1), assuming the surfaces are quite similar in
shape but having different meshes (non-isotopic).
This is done by projecting each node (nj) of S1 along the normal
at nj and finding the closest triangle t of S2 that is intersected
by this projection. Projection is actually bidirectional.
If such a triangle t is found, the nodes (of S2) forming it are
considered to be the neighbors of nj.
Values (arbitrary data, or coordinates) at these neighboring nodes
are then transfered to nj using barycentric interpolation or
nearest-node interpolation.
Nodes whose projections fail to intersect triangles in S2 are given
nonsensical values of -1 and 0.0 in the output.
Mandatory input:
Two surfaces are required at input. See -i_TYPE options
below for more information.
Optional input:
-prefix PREFIX: Specify the prefix of the output file.
The output file is in 1D format at the moment.
Default is SurfToSurf
-output_params PARAM_LIST: Specify the list of mapping
parameters to include in output
PARAM_LIST can have any or all of the following:
NearestTriangleNodes: Use Barycentric interpolation (default)
and output indices of 3 nodes from S2
that neighbor nj of S1
NearestNode: Use only the closest node from S2 (of the three
closest neighbors) to nj of S1 for interpolation
and output the index of that closest node.
NearestTriangle: Output index of triangle t from S2 that
is the closest to nj along its projection
direction.
DistanceToSurf: Output distance (signed) from nj, along
projection direction to S2.
This is the parameter output by the precursor
program CompareSurfaces
ProjectionOnSurf: Output coordinates of projection of nj onto
triangle t of S2.
Data: Output the data from S2, interpolated onto S1
If no data is specified via the -data option, then
the XYZ coordinates of SO2's nodes are considered
the data.
-data DATA: 1D file containing data to be interpolated.
Each row i contains data for node i of S2.
You must have one row for each node making up S2.
In other terms, if S2 has N nodes, you need N rows
in DATA.
Each column of DATA is processed separately (think
sub-bricks, and spatial interpolation).
You can use [] selectors to choose a subset
of columns.
If -data option is not specified and Data is in PARAM_LIST
then the XYZ coordinates of SO2's nodes are the data.
-node_indices NODE_INDICES: 1D file containing the indices of S1
to consider. The default is all of the
nodes in S1. Only one column of values is
allowed here, use [] selectors to choose
the column of node indices if NODE_INDICES
has multiple columns in it.
-proj_dir PROJ_DIR: 1D file containing projection directions to use
instead of the node normals of S1.
Each row should contain one direction for each
of the nodes forming S1.
-make_consistent: Force a consistency check and correct triangle
orientation of S1 if needed. Triangles are also
oriented such that the majority of normals point
away from center of surface.
The program might not succeed in repairing some
meshes with inconsistent orientation.
Specifying input surfaces using -i_TYPE options:
-i_TYPE inSurf specifies the input surface,
TYPE is one of the following:
fs: FreeSurfer surface.
If surface name has .asc it is assumed to be
in ASCII format. Otherwise it is assumed to be
in BINARY_BE (Big Endian) format.
Patches in Binary format cannot be read at the moment.
sf: SureFit surface.
You must specify the .coord followed by the .topo file.
vec (or 1D): Simple ascii matrix format.
You must specify the coord (NodeList) file followed by
the topo (FaceSetList) file.
coord contains 3 floats per line, representing
X Y Z vertex coordinates.
topo contains 3 ints per line, representing
v1 v2 v3 triangle vertices.
ply: PLY format, ascii or binary.
Only vertex and triangulation info is preserved.
bv: BrainVoyager format.
Only vertex and triangulation info is preserved.
dx: OpenDX ascii mesh format.
Only vertex and triangulation info is preserved.
Requires presence of 3 objects, the one of class
'field' should contain 2 components 'positions'
and 'connections' that point to the two objects
containing node coordinates and topology, respectively.
Specifying surfaces using -t* options:
-tn TYPE NAME: specify surface type and name.
See below for help on the parameters.
-tsn TYPE STATE NAME: specify surface type state and name.
TYPE: Choose from the following (case sensitive):
1D: 1D format
FS: FreeSurfer ascii format
PLY: ply format
SF: Caret/SureFit format
BV: BrainVoyager format
NAME: Name of surface file.
For SF and 1D formats, NAME is composed of two names
the coord file followed by the topo file
STATE: State of the surface.
Default is S1, S2.... for each surface.
Specifying a Surface Volume:
-sv SurfaceVolume [VolParam for sf surfaces]
If you supply a surface volume, the coordinates of the input surface.
are modified to SUMA's convention and aligned with SurfaceVolume.
You must also specify a VolParam file for SureFit surfaces.
Specifying a surface specification (spec) file:
-spec SPEC: specify the name of the SPEC file.
Specifying a surface using -surf_? method:
-surf_A SURFACE: specify the name of the first
surface to load. If the program requires
or allows multiple surfaces, use -surf_B
... -surf_Z .
You need not use _A if only one surface is
expected.
SURFACE is the name of the surface as specified
in the SPEC file. The use of -surf_ option
requires the use of -spec option.
Specifying output surfaces using -o_TYPE options:
-o_TYPE outSurf specifies the output surface,
TYPE is one of the following:
fs: FreeSurfer ascii surface.
fsp: FeeSurfer ascii patch surface.
In addition to outSurf, you need to specify
the name of the parent surface for the patch.
using the -ipar_TYPE option.
This option is only for ConvertSurface
sf: SureFit surface.
