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

Output

--------------------------------------------------------------
preproc-sess logfile is log/preproc-sess.FS_T1_501.log
--------------------------------------------------------------
$Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $
chris
setenv FREESURFER_HOME /usr/local/freesurfer
setenv SUBJECTS_DIR /home/chris/ubfs/cpmcnorg/openfmri/booth
Linux wernickesarea 3.13.0-85-generic #129-Ubuntu SMP Thu Mar 17 20:50:15 UTC 2016 x86_64 x86_64 x86_64  GNU/Linux
/home/chris/ubfs/cpmcnorg/openfmri/booth
/usr/local/freesurfer/fsfast/bin/preproc-sess -s FS_T1_501 -df ./ -surface self lhrh -fwhm 6 -per-run -fsd bold
Fri Apr 15 12:41:05 EDT 2016
instem   f 
mc   1     f fmcpr 
stc  0     fmcpr
sm   0   
mask 1   brain
FS_T1_501 Template -----------------------------
mktemplate-sess -s FS_T1_501 -d /home/chris/ubfs/cpmcnorg/openfmri/booth -fsd bold -update
 
Session: /home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T1_501 ----------------
Fri Apr 15 12:41:05 EDT 2016
Detected input format at nii
FS_T1_501 Update not needed
 Run: 005 ----------------
 Fri Apr 15 12:41:06 EDT 2016
 FS_T1_501 005 Update not needed
 Run: 006 ----------------
 Fri Apr 15 12:41:06 EDT 2016
 FS_T1_501 006 Update not needed
Fri Apr 15 12:41:06 EDT 2016
mktemplate-sess completed 
FS_T1_501 Mask ------------------------
mkbrainmask-sess -maskstem brain -fsd bold -s FS_T1_501 -d /home/chris/ubfs/cpmcnorg/openfmri/booth -update
------------------------------------------------
/home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T1_501 
Fri Apr 15 12:41:06 EDT 2016
mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil 1 -nerode 0
FSLMATHS fslmaths.fsl
Scratch Dir is /tmp/mkbrainmask_3238
/home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T1_501/bold
mri_convert template.nii.gz /tmp/mkbrainmask_3238/in.nii
mri_convert template.nii.gz /tmp/mkbrainmask_3238/in.nii 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from template.nii.gz...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998676, 0.0474253, -0.019947)
j_ras = (0.0460224, 0.996776, 0.0657189)
k_ras = (-0.0229995, -0.0647138, 0.997639)
writing to /tmp/mkbrainmask_3238/in.nii...
# ---------- Using FSL's BET to Extract Brain------------------ #
/home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T1_501/bold
bet.fsl /tmp/mkbrainmask_3238/in.nii /tmp/mkbrainmask_3238/brain -m -f 0.1
/usr/local/freesurfer/bin/bet.fsl: 1: /usr/local/freesurfer/bin/bet.fsl: /bin/remove_ext: not found
/usr/local/freesurfer/bin/bet.fsl: 1: /usr/local/freesurfer/bin/bet.fsl: /bin/remove_ext: not found
/usr/local/freesurfer/bin/bet.fsl: 1: /usr/local/freesurfer/bin/bet.fsl: /bin/imtest: not found
/usr/local/freesurfer/bin/bet.fsl: 153: [: =: unexpected operator
/usr/local/freesurfer/bin/bet.fsl: 231: /usr/local/freesurfer/bin/bet.fsl: /bin/bet2: not found
mri_binarize --i /tmp/mkbrainmask_3238/brain_mask.nii --min .01 --o /tmp/mkbrainmask_3238/brain_mask.nii
niiRead(): error opening file /tmp/mkbrainmask_3238/brain_mask.nii

$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T1_501/bold
cmdline mri_binarize --i /tmp/mkbrainmask_3238/brain_mask.nii --min .01 --o  /tmp/mkbrainmask_3238/brain_mask.nii  
sysname  Linux
hostname wernickesarea
machine  x86_64
user     chris

input      /tmp/mkbrainmask_3238/brain_mask.nii
frame      0
nErode3d   0
nErode2d   0
output     /tmp/mkbrainmask_3238/brain_mask.nii
Binarizing based on threshold
min        0.01
max        +infinity
binval        1
binvalnot     0