Configure preproc-sess

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

Create a subjectname file

The first thing you will need to do is create a file called subjectname in the folders for each of the participants you will be preprocessing. This file contains only a single line, indicating the Freesurfer subjectid by which that subject is known. For example, for the subject whose data is in $SUBJECTS_DIR/FS_T1_501/, there should be a file called subjectname that contains just a single line:

FS_T1_501

If such a file does not exist, create it:

cd $SUBJECTS_DIR/FS_T1_501
echo FS_T1_501 > subjectname

Or, if you want to be fancy and not have to type out the name of the participant, you can use the output of the 'basename' linux command to generate the name of your directory, which should match your participant name:

cd $SUBJECTS_DIR/FS_T1_501
echo `basename "$PWD"` > subjectname

Using this method, the second command will always be the same for any participant.

Run preproc-sess

This command does motion correction, spatial smoothing (to reduce noise, thereby increasing the signal-to-noise ratio), and slice-time correction on your functional (BOLD) data. It can be run on a batch of participants or on individuals.

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

Other options

Slice time correction

Slice time correction adjusts the functional data to account for the fact that, when you acquire an entire 3D volume as a series of 2-D planes (slices) over the span of 1 TR (commonly 2 seconds), then the very last slice you acquire is going to be delayed 2 seconds relative to the very first slice you acquire. There is a -stc switch that you can provide telling Freesurfer what order the slices were acquired, which the software uses to algorithmically adjust the signals for each slice to account for the fact that they occurred earlier vs. later within that 1 TR time window. Using this switch requires you to know something about the scanner. It is prudent to check with the scanner technician to verify the slice acquisition order so that you can provide the correct value to go along with the -stc switch. If you omit the -stc switch, slice time correction is not performed on the data.

Problems

Unsupported slice timing 5

Running preproc-sess on an existing dataset, I ran into

nifti1Read(): unsupported slice timing pattern 5 in /home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T2_501/bold/029/f.nii

A suggested fix is to convert the data to .mgz using Slicer. Opening up the f.nii file and resaving it as an f.mgz file (deleting the source .nii file to avoid confusion) resolves the problem.