For most programs, you are expected to specify prefix:
i.e. -o_sf brain. In some programs, you are allowed to
specify both .coord and .topo file names:
i.e. -o_sf XYZ.coord TRI.topo
The program will determine your choice by examining
the first character of the second parameter following
-o_sf. If that character is a '-' then you have supplied
a prefix and the program will generate the coord and topo names.
vec (or 1D): Simple ascii matrix format.
For most programs, you are expected to specify prefix:
i.e. -o_1D brain. In some programs, you are allowed to
specify both coord and topo file names:
i.e. -o_1D brain.1D.coord brain.1D.topo
coord contains 3 floats per line, representing
X Y Z vertex coordinates.
topo contains 3 ints per line, representing
v1 v2 v3 triangle vertices.
ply: PLY format, ascii or binary.
Common Debugging Options:
[-trace]: Turns on In/Out debug and Memory tracing.
For speeding up the tracing log, I recommend
you redirect stdout to a file when using this option.
For example, if you were running suma you would use:
suma -spec lh.spec -sv ... > TraceFile
This option replaces the old -iodbg and -memdbg.
[-TRACE]: Turns on extreme tracing.
[-nomall]: Turn off memory tracing.
[-yesmall]: Turn on memory tracing (default).
[-novolreg]: Ignore any Volreg or Tagalign transformations
present in the Surface Volume.
NOTE: For programs that output results to stdout
(that is to your shell/screen), the debugging info
might get mixed up with your results.
++ SUMA version 2004_12_29
CVS tag:
SUMA_2005_04_29_1733
Compile Date:
Aug 25 2005
Ziad S. Saad SSCC/NIMH/NIH ziad@nih.gov
Shruti Japee LBC/NIMH/NIH shruti@codon.nih.gov
This page auto-generated on Thu Aug 25 16:49:43 EDT 2005
|
| tfim |
MCW TFIM: t-tests on sets of functional images, by RW Cox
Usage 1: tfim [options] -set1 image_files ... -set2 image_files ...
Usage 2: tfim [options] -base1 bval -set2 image_files ...
In usage 1, the collection of images files after '-set1' and the
collection after '-set2' are averaged and differenced, and the
difference is tested for significance with a 2 sample Student t-test.
In usage 2, the collection of image files after '-set2' is averaged
and then has the constant numerical value 'bval' subtracted, and the
difference is tested for significance with a 1 sample Student t-test.
N.B.: The input images can be in the usual 'short' or 'byte'
formats, or in the floating point 'flim' format.
N.B.: If in either set of images, a given pixel has zero variance
(i.e., is constant), then the t-test is not performed.
In that pixel, the .tspm file will be zero.
Options are:
-prefix pname: 'pname' is used as the prefix for the output
filenames. The output image files are
+ pname.diff = average of set2 minus average of set1
(or minus 'bval')
+ pname.tspm = t-statistic of difference
Output images are in the 'flim' (floating pt. image)
format, and may be converted to 16 bit shorts using
the program 'ftosh'.
*** The default 'pname' is 'tfim', if -prefix isn't used.
-pthresh pval: 'pval' is a numeric value between 0 and 1, giving
the significance level (per voxel) to threshold the
output with; voxels with (2-sided) t-statistic
less significant than 'pval' will have their diff
output zeroed.
*** The default is no threshold, if -pthresh isn't used.
-eqcorr dval: If present, this option means to write out the file
pname.corr = equivalent correlation statistic
= t/sqrt(dof+t^2)
The number 'dval' is the value to use for 'dof' if
dval is positive. This would typically be the total
number of data images used in forming the image sets,
if the image sets are from sfim or fim.
If dval is zero, then dof is computed from the number
of images in -set1 and -set2; if these are averages
from program sfim, then dof will be smallish, which in
turn means that significant corr values will be higher
than you may be used to from using program fim.
*** The default is not to write, if -eqcorr isn't used.
-paired: If present, this means that -set1 and -set2 should be
compared using a paired sample t-test. This option is
illegal with the -base1 option. The number of samples
in the two sets of images must be equal.
[This test is implemented by subtracting -set1 images
from the -set2 images, then testing as in '-base1 0'.]
*** The default is to do an unpaired test, if -paired isn't
used. In that case, -set1 and -set2 don't need to have
the same number of images.
This page auto-generated on Thu Aug 25 16:49:43 EDT 2005
|
| to3d |
to3d: 2D slices into 3D datasets for AFNI, by RW Cox
Usage: to3d [options] image_files ...
