Last edit: 06-06-02 Graham Wideman

FreeSurfer

FreeSurfer Data Flow

The following table presents a condensed view of the basic FreeSurfer data flow:

Also available as Excel spreadsheet for prettier printing.

How to read:

• Left Columns = Process Steps: FreeSurfer provides an environment in which to work through a series of steps, starting with raw data and eventually producing a number of useful surfaces. This series of steps is presented in order in the leftmost column.
   
• Headings = Directories/Files: The files involved in this process are listed across the top. The directories are those appearing in the $FREESURFER/subjects/subjectname/ branch.
  A single volume dataset consists of a set of files (typically 256 slices plus info file). These files are segregated into separate directories for each volume,  so for volumes it is the directory names which are significant. Surfaces are stored in single files, so these are all contained in the single surf directory and distinguished by file name.
   
• 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) or Rewritten (R).
   
• Top-Left to Bottom-Right Flow: I've ordered the directories and files so that there is a basic top-left to bottom-right flow of "I"s and "O"s. This makes it easier to visually appreciate the general flow of data from raw to final products.

Additional Notes

• Scripts and Logs: Not documented above is that a number of the programs and scripts also write some information (such as parameters calculated) into files in the directories:
  $FREESURFER/subjects/subjectname/scripts
  $FREESURFER/subjects/subjectname/tmp
  $FREESURFER/subjects/subjectname/mri/tmp
  
  ...and possibly elsewhere.

 
• Register Surface involves other input files beyond those shown in the table above, providing data for the "average" reference surface.
   
• Flatten: The flattening functionality is not covered in the table above.
   
• Other Functionality: FreeSurfer includes other functionality not described in the above basic process, for example the fs-fast functionality (Functional Analysis Stream).

Source of Information in Table

The input/output information was distilled from the log information captured in CSurf's window, while running through the entire process from start to finish. Possible inaccuracies may exist if the logging information produced by the numerous scripts and programs was incomplete. Time information was recorded while processing the sample bert data on a 2 GHz P4, 512 MB Linux machine.

Go to:   or back to Understanding FreeSurfer