can you tell us what your FREESURFER_HOME is and what your SUBJECTS_DIR is? You will need to remove the broken link probably
On Fri, 19 Sep 2014, Mahmoud wrote:
Hi Bruce,
Actually I couldn't. It says: ls: cannot access
/usr/local/freesurfer/subjects/fsaverage: Too many levels of symbolic links
And even I couldn't cd to fsaverage !
In fact there is no directory under SUBJETCS_DIR named fsaverage, it seems
the fsaverage under SUBJETCS_DIR is just a broken link, and I have no idea
why the the link is broken and how to fix it.
Any help would be highly appreciated !
Thank you,
Mahmoud
On Fri, Sep 19, 2014 at 8:21 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>
wrote:
Hi Mahmoud
were you able to create a symlink to fsaverage in your
SUBJECTS_DIR? If not, that is the reason for this error
Bruce
On Thu, 18 Sep 2014, Mahmoud wrote:
Dear all,
After running "recon-all -i
$SUBJECTS_DIR/Case018/case018_tp2/22-1.dcm
-subject case018_tp2 -all" I'm always getting the
following error and really
don't know how to fix.
Could anybody please help me. The recon-all.log file
is attached.
Thank you,
Mahmoud
Reporting on 70 segmentations
mri_segstats done
/usr/local/freesurfer/subjects/case018_tp2/label
#--------------------------------------------
#@# BA Labels lh Thu Sep 18 20:23:27 EDT 2014
INFO: fsaverage subject does not exist in
SUBJECTS_DIR
INFO: Creating symlink to fsaverage subject...
cd /usr/local/freesurfer/subjects; ln -s
/usr/local/freesurfer/subjects/fsaverage; cd -
mri_label2label --srcsubject fsaverage --srclabel
/usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label
--trgsubject
case018_tp2 --trglabel ./lh.BA1.label --hemi lh
--regmethod surface
Too many levels of symbolic links
mri_label2label: could not open label file
/usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label
srclabel =
/usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label
srcsubject = fsaverage
trgsubject = case018_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 /usr/local/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Invalid argument
ERROR reading
/usr/local/freesurfer/subjects/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 case018_tp2 exited with ERRORS at Thu
Sep 18 20:23:27 EDT 2014
For more details, see the log file
/usr/local/freesurfer/subjects/case018_tp2/scripts/recon-all.log
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