Yeah, I was starting to wonder if he was having permissions issues as well.
On Wed, Sep 17, 2014 at 10:16 AM, Mahmoud <zeydab...@gmail.com> wrote: > Paul, > > I am using bash instead of tcsh. Does it make any difference ? > > Mahmoud > > On Wed, Sep 17, 2014 at 7:09 AM, Paul Beach <pabea...@gmail.com> wrote: > >> Hmm. Well I'm stumped. Sorry. :-/ >> >> Any Freesurfer gurus have some ideas here? >> >> On Wed, Sep 17, 2014 at 9:59 AM, Mahmoud <zeydab...@gmail.com> wrote: >> >>> 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. >>>> >>>> >>> >>> _______________________________________________ >>> 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.
