Paul it shows again: ln: failed to create symbolic link ‘./fsaverage’: Operation not supported
!!! On Wed, Sep 17, 2014 at 6:50 AM, Paul Beach <pabea...@gmail.com> wrote: > 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. > >
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