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.
