Mark,

How was the .gca file created?  Can you send us this file?

Nick

On Tue, 2013-08-20 at 14:15 -0500, Mark Plantz wrote:
> 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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