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. > >
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