gw_logo_08.gif (1982 bytes)  
Last edit: 06-06-02 Graham Wideman


FreeSurfer 3.0.3 (2006)  Process vs Data Files
Article created: 2006-06-01

FreeSurfer Data Flow

The following table presents a condensed view of the "recon-all" FreeSurfer data flow distilled from FreeSurfer Wiki - ReconAllDevTable.


1. If your web browser shrinks this image to a blurry mess to fit the browser window, look for a function (eg: right-click on image) which forces the image to show full size.

2. Printing: Also available as Excel spreadsheet, which you can adjust to print nicely.

How to read:

Topic and Link Description
Left Columns = Process Steps The left columns show to several levels of detail the progression of steps followed in the "recon-all" script. (See FreeSurfer Wiki - ReconAllDevTable for details.)
Headings =Files The files involved in this process are listed across the top. (These are indvidual subjects's data files, located in one branch or another of a subject's directory.
Body of Table = File I/O For each process step (row), the table shows which files are used as input (I), and which are produced as output (O).  (I believe there are no files read AND written by the same program
Top-Left to Bottom-Right Flow The table lists the steps in the order they are performed, and in general each step produces files which are used by the next step, creating the mostly diagonal pattern of output and input activity.

Additional Notes

Issue Description
Source of data Based on 2005-06-01
Processing Semi-automatically transformed into the table above. (Note to self: reconall01.mdb)
Simplification Deleted all lh-only columns, as rh versions are representative
Simplification talairach_m3z_inv_[x,y,z]_mgz stands for three separate files
Simplification Deleted "transform/" from talairach transform file column heads


Go to:  gw_logo_08.gif (1982 bytes)  or back to Understanding FreeSurfer