Hi Doug,

It is writing to the trumpet directory which is not full.
It does write out the output file aparc.annot.ctab, but seg faults at the end.

Here is the df -h output for the trumpet directory (775Gb are available):

[jdrozd@trumpet label]$ df -h
Filesystem            Size  Used Avail Use% Mounted on
/dev/md2               50G  7.7G   40G  17% /
/dev/md3              862G   43G  775G   6% /trumpet
/dev/md0              122M   21M   95M  19% /boot
tmpfs                 3.0G  952K  3.0G   1% /dev/shm
nil:/people/j         185G  180G  3.1G  99% /people/j
nil:/scratch           62G   60G  1.1G  99% /scratch
nil:/irus              40G   38G  2.0G  95% /net/nil/irus
nil:/local             40G   38G  2.0G  95% /localaparc.annot.ctab

The subject is not an average subject but is part of an Alzheimer's study.
I have not done any manual interventions/corrections in freesurfer (maybe I should at this stage).
I am just running the commands for a first try.

Thanks,
john

On Tue, May 26, 2009 at 3:13 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:
Can you verify that the disk it is writing to is not full?

Is this an average subject?

doug

John Drozd wrote:
Hello again,

Sorry, I forgot to include the required info:

john

FREESURFER_HOME: /trumpet/downloads/FreeSurfer/freesurfer

Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0

RedHat release: Fedora release 10 (Cambridge)

Kernel info: Linux 2.6.27.21-170.2.56.fc10.x86_64 x86_64

---------------------------------------------------------------------
Please include the following additional information in your report:

 1) subject name: convertedfile

 2) the entire command-line executed:
     mris_anatomical_stats -mgz -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -cf ../label/aparc.annot.ctab convertedfile lh

 3) the error message generated:
     Segmentation fault

 4) optionally include the subject's /script/recon-all.log


On Tue, May 26, 2009 at 2:23 PM, John Drozd <john.drozd@gmail.com <mailto:john.drozd@gmail.com>> wrote:

   Hello,

   I am running the reconall steps individually for a firts try.

   I noticed that I get a segmentation fault when I run
   mris_anatomical_stats as whown below:

   [jdrozd@trumpet mri]$ mris_anatomical_stats -mgz -f
   ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -cf
   ../label/aparc.annot.ctab convertedfile lh                            INFO: assuming MGZ format for
   volumes.                                                      computing statistics for each annotation in ../label/lh.aparc.annot.
   reading volume
   /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/mri/wm.mgz...
   reading input surface
   /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/surf/lh.white...
   reading input pial surface
   /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/surf/lh.pial...
   reading input white surface
   /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/surf/lh.white...
   reading colortable from annotation file...
   colortable with 35 entries read (originally
   /space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt)
   Saving annotation colortable ../label/aparc.annot.ctab

   table columns are:
       number of vertices
       total surface area (mm^2)
       total gray matter volume (mm^3)
       average cortical thickness +- standard deviation (mm)
       integrated rectified mean curvature
       integrated rectified Gaussian curvature
       folding index
       intrinsic curvature index
       structure name

   Segmentation fault

   john


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