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 <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> > 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 > > > > 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 . 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. > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
