Configure preproc-sess

You can preprocess multiple participants in a batch or individual participants, depending on how you invoke the preproc-sess command.

Batch processing

Batch processing requires a sessid file containing the session names (i.e., the names of all the Freesurfer folders) for all your participants. The sessid file can be called anything you wish, and is simply a plain text file with one folder name on each line. For example:

chris_subjects.txt:
 FS_T1_501
 FS_T2_501
 FS_T1_505
 FS_T2_505

When doing a batch, you call using the -sf switch:

preproc-sess -sf <sessidfile> -df <srchdirfile> [options]

e.g.,

preproc-sess -sf chris_subjects.txt -surface self lhrh –fwhm 6 -per-run –fsd bold

If the -df switch isn't provided (it doesn't seem to be mandatory) then it uses a default directory (possibly $SUBJECTS_DIR, or possibly your current working directory) to start in.

Individuals

Preprocessing individuals works pretty much the same, except you do not require a sessid file. Instead, you provide it with the name of one of the session folders, and use the -s switch, rather than the -sf switch:

preproc-sess -s FS_T1_501 -surface self lhrh –fwhm 6 -per-run –fsd bold