Creates 3D datasets for use with AFNI from 2D image files
The available options are
-help show this message
-'type' declare images to contain data of a given type
where 'type' is chosen from the following options:
ANATOMICAL TYPES
spgr == Spoiled GRASS
fse == Fast Spin Echo
epan == Echo Planar
anat == MRI Anatomy
ct == CT Scan
spct == SPECT Anatomy
pet == PET Anatomy
mra == MR Angiography
bmap == B-field Map
diff == Diffusion Map
omri == Other MRI
abuc == Anat Bucket
FUNCTIONAL TYPES
fim == Intensity
fith == Inten+Thr
fico == Inten+Cor
fitt == Inten+Ttest
fift == Inten+Ftest
fizt == Inten+Ztest
fict == Inten+ChiSq
fibt == Inten+Beta
fibn == Inten+Binom
figt == Inten+Gamma
fipt == Inten+Poisson
fbuc == Func-Bucket
[for paired (+) types above, images are fim first,]
[then followed by the threshold (etc.) image files]
-statpar value value ... value [* NEW IN 1996 *]
This option is used to supply the auxiliary statistical parameters
needed for certain dataset types (e.g., 'fico' and 'fitt'). For
example, a correlation coefficient computed using program 'fim2'
from 64 images, with 1 ideal, and with 2 orts could be specified with
-statpar 64 1 2
-prefix name will write 3D dataset using prefix 'name'
-session name will write 3D dataset into session directory 'name'
-geomparent fname will read geometry data from dataset file 'fname'
N.B.: geometry data does NOT include time-dependence
-anatparent fname will take anatomy parent from dataset file 'fname'
-nosave will suppress autosave of 3D dataset, which normally occurs
when the command line options supply all needed data correctly
-view type [* NEW IN 1996 *]
Will set the dataset's viewing coordinates to 'type', which
must be one of these strings: orig acpc tlrc
TIME DEPENDENT DATASETS [* NEW IN 1996 *]
-time:zt nz nt TR tpattern OR -time:tz nt nz TR tpattern
These options are used to specify a time dependent dataset.
'-time:zt' is used when the slices are input in the order
z-axis first, then t-axis.
'-time:tz' is used when the slices are input in the order
t-axis first, then z-axis.
nz = number of points in the z-direction (minimum 1)
nt = number of points in the t-direction
(thus exactly nt * nz slices must be read in)
TR = repetition interval between acquisitions of the
same slice, in milliseconds (or other units, as given below)
tpattern = Code word that identifies how the slices (z-direction)
were gathered in time. The values that can be used:
alt+z = altplus = alternating in the plus direction
alt+z2 = alternating, starting at slice #1
alt-z = altminus = alternating in the minus direction
alt-z2 = alternating, starting at slice #nz-2
seq+z = seqplus = sequential in the plus direction
seq-z = seqminus = sequential in the minus direction
zero = simult = simultaneous acquisition
@filename = read temporal offsets from 'filename'
For example if nz = 5 and TR = 1000, then the inter-slice
time is taken to be dt = TR/nz = 200. In this case, the
slices are offset in time by the following amounts:
S L I C E N U M B E R
tpattern 0 1 2 3 4 Comment
---------- ---- ---- ---- ---- ---- -------------------------------
altplus 0 600 200 800 400 Alternating in the +z direction
alt+z2 400 0 600 200 800 Alternating, but starting at #1
altminus 400 800 200 600 0 Alternating in the -z direction
alt-z2 800 200 600 0 400 Alternating, starting at #nz-2
seqplus 0 200 400 600 800 Sequential in the +z direction
seqminus 800 600 400 200 0 Sequential in the -z direction
simult 0 0 0 0 0 All slices acquired at once
If @filename is used for tpattern, then nz ASCII-formatted numbers are
read from the file. These are used to indicate the time offsets (in ms)
for each slice. For example, if 'filename' contains
0 600 200 800 400
then this is equivalent to 'altplus' in the above example.
Notes:
* Time-dependent functional datasets are not yet supported by
to3d or any other AFNI package software. For many users,
the proper dataset type for these datasets is '-epan'.
* Time-dependent datasets with more than one value per time point
(e.g., 'fith', 'fico', 'fitt') are also not allowed by to3d.
* If you use 'abut' to fill in gaps in the data and/or to
subdivide the data slices, you will have to use the @filename
form for tpattern, unless 'simult' or 'zero' is acceptable.
* At this time, the value of 'tpattern' is not actually used in
any AFNI program. The values are stored in the dataset
.HEAD files, and will be used in the future.
* The values set on the command line can't be altered interactively.
* The units of TR can be specified by the command line options below:
-t=ms or -t=msec --> milliseconds (the default)
-t=s or -t=sec --> seconds
-t=Hz or -t=Hertz --> Hertz (for chemical shift images?)
Alternatively, the units symbol ('ms', 'msec', 's', 'sec',
'Hz', or 'Hertz') may be attached to TR in the '-time:' option,
as in '-time:zt 16 64 4.0sec alt+z'
****** 15 Aug 2005 ******
* Millisecond time units are no longer stored in AFNI dataset
header files. For backwards compatibility, the default unit
of TR (i.e., without a suffix 's') is still milliseconds, but
this value will be converted to seconds when the dataset is
written to disk. Any old AFNI datasets that have millisecond
units for TR will be read in to all AFNI programs with the TR
converted to seconds.
-Torg ttt = set time origin of dataset to 'ttt' [default=0.0]
COMMAND LINE GEOMETRY SPECIFICATION [* NEW IN 1996 *]
-xFOV <DIMEN1><DIREC1>-<DIMEN2><DIREC2>
or or
-xSLAB <DIMEN1><DIREC1>-<DIREC2>
(Similar -yFOV, -ySLAB, -zFOV and -zSLAB option are also present.)
These options specify the size and orientation of the x-axis extent
of the dataset. <DIMEN#> means a dimension (in mm); <DIREC> is
an anatomical direction code, chosen from
A (Anterior) P (Posterior) L (Left)
I (Inferior) S (Superior) R (Right)
Thus, 20A-30P means that the x-axis of the input images runs from
20 mm Anterior to 30 mm Posterior. For convenience, 20A-20P can be
abbreviated as 20A-P.
-xFOV is used to mean that the distances are from edge-to-edge of
the outermost voxels in the x-direction.
