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arnaud
New Member
USA
14 Posts |
 Posted - Sep 06 2011 : 11:06:11 AM
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Hi,
I submitted a job that calls a simple script that sets the freesurfer SUBJECTS_DIR variable to a subfolder of my EXPERIMENT folder and then calls recon_all. It runs well up to mri_label2label.
At that point recon_all fails to create a symlink in $SUBJECTS_DIR/. The symlink would normally point to $FREESURFER_HOME/subjects/fsaverage but instead I get this error message:
ln: creating symbolic link `./fsaverage': Operation not supported
Anyone knows a workaround? Thanks.
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petty
BIAC Staff
USA
453 Posts |
Posted - Sep 06 2011 : 11:36:17 AM
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your workaround would be to write your freesurfer results to your temporary directory ( $TMP ), then copy them back to your normal experiment directory when you are finished.
All the mounts are cifs/smb mounts, which don't allow symbolic linking ... the temporary directories are nfs |
Edited by - petty on Sep 06 2011 11:49:19 AM |
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Sep 06 2011 : 11:57:09 AM
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| I just asked Doug Greve about this -- he suggests explicitly copying the $FREESURFER_HOME/subjects/fsaverage directory to your $SUBJECTS_DIR, and then it won't attempt to symbolically link it. He also says the other symbolic links in recon-all are generally only encountered in their testing. Hopefully this will work. |
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petty
BIAC Staff
USA
453 Posts |
Posted - Sep 06 2011 : 12:05:46 PM
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quote:
Originally posted by syam.gadde
I just asked Doug Greve about this -- he suggests explicitly copying the $FREESURFER_HOME/subjects/fsaverage directory to your $SUBJECTS_DIR, and then it won't attempt to symbolically link it. He also says the other symbolic links in recon-all are generally only encountered in their testing. Hopefully this will work.
that would make the most sense ... if something went wrong, your progress wouldn't get deleted at the end of the job ( which is what happens to $TMP ) |
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arnaud
New Member
USA
14 Posts |
Posted - Sep 06 2011 : 1:44:26 PM
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Thanks to both of you. The solution of explicitly copying the following folders in my $SUBJECTS_DIR worked.
In case other users run into this problem, just do the following thing in interactive mode:
cd $SUBJECTS_DIR
cp -rf $FREESURFER_HOME/subjects/fsaverage .
cp -rf $FREESURFER_HOME/subjects/lh.EC_average .
cp -rf $FREESURFER_HOME/subjects/rh.EC_average .
cp -rf $FREESURFER_HOME/subjects/V1_average . [ not sure if that one is necessary but in doubt...]
Then adapt your master script to resume recon-all from where it failed using the following arguments (<5min):
recon-all -s $subjectid -no-isrunning -autorecon3 -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -surfvolume -noparcstats -nocortparc2 -noparcstats2 -nocortribbon -nosegstats -noaparc2aseg -nowmparc -balabels -label-exvivo-ec
Note: it's tempting to use -nosurfvolume but it is not available in FreeSurfer5.1 (oversight?). In any case, the surfvolume step is very quick. |
Edited by - arnaud on Sep 06 2011 1:47:10 PM |
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petty
BIAC Staff
USA
453 Posts |
Posted - Sep 07 2011 : 09:07:59 AM
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Also, there's a general freesurfer template script on the head node which anyone can run.
I've included copying these directories over if they don't exist:
/usr/local/packages/qsub_templates/RunFreeSurf.sh
to run it, just:
qsub -v EXPERIMENT=Something.01 /usr/local/packages/qsub_templates/RunFreeSurf.sh SUBJNUM Path/to/Anat/Series
(ie: qsub -v EXPERIMENT=Something.01 /usr/local/packages/qsub_templates/RunFreeSurf.sh 12345 Data/Anat/20110907_12345/series007 )
The results will be in Something.01/Analysis/freesurfer/12345 |
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recon_all FreeSurfer 5.1.0
