Hi, I'm having problems reconstructing the surface for one individual on an older version of recon-all (v. 1.104). It always seems to exit with no error message during mris_fix_topology. I've tried to re-run this subject several times, and even starting from scratch does not seem to help. I'm not sure why this is happening, as I've used this version of recon-all on hundreds of other images without any problem. There's no obvious difference between this image and any of the others that I can see by looking at the T1 (e.g., no apparent artifacts, etc.). I've attached recon-all.log. Any suggestions? Thanks, Alex
Alex Fornito JN Peters Research Fellow Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1861 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
Hi Alex,
the initial Euler number is huge (-609):
efore topology correction, eno=-609 (nv=178409, nf=358124, ne=537142, g=305) using quasi-homeomorphic spherical map to tessellate cortical surface...
check to see if the cerebellum or skull is attached (178409 vertices is also way too many).
cheers, Bruce
On Wed, 14 Feb 2007, Fornito, Alexander wrote:
Hi, I'm having problems reconstructing the surface for one individual on an older version of recon-all (v. 1.104). It always seems to exit with no error message during mris_fix_topology. I've tried to re-run this subject several times, and even starting from scratch does not seem to help. I'm not sure why this is happening, as I've used this version of recon-all on hundreds of other images without any problem. There's no obvious difference between this image and any of the others that I can see by looking at the T1 (e.g., no apparent artifacts, etc.). I've attached recon-all.log. Any suggestions? Thanks, Alex
Alex Fornito JN Peters Research Fellow Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1861 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
p.s. also the last defect it gets to is a really big one:
retessellating defect 105 with 13082 vertices (convex hull=6596).
which may cause it to run out of memory. In any case, my guess is something is pretty seriousll wrong with this surface.
On Wed, 14 Feb 2007, Fornito, Alexander wrote:
Hi, I'm having problems reconstructing the surface for one individual on an older version of recon-all (v. 1.104). It always seems to exit with no error message during mris_fix_topology. I've tried to re-run this subject several times, and even starting from scratch does not seem to help. I'm not sure why this is happening, as I've used this version of recon-all on hundreds of other images without any problem. There's no obvious difference between this image and any of the others that I can see by looking at the T1 (e.g., no apparent artifacts, etc.). I've attached recon-all.log. Any suggestions? Thanks, Alex
Alex Fornito JN Peters Research Fellow Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1861 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Fornito, Alexander