-xSLAB is used to mean that the distances are from center-to-center
of the outermost voxels in the x-direction.
Under most circumstance, -xFOV , -yFOV , and -zSLAB would be the
correct combination of geometry specifiers to use. For example,
a common type of run at MCW would be entered as
-xFOV 120L-R -yFOV 120A-P -zSLAB 60S-50I
Z-AXIS SLICE OFFSET ONLY
-zorigin distz Puts the center of the 1st slice off at the
given distance ('distz' in mm). This distance
is in the direction given by the corresponding
letter in the -orient code. For example,
-orient RAI -zorigin 30
would set the center of the first slice at
30 mm Inferior.
N.B.: This option has no effect if the FOV or SLAB options
described above are used.
INPUT IMAGE FORMATS [* SIGNIFICANTLY CHANGED IN 1996 *]
Image files may be single images of unsigned bytes or signed shorts
(64x64, 128x128, 256x256, 512x512, or 1024x1024) or may be grouped
images (that is, 3- or 4-dimensional blocks of data).
In the grouped case, the string for the command line file spec is like
3D:hglobal:himage:nx:ny:nz:fname [16 bit input]
3Ds:hglobal:himage:nx:ny:nz:fname [16 bit input, swapped bytes]
3Db:hglobal:himage:nx:ny:nz:fname [ 8 bit input]
3Di:hglobal:himage:nx:ny:nz:fname [32 bit input]
3Df:hglobal:himage:nx:ny:nz:fname [floating point input]
3Dc:hglobal:himage:nx:ny:nz:fname [complex input]
3Dd:hglobal:himage:nx:ny:nz:fname [double input]
where '3D:' or '3Ds': signals this is a 3D input file of signed shorts
'3Db:' signals this is a 3D input file of unsigned bytes
'3Di:' signals this is a 3D input file of signed ints
'3Df:' signals this is a 3D input file of floats
'3Dc:' signals this is a 3D input file of complex numbers
(real and imaginary pairs of floats)
'3Dd:' signals this is a 3D input file of double numbers
(will be converted to floats)
hglobal = number of bytes to skip at start of whole file
himage = number of bytes to skip at start of each 2D image
nx = x dimension of each 2D image in the file
ny = y dimension of each 2D image in the file
nz = number of 2D images in the file
fname = actual filename on disk to read
* The ':' separators are required. The k-th image starts at
BYTE offset hglobal+(k+1)*himage+vs*k*nx*ny in file 'fname'
for k=0,1,...,nz-1.
* Here, vs=voxel length=1 for bytes, 2 for shorts, 4 for ints and floats,
and 8 for complex numbers.
* As a special case, hglobal = -1 means read data starting at
offset len-nz*(vs*nx*ny+himage), where len=file size in bytes.
(That is, to read the needed data from the END of the file.)
* Note that there is no provision for skips between data rows inside
a 2D slice, only for skips between 2D slice images.
* The int, float, and complex formats presume that the data in
the image file are in the 'native' format for this CPU; that is,
there is no provision for data conversion (unlike the 3Ds: format).
* Double input will be converted to floats (or whatever -datum is)
since AFNI doesn't support double precision datasets.
* Whether the 2D image data is interpreted as a 3D block or a 3D+time
block depends on the rest of the command line parameters. The
various 3D: input formats are just ways of inputting multiple 2D
slices from a single file.
* SPECIAL CASE: If fname is ALLZERO, then this means not to read
data from disk, but instead to create nz nx*ny images filled
with zeros. One application of this is to make it easy to create
a dataset of a specified geometry for use with other programs.
The 'raw pgm' image format is also supported; it reads data into 'byte' images.
* ANALYZE (TM) .hdr/.img files can now be read - give the .hdr filename on
the command line. The program will detect if byte-swapping is needed on
these images, and can also set the voxel grid sizes from the first .hdr file.
If the 'funused1' field in the .hdr is positive, it will be used to scale the
input values. If the environment variable AFNI_ANALYZE_FLOATIZE is YES, then
.img files will be converted to floats on input.
* Siemens .ima image files can now be read. The program will detect if
byte-swapping is needed on these images, and can also set voxel grid
sizes and orientations (correctly, I hope).
* Some Siemens .ima files seems to have their EPI slices stored in
spatial order, and some in acquisition (interleaved) order. This
program doesn't try to figure this out. You can use the command
line option '-sinter' to tell the program to assume that the images
in a single .ima file are interleaved; for example, if there are
7 images in a file, then without -sinter, the program will assume
their order is '0 1 2 3 4 5 6'; with -sinter, the program will
assume their order is '0 2 4 6 1 3 5' (here, the number refers
to the slice location in space).
* GEMS I.* (IMGF) 16-bit files can now be read. The program will detect
if byte-swapping is needed on these images, and can also set voxel
grid sizes and orientations. It can also detect the TR in the
image header. If you wish to rely on this TR, you can set TR=0
in the -time:zt or -time:tz option.
* If you use the image header's TR and also use @filename for the
tpattern, then the values in the tpattern file should be fractions
of the true TR; they will be multiplied by the true TR once it is
read from the image header.
NOTES:
* Not all AFNI programs support all datum types. Shorts and
floats are safest. (See the '-datum' option below.)
* If '-datum short' is used or implied, then int, float, and complex
data will be scaled to fit into a 16 bit integer. If the '-gsfac'
option below is NOT used, then each slice will be SEPARATELY
scaled according to the following choice:
(a) If the slice values all fall in the range -32767 .. 32767,
then no scaling is performed.
