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 <zkauf...@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> >> <http://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 >> >> >> >> ______________________________**_________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. > If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >
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