Bruce,

Here is the info when I open a new terminal:

-------- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME       /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /usr/local/freesurfer/subjects
MNI_DIR           /usr/local/freesurfer/mni
ubuntu:~>

On Fri, Sep 19, 2014 at 8:56 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

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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