(b) Otherwise, the image values are scaled to lie in the range
0 .. 10000 (original slice min -> 0, original max -> 10000).
This latter option is almost surely not what you want! Therefore,
if you use the 3Di:, 3Df:, or 3Dc: input methods and store the
data as shorts, I suggest you supply a global scaling factor.
Similar remarks apply to '-datum byte' scaling, with even more force.
* To3d now incoporates POSIX filename 'globbing', which means that
you can input filenames using 'escaped wildcards', and then to3d
will internally do the expansion to the list of files. This is
only desirable because some systems limit the number of command-line
arguments to a program. It is possible that you would wish to input
more slice files than your computer supports. For example,
to3d exp.?.*
might overflow the system command line limitations. The way to do
this using internal globbing would be
to3d exp.\?.\*
where the \ characters indicate to pass the wildcards ? and *
through to the program, rather than expand them in the shell.
(a) Note that if you choose to use this feature, ALL wildcards in
a filename must be escaped with \ or NONE must be escaped.
(b) Using the C shell, it is possible to turn off shell globbing
by using the command 'set noglob' -- if you do this, then you
do not need to use the \ character to escape the wildcards.
(c) Internal globbing of 3D: file specifiers is supported in to3d.
For example, '3D:0:0:64:64:100:sl.\*' could be used to input
a series of 64x64x100 files with names 'sl.01', 'sl.02' ....
This type of expansion is specific to to3d; the shell will not
properly expand such 3D: file specifications.
(d) In the C shell (csh or tcsh), you can use forward single 'quotes'
to prevent shell expansion of the wildcards, as in the command
to3d '3D:0:0:64:64:100:sl.*'
The globbing code is adapted from software developed by the
University of California, Berkeley, and is copyrighted by the
Regents of the University of California (see file mcw_glob.c).
RGB datasets [Apr 2002]
-----------------------
You can now create RGB-valued datasets. Each voxel contains 3 byte values
ranging from 0..255. RGB values may be input to to3d in one of two ways:
* Using raw PPM formatted 2D image files.
* Using JPEG formatted 2D files.
* Using TIFF, BMP, GIF, PNG formatted 2D files [if netpbm is installed].
* Using the 3Dr: input format, analogous to 3Df:, etc., described above.
RGB datasets can be created as functional FIM datasets, or as anatomical
datasets:
* RGB fim overlays are transparent in AFNI only where all three
bytes are zero - that is, you can't overlay solid black.
* At present, there is limited support for RGB datasets.
About the only thing you can do is display them in 2D slice
viewers in AFNI.
You can also create RGB-valued datasets using program 3dThreetoRGB.
Other Data Options
------------------
-2swap
This option will force all input 2 byte images to be byte-swapped
after they are read in.
-4swap
This option will force all input 4 byte images to be byte-swapped
after they are read in.
-8swap
This option will force all input 8 byte images to be byte-swapped
after they are read in.
BUT PLEASE NOTE:
Input images that are auto-detected to need byte-swapping
(GEMS I.*, Siemens *.ima, ANALYZE *.img, and 3Ds: files)
will NOT be swapped again by one of the above options.
If you want to swap them again for some bizarre reason,
you'll have to use the 'Byte Swap' button on the GUI.
That is, -2swap/-4swap will swap bytes on input files only
if they haven't already been swapped by the image input
function.
-zpad N OR
-zpad Nmm
This option tells to3d to write 'N' slices of all zeros on each side
in the z-direction. This will make the dataset 'fatter', but make it
simpler to align with datasets from other scanning sessions. This same
function can be accomplished later using program 3dZeropad.
N.B.: The zero slices will NOT be visible in the image viewer in to3d, but
will be visible when you use AFNI to look at the dataset.
N.B.: If 'mm' follows the integer N, then the padding is measured in mm.
The actual number of slices of padding will be rounded up. So if
the slice thickness is 5 mm, then '-zpad 16mm' would be the equivalent
of '-zpad 4' -- that is, 4 slices on each z-face of the volume.
N.B.: If the geometry parent dataset was created with -zpad, the spatial
location (origin) of the slices is set using the geometry dataset's
origin BEFORE the padding slices were added. This is correct, since
you need to set the origin on the current dataset as if the padding
slices were not present.
N.B.: Unlike the '-zpad' option to 3drotate and 3dvolreg, this adds slices
only in the z-direction.
N.B.: You can set the environment variable 'AFNI_TO3D_ZPAD' to provide a
default for this option.
-gsfac value
will scale each input slice by 'value'. For example,
'-gsfac 0.31830989' will scale by 1/Pi (approximately).
This option only has meaning if one of '-datum short' or
'-datum byte' is used or implied. Otherwise, it is ignored.
-datum type
will set the voxel data to be stored as 'type', which is currently
allowed to be short, float, byte, or complex.
If -datum is not used, then the datum type of the first input image
will determine what is used. In that case, the first input image will
determine the type as follows:
byte --> byte
short --> short
int, float --> float
complex --> complex
If -datum IS specified, then all input images will be converted
to the desired type. Note that the list of allowed types may
grow in the future, so you should not rely on the automatic
conversion scheme. Also note that floating point datasets may
not be portable between CPU architectures.
-nofloatscan
tells to3d NOT to scan input float and complex data files for
illegal values - the default is to scan and replace illegal
floating point values with zeros (cf. program float_scan).
