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. > >
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