Thanks for the responses.

I think I have determined the cause of the error. I thought it would be OK to run recon-all with a .gca atlas that contained some different ROI's from the default .gca atlas. I think that this may be throwing off the subcortical segmentation.

Does anyone know if the gca atlas must contain the exact same ROI's as the default atlas? I was under the impression that the values of the non-included and/or different ROI's would simply be ignored or set to zero; however, it actually caused recon-all to fail entirely.

-MP

On Tue, Aug 20, 2013 at 1:40 PM, Z K <zkaufman@nmr.mgh.harvard.edu> wrote:

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 following
error 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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