-in:1
Input of huge 3D: files (with all the data from a 3D+time run, say)
can cause to3d to fail from lack of memory. The reason is that
the images are from a file are all read into RAM at once, and then
are scaled, converted, etc., as needed, then put into the final
dataset brick. This switch will cause the images from a 3D: file
to be read and processed one slice at a time, which will lower the
amount of memory needed. The penalty is somewhat more I/O overhead.
NEW IN 1997:
-orient code
Tells the orientation of the 3D volumes. The code must be 3 letters,
one each from the pairs {R,L} {A,P} {I,S}. The first letter gives
the orientation of the x-axis, the second the orientation of the
y-axis, the third the z-axis:
R = right-to-left L = left-to-right
A = anterior-to-posterior P = posterior-to-anterior
I = inferior-to-superior S = superior-to-inferior
Note that the -xFOV, -zSLAB constructions can convey this information.
NEW IN 2001:
-skip_outliers
If present, this tells the program to skip the outlier check that is
automatically performed for 3D+time datasets. You can also turn this
feature off by setting the environment variable AFNI_TO3D_OUTLIERS
to "No".
-text_outliers
If present, tells the program to only print out the outlier check
results in text form, not graph them. You can make this the default
by setting the environment variable AFNI_TO3D_OUTLIERS to "Text".
N.B.: If to3d is run in batch mode, then no graph can be produced.
Thus, this option only has meaning when to3d is run with the
interactive graphical user interface.
-save_outliers fname
Tells the program to save the outliers count into a 1D file with
name 'fname'. You could graph this file later with the command
1dplot -one fname
If this option is used, the outlier count will be saved even if
nothing appears 'suspicious' (whatever that means).
NOTES on outliers:
* See '3dToutcount -help' for a description of how outliers are
defined.
* The outlier count is not done if the input images are shorts
and there is a significant (> 1%) number of negative inputs.
* There must be at least 6 time points for the outlier count to
be carried out.
OPTIONS THAT AFFECT THE X11 IMAGE DISPLAY
-gamma gg the gamma correction factor for the
monitor is 'gg' (default gg is 1.0; greater than
1.0 makes the image contrast larger -- this may
also be adjusted interactively)
-ncolors nn use 'nn' gray levels for the image
displays (default is 80)
-xtwarns turn on display of Xt warning messages
This page auto-generated on Thu Aug 25 16:49:43 EDT 2005
|
| @TTxform_anat |
A script to transform an antomical dataset
to match a template in TLRC space.
Usage: @TTxform_anat [options] <-base template> <-input anat>
Mandatory parameters:
-base template : Skull-stripped volume in TLRC space (+tlrc)
-input anat : Original (with skull) anatomical volume (+orig)
Optional parameters:
-no_ss : Do not stip skull of input data set
(because skull has already been removed
or because template still has the skull)
-keep_view : Do not mark output dataset as +tlrc
-pad_base MM : Pad the base dset by MM mm in each directions.
That is needed to make sure that datasets
requiring wild rotations do not get cropped
Default is MM = 30
-verb : Yakiti yak yak
Example:
@TTxform_anat -base N27_SurfVol_NoSkull+tlrc. -input DemoSubj_spgrsa+orig.
This page auto-generated on Thu Aug 25 16:49:43 EDT 2005
|
| @UpdateAfni |
\012Usage: @UpdateAfni Updates AFNI on your computer using wget \012If you are using the program for the first time, you must add some info about your computer into the script You can easily do so by modifying the template in the block SETDESTIN. \012IMPORTANT: Rename this script once you modify it. Otherwise, it will get overwritten whenever you update your AFNI distribution. \012Before the update begins, executables from the current version are copied into $localBIN.bak directory \012For more info, see: http://afni.nimh.nih.gov/~cox/afni_wget.html \012Ziad Saad (ziad@nih.gov)\012LBC/NIMH/ National Institutes of Health, Bethesda Maryland\012This page auto-generated on Thu Aug 25 16:49:44 EDT 2005 |
| Vecwarp |
Usage: Vecwarp [options]
Transforms (warps) a list of 3-vectors into another list of 3-vectors
according to the options. Error messages, warnings, and informational
messages are written to stderr. If a fatal error occurs, the program
exits with status 1; otherwise, it exits with status 0.
OPTIONS:
-apar aaa = Use the AFNI dataset 'aaa' as the source of the
transformation; this dataset must be in +acpc
or +tlrc coordinates, and must contain the
attributes WARP_TYPE and WARP_DATA which describe
the forward transformation from +orig coordinates
to the 'aaa' coordinate system.
N.B.: The +orig version of this dataset must also be
readable, since it is also needed when translating
vectors between SureFit and AFNI coordinates.
Only the .HEAD files are actually used.
-matvec mmm = Read an affine transformation matrix-vector from file
'mmm', which must be in the format
u11 u12 u13 v1
u21 u22 u23 v2
u31 u32 u33 v3
where each 'uij' and 'vi' is a number. The forward
transformation is defined as
[ xout ] [ u11 u12 u13 ] [ xin ] [ v1 ]
[ yout ] = [ u21 u22 u23 ] [ yin ] + [ v2 ]
[ zout ] [ u31 u32 u33 ] [ zin ] [ v3 ]
Exactly one of -apar or -matvec must be used to specify the
transformation.
-forward = -forward means to apply the forward transformation;
*OR* -backward means to apply the backward transformation
-backward * For example, if the transformation is specified by
'-apar fred+tlrc', then the forward transformation
is from +orig to +tlrc coordinates, and the backward
transformation is from +tlrc to +orig coordinates.
