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*)
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