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*)
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