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.dr...@gmail.com
<mailto:john.dr...@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:
[jdr...@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
gr...@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
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