you have to tell the symbolic link where to put the directory copy this exactly into your terminal, including the period at the end
SUBJECTS_DIR=/mnt/hgfs/DBSI/volumetric/MGZ cd $SUBJECTS_DIR ln -s $FREESURFER_HOME/subjects/fsaverage . On Wed, Sep 17, 2014 at 9:46 AM, Mahmoud <zeydab...@gmail.com> wrote: > 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. >> >> > > _______________________________________________ > 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.
