And here is a screen shot of subjects directory ...
On Fri, Sep 19, 2014 at 9:07 AM, Mahmoud zeydabadi@gmail.com wrote:
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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