On Tue, May 26, 2009 at 3:43 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

Does ../stats/lh.aparc.stats exist and do you have write perms to the file and directory?

John Drozd wrote:

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 <mailto: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>
<mailto: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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-- Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>

Phone Number: 617-724-2358 Fax: 617-726-7422

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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 Fax: 617-726-7422

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting