I think the best way to diagnose the issue would be to run the subject using the standard atlas provided with freesurfer. If that runs to completion that the .gca is almost certainly the source of the problem.
-Zeke
On 08/19/2013 03:07 PM, Mark Plantz wrote:
Hello all,
While running recon-all for a subject, I ran into the followingerror message:
*reading aseg from /Users/IngvalsonLab/Desktop/avgseg_seg_test/mri/aseg.auto_noCCseg.mgz*
*reading norm from /Users/IngvalsonLab/Desktop/avgseg_seg_test/mri/norm.mgz*
*0 voxels in left wm, 0 in right wm, xrange [-1, 257]*
*searching rotation angles z=[-7 7], y=[83 97]*
*searching scale 1 Z rot 6.8 global minimum found at slice 0.0, rotations (90.00, -0.00)*
*final transformation (x=0.0, yr=90.000, zr=-0.000):*
*-0.000 0.000 1.000 128.000;*
*-0.000 1.000 -0.000 128.000;*
*-1.000 0.000 0.000 128.000;*
- 0.000 0.000 0.000 1.000;*
*Segmentation fault*
*Darwin dhcp-165-124-23-248.prevmed.northwestern.edu http://dhcp-165-124-23-248.prevmed.northwestern.edu 12.4.0 Darwin Kernel Version 12.4.0: Wed May 1 17:57:12 PDT 2013; root:xnu-2050.24.15~1/RELEASE_X86_64 x86_64*
*recon-all -s avgseg_seg_test exited with ERRORS at Mon Aug 19 13:32:28 CDT 2013*
I don't know if this error is directly related to the actual brain segmentation, but recon-all was run with a different gca atlas. The command was:
recon-all -gca atlas.gca -all -s <subjID>
My best guess is that the .gca file is the source of the problem, but I am not sure why recon-all would make it to the final transformation and then throw an error.
Any ideas?
Thanks in advance.
MP
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