* If the transformation is specified by -matvec, then
the matrix-vector read in defines the forward
transform as above, and the backward transformation
is defined as the inverse.
* If neither -forward nor -backward is given, then
-forward is the default.
-input iii = Read input 3-vectors from file 'iii' (from stdin if
'iii' is '-' or the -input option is missing). Input
data may be in one of the following ASCII formats:
* SureFit .coord files:
BeginHeader
lines of text ...
EndHeader
count
int x y z
int x y z
et cetera...
In this case, everything up to and including the
count is simply passed through to the output. Each
(x,y,z) triple is transformed, and output with the
int label that precedes it. Lines that cannot be
scanned as 1 int and 3 floats are treated as comments
and are passed to through to the output unchanged.
N.B.: SureFit coordinates are
x = distance Right of Left-most dataset corner
y = distance Anterior to Posterior-most dataset corner
z = distance Superior to Inferior-most dataset corner
For example, if the transformation is specified by
-forward -apar fred+tlrc
then the input (x,y,z) are relative to fred+orig and the
output (x,y,z) are relative to fred+tlrc. If instead
-backward -apar fred+tlrc
is used, then the input (x,y,z) are relative to fred+tlrc
and the output (x,y,z) are relative to fred+orig.
For this to work properly, not only fred+tlrc must be
readable by Vecwarp, but fred+orig must be as well.
If the transformation is specified by -matvec, then
the matrix-vector transformation is applied to the
(x,y,z) vectors directly, with no coordinate shifting.
* AFNI .1D files with 3 columns
x y z
x y z
et cetera...
In this case, each (x,y,z) triple is transformed and
written to the output. Lines that cannot be scanned
as 3 floats are treated as comments and are passed
through to the output unchanged.
N.B.: AFNI (x,y,z) coordinates are in DICOM order:
-x = Right +x = Left
-y = Anterior +y = Posterior
-z = Inferior +z = Superior
-output ooo = Write the output to file 'ooo' (to stdout if 'ooo'
is '-', or if the -output option is missing). If the
file already exists, it will not be overwritten unless
the -force option is also used.
-force = If the output file already exists, -force can be
used to overwrite it. If you want to use -force,
it must come before -output on the command line.
EXAMPLES:
Vecwarp -apar fred+tlrc -input fred.orig.coord > fred.tlrc.coord
This transforms the vectors defined in original coordinates to
Talairach coordinates, using the transformation previously defined
by AFNI markers.
Vecwarp -apar fred+tlrc -input fred.tlrc.coord -backward > fred.test.coord
This does the reverse transformation; fred.test.coord should differ from
fred.orig.coord only by roundoff error.
Author: RWCox - October 2001
This page auto-generated on Thu Aug 25 16:49:44 EDT 2005
|
| waver |
Usage: waver [options] > output_filename
Creates an ideal waveform timeseries file.
The output goes to stdout, and normally would be redirected to a file.
Options: (# refers to a number; [xx] is the default value)
-WAV = Sets waveform to Cox special [default]
(cf. AFNI FAQ list for formulas)
-GAM = Sets waveform to form t^b * exp(-t/c)
(cf. Mark Cohen)
-EXPR "expression" = Sets waveform to the expression given,
which should depend on the variable 't'.
e.g.: -EXPR "step(t-2)*step(12-t)*(t-2)*(12-t)"
N.B.: The peak value of the expression on the '-dt' grid will
be scaled to the value given by '-peak'; if this is not
desired, set '-peak 0', and the 'natural' peak value of
the expression will be used.
-FILE dt wname = Sets waveform to the values read from the file
'wname', which should be a single column .1D file
(i.e., 1 ASCII number per line). The 'dt value
is the time step (in seconds) between lines
in 'wname'; the first value will be at t=0, the
second at t='dt', etc. Intermediate time values
will be linearly interpolated. Times past the
the end of the 'wname' file length will have
the waveform value set to zero.
*** N.B.: If the -peak option is used AFTER -FILE,
its value will be multiplied into the result.
These options set parameters for the -WAV waveform.
-delaytime # = Sets delay time to # seconds [2]
-risetime # = Sets rise time to # seconds [4]
-falltime # = Sets fall time to # seconds [6]
-undershoot # = Sets undershoot to # times the peak [0.2]
(this should be a nonnegative factor)
-restoretime # = Sets time to restore from undershoot [2]
These options set parameters for the -GAM waveform:
-gamb # = Sets the parameter 'b' to # [8.6]
-gamc # = Sets the parameter 'c' to # [0.547]
-gamd # = Sets the delay time to # seconds [0.0]
These options apply to all waveform types:
-peak # = Sets peak value to # [100]
-dt # = Sets time step of output AND input [0.1]
-TR # = '-TR' is equivalent to '-dt'
The default is just to output the waveform defined by the parameters
above. If an input file is specified by one the options below, then
the timeseries defined by that file will be convolved with the ideal
waveform defined above -- that is, each nonzero point in the input
timeseries will generate a copy of the waveform starting at that point
in time, with the amplitude scaled by the input timeseries value.
