Configure preproc-sess: Difference between revisions
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preproc-sess -sf <sessidfile> -df <srchdirfile> [options] | preproc-sess -sf <sessidfile> -df <srchdirfile> [options] | ||
e.g., | e.g., | ||
preproc-sess -sf chris_subjects.txt -surface self lhrh | preproc-sess -sf chris_subjects.txt -surface self lhrh -fwhm 6 -per-run -fsd bold | ||
If the <code>-df</code> 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. | If the <code>-df</code> 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. | ||
Revision as of 11:10, 19 April 2016
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 -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