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