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.

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