Paul, I tried this: SUBJECTS_DIR=/mnt/hgfs/DBSI/volumetric/MGZ cd $SUBJECTS_DIR ln -s $FREESURFER_HOME/subjects/fsaverage
and got this: ln: failed to create symbolic link ‘./fsaverage’: Operation not supported any idea ? Mahmoud On Wed, Sep 17, 2014 at 6:27 AM, Paul Beach <pabea...@gmail.com> wrote: > Try something like: > > cd $SUBJECTS_DIR > ln -s $FREESURFER_HOME/subjects/fsaverage . > > Confirm the linked directory is now in your $SUBJECTS_DIR, then try > running your script. > > On Wed, Sep 17, 2014 at 9:20 AM, Mahmoud <zeydab...@gmail.com> wrote: > >> Paul, >> >> The fsaverages are in $FREESURFER_HOME/subjects. So does it mean that >> the program couldn't make a link between my actual image places and >> $FREESURFER_HOME/subjects/fsaverage >> ? >> what can I do to fix it ? >> >> Thank you, >> Mahmoud >> >> On Wed, Sep 17, 2014 at 9:16 AM, Paul Beach <pabea...@gmail.com> wrote: >> >>> The general fsaverage (as well as it's other iterations, fsaverages 3-6) >>> should be located in your $FREESURFER_HOME/subjects directory. You could >>> symbolically link it over to your $SUBJECTS_DIR. >>> >>> On Wed, Sep 17, 2014 at 9:09 AM, Mahmoud <zeydab...@gmail.com> wrote: >>> >>>> Dear All, >>>> >>>> I ran the following script: >>>> >>>> #!/bin/bash >>>> SUBJECTS_DIR=/mnt/hgfs/DBSI/volumetric/MGZ >>>> recon-all -i /mnt/hgfs/DBSI/volumetric/Case022/Case022_tp2/3-1.dcm >>>> -subject case022_tp2 -all >>>> >>>> and got the error below at the end. Could anybody please let me know >>>> how to fix it. >>>> >>>> Thank you, >>>> Mahmoud >>>> >>>> >>>> Reporting on 70 segmentations >>>> mri_segstats done >>>> /mnt/hgfs/DBSI/volumetric/MGZ/case022_tp2/label >>>> #-------------------------------------------- >>>> #@# BA Labels lh Tue Sep 16 19:26:47 PDT 2014 >>>> INFO: *fsaverage subject does not exist in SUBJECTS_DIR* >>>> INFO: Creating symlink to fsaverage subject... >>>> >>>> cd /mnt/hgfs/DBSI/volumetric/MGZ; ln -s >>>> /usr/local/freesurfer/subjects/fsaverage; cd - >>>> >>>> ln: *failed to create symbolic link './fsaverage': Operation not >>>> supported* >>>> >>>> mri_label2label --srcsubject fsaverage --srclabel >>>> /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label --trgsubject >>>> case022_tp2 --trglabel ./lh.BA1.label --hemi lh --regmethod surface >>>> >>>> No such file or directory >>>> mri_label2label: could not open label file >>>> /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label >>>> >>>> srclabel = /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label >>>> srcsubject = fsaverage >>>> trgsubject = case022_tp2 >>>> trglabel = ./lh.BA1.label >>>> regmethod = surface >>>> >>>> srchemi = lh >>>> trghemi = lh >>>> trgsurface = white >>>> srcsurfreg = sphere.reg >>>> trgsurfreg = sphere.reg >>>> usehash = 1 >>>> Use ProjAbs = 0, 0 >>>> Use ProjFrac = 0, 0 >>>> DoPaint 0 >>>> >>>> SUBJECTS_DIR /mnt/hgfs/DBSI/volumetric/MGZ >>>> FREESURFER_HOME /usr/local/freesurfer >>>> Loading source label. >>>> Invalid argument >>>> ERROR reading /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label >>>> Linux ubuntu 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC >>>> 2014 x86_64 x86_64 x86_64 GNU/Linux >>>> >>>> recon-all -s case022_tp2 exited with ERRORS at Tue Sep 16 19:26:47 PDT >>>> 2014 >>>> >>>> For more details, see the log file >>>> /mnt/hgfs/DBSI/volumetric/MGZ/case022_tp2/scripts/recon-all.log >>>> To report a problem, see >>>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> The information in this e-mail is intended only for the person to whom >>>> it is >>>> addressed. If you believe this e-mail was sent to you in error and the >>>> e-mail >>>> contains patient information, please contact the Partners Compliance >>>> HelpLine at >>>> http://www.partners.org/complianceline . If the e-mail was sent to you >>>> in error >>>> but does not contain patient information, please contact the sender and >>>> properly >>>> dispose of the e-mail. >>>> >>>> >>> >>> >>> -- >>> Paul Beach >>> DO/PhD candidate - Year VI >>> Michigan State University >>> - College of Osteopathic Medicine >>> - Neuroscience Program >>> - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*) >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> The information in this e-mail is intended only for the person to whom >>> it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you >>> in error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >>> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> > > > -- > Paul Beach > DO/PhD candidate - Year VI > Michigan State University > - College of Osteopathic Medicine > - Neuroscience Program > - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*) > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >
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