Absolutely, sorry about that, the group is now cc'd.

the ls -l says: -rw-rw-r-- 1 vhasfcwui cind       0 Nov  6 15:57 lh.sphere

so it has 0 size to it, and I can't open it in tksurfer

-bash-3.2$ tksurfer PPMI_290_S_3829m12_i395612 lh sphere
Using Freesurfer version 5.1.

subject is PPMI_290_S_3829m12_i395612
hemi    is lh
surface is sphere
surfer: current subjects dir: /cind/00/PPMI/Freesurfer/subjects
surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($session) set to:
surfer:     /cind/07/PPMI/Freesurfer/subjects
checking for nofix files in 'sphere'
Reading image info (/cind/00/PPMI/Freesurfer/subjects/PPMI_290_S_3829m12_i395612)
Reading /cind/00/PPMI/Freesurfer/subjects/PPMI_290_S_3829m12_i395612/mri/orig.mgz
surfer: Reading header info from /cind/00/PPMI/Freesurfer/subjects/PPMI_290_S_3829m12_i395612/mri/orig.mgz
ERROR: reading /cind/00/PPMI/Freesurfer/subjects/PPMI_290_S_3829m12_i395612/surf/lh.sphere
Read 0 bytes, expected 1


Perhaps I should first try deleting the file and rerun as you recommended?

Thanks,
Adam


On Fri, Nov 8, 2013 at 2:36 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
Hi Adam

can you cc the list on your replies so that others can answer? What does ls -l say about the sphere? Can you open it in tksurfer? Maybe the partition filled at some point when it was being written but things opened up later? You might just deleted the lh.sphere file and run

recon-all -make all -s <subject>

cheers

Bruce


On Fri, 8 Nov 2013, Adam Mezher wrote:

Hi Bruce,

Yes I checked and the partition is not full, there should be ample space available.
Do you have any other ideas? I've never come across this error before.

Thanks,
-Adam


Filesystem            Size  Used Avail Use% Mounted on
cosf:/cind/07         2.3T  2.0T  167G  93% /cind/07

On Fri, Nov 8, 2013 at 2:22 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
      Hi Adam

      can you check to make sure that the partition isn't full?

      Bruce
      On Fri, 8 Nov 2013, Adam Mezher wrote:

            Hi FreeSurfer experts,

            I am repeatedly running into an autorecon3 error (see below).
            Any ideas how to fix
            this? It appears that the software is having an issue reading
            /surf/lh.sphere and
            immediately exits afterward.

            Thank you,
            Adam

             

            Adam Mezher

            Staff Research Associate II

            Center for Imaging of Neurodegenerative Diseases

            San Francisco VA Medical Center

            4150 Clement St. (114M)

            San Francisco, CA 94121

            Tel: 415-221-4810 Ext. 4629

            Fax: 415-668-2864

             



            using smoothwm curvature for final alignment
            $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $
              $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $
            reading surface from ../surf/lh.sphere...
            mris_register: could not read surface file ../surf/lh.sphere
            ERROR: reading ../surf/lh.sphere
            Read 0 bytes, expected 1
            Linux aldebaran 2.6.18-194.17.4.el5 #1 SMP Mon Oct 25
            15:50:53 EDT 2010 x86_64 x86_64
            x86_64 GNU/Linux

            recon-all -s PPMI_290_S_3829m12_i395612 exited with ERRORS at
            Wed Nov  6 15:57:07 PST
            2013




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