-xyout = Output data in 2 columns:
1=time 2=waveform (useful for graphing)
[default is 1 column=waveform]
-input infile = Read timeseries from *.1D formatted 'infile';
convolve with waveform to produce output
N.B.: you can use a sub-vector selector to choose
a particular column of infile, as in
-input 'fred.1D[3]'
-inline DATA = Read timeseries from command line DATA;
convolve with waveform to produce output
DATA is in the form of numbers and
count@value, as in
-inline 20@0.0 5@1.0 30@0.0 1.0 20@0.0 2.0
which means a timeseries with 20 zeros, then 5 ones, then 30 zeros,
a single 1, 20 more zeros, and a final 2.
[The '@' character may actually be any of: '@', '*', 'x', 'X'.
Note that * must be typed as \* to prevent the shell from
trying to interpret it as a filename wildcard.]
-tstim DATA = Read discrete stimulation times from the command line
and convolve the waveform with delta-functions at
those times. In this input format, the times do
NOT have to be at intervals of '-dt'. For example
-dt 2.0 -tstim 5.6 9.3 13.7 16.4
specifies a TR of 2 s and stimuli at 4 times
(5.6 s, etc.) that do not correspond to integer
multiples of TR. DATA values cannot be negative.
If the DATA is stored in a file, you can read it
onto the command line using something like
-tstim `cat filename`
where using the backward-single-quote operator
of the usual Unix shells.
** 12 May 2003: The times after '-tstim' can now also be specified
in the format 'a:b', indicating a continuous ON
period from time 'a' to time 'b'. For example,
-dt 2.0 -tstim 13.2:15.7 20.3:25.3
The amplitude of a response of duration equal to
'dt' is equal the the amplitude of a single impulse
response (which is the special case a=b). N.B.: This
means that something like '5:5.01' is very different
from '5' (='5:5'). The former will have a small amplitude
because of the small duration, but the latter will have
a large amplitude because the case of an instantaneous
input is special. It is probably best NOT to mix the
two types of input to '-tstim' for this reason.
Compare the graphs from the 2 commands below:
waver -dt 1.0 -tstim 5:5.1 | 1dplot -stdin
waver -dt 1.0 -tstim 5 | 1dplot -stdin
If you prefer, you can use the form 'a%c' to indicate
an ON interval from time=a to time=a+c.
** 13 May 2005: You can now add an amplitude to each response individually.
For example
waver -dt 1.0 -peak 1.0 -tstim 3.2 17.9x2.0 23.1x-0.5
puts the default response amplitude at time 3.2,
2.0 times the default at time 17.9, and -0.5 times
the default at time 23.1.
-when DATA = Read time blocks when stimulus is 'on' (=1) from the
command line and convolve the waveform with with
a zero-one input. For example:
-when 20..40 60..80
means that the stimulus function is 1.0 for time
steps number 20 to 40, and 60 to 80 (inclusive),
and zero otherwise. (The first time step is
numbered 0.)
-numout NN = Output a timeseries with NN points; if this option
is not given, then enough points are output to
let the result tail back down to zero.
At least one option is required, or the program will just print this message
to stdout. Only one of the 3 timeseries input options above can be used.
If you have the 'xmgr' graphing program, then a useful way to preview the
results of this program is through a command pipe like
waver -dt 0.25 -xyout -inline 16@1 40@0 16@1 40@0 | xmgr -source stdin
Using the cruder AFNI package program 1dplot, you can do something like:
waver -GAM -tstim 0 7.7 | 1dplot -stdin
If a square wave is desired, see the 'sqwave' program.
This page auto-generated on Thu Aug 25 16:49:44 EDT 2005
|
| whereami |
** bad option -helpThis page auto-generated on Thu Aug 25 16:49:44 EDT 2005 |
| whirlgif |
whirlgif Rev 1.00 (C) 1996 by Kevin Kadow
(C) 1991,1992 by Mark Podlipec
whirlgif is a quick program that reads a series of GIF files, and produces
a single gif file composed of those images.
Usage: whirlgif [-v] [-trans index ] [-time delay] [-o outfile]
[-loop] [-i incfile] file1 [ -time delay] file2
options:
-v verbose mode
-loop [count] add the Netscape 'loop' extension.
-time delay inter-frame timing.
-trans index set the colormap index 'index' to be transparent
-o outfile write the results to 'outfile'
-i incfile read a list of names from 'incfile'
TIPS
If you don't specify an output file, the GIF will be sent to stdout. This is
a good thing if you're using this in a CGI script, a very bad thing if you
run this from a terminal and forget to redirect stdout.
The output file (if any) and -loop _MUST_ be specified before any gif images.
You can specify several delay statements on the command line to change
the delay between images in the middle of an animation, e.g.
whirlgif -time 5 a.gif b.gif c.gif -time 100 d.gif -time 5 e.gif f.gif
Although it's generally considered to be evil, you can also specify
several transparency statements on the command line, to change the transparent
color in the middle of an animation. This may cause problems for some programs.
BUGS
+ The loop 'count' is ineffective because Netspcape always loops infinitely.
+ Should be able to specify delay in an 'incfile' list (see next bug).
+ Does not handle filenames starting with a - (hypen), except in 'incfile'.
This program is available from http://www.msg.net/utility/whirlgif/
-------------------------------------------------------------------
Kevin Kadow kadokev@msg.net
Based on 'txtmerge' written by:
Mark Podlipec podlipec@wellfleet.com
This page auto-generated on Thu Aug 25 16:49:44 EDT 2005
|
| Xphace |
Usage: Xphace im1 [im2] Image mergerizing. Image files are in PGM format.This page auto-generated on Thu Aug 25 16:49:44 EDT 2005 |
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