Hi Sasha,
check to see if the cerebellum or skull is attached. An initial euler number of -1360 is ridiculous (probably shouldn't be <-100)
Bruce
On Thu, 10 Nov 2005, Sasha Wolosin wrote:
Dear all, I ran into a problem with the mris_fix_topology step of recon-all. Below is the output of mris_fix_topology. Does anyone know what this might mean? Any help is greatly appreciated, Thanks, Sasha
Fix Topology lh Wed Nov 9 23:53:11 EST 2005 /data/Sasha_subjects/0248_corffe/scripts mris_fix_topology 0248_corffe lh
Setting options
Topology Correction Parameters retessellation mode : greedy search ordering dependant retessellation: 0 initial patch selection : 0 use precomputed edge table : 0 smooth retessellated patch : 0 match retessellated patch : 0 verbose mode : 0
reading input surface /data/Sasha_subjects/0248_corffe/surf/lh.qsphere... INFO: Volume /tmp/mritotal_24375/nu_8_dxyz.mnc cannot be found. INFO: found the orig volume info on /data/Sasha_subjects/0248_corffe/mri/filled in the surface data. before topology correction, eno=-1360 (nv=257430, nf=517668, ne=776458, g=681) using quasi-homeomorphic spherical map to tessellate cortical surface... Too many intersected faces for face 347232 (171859, 173622, 173623) No such file or directory reading T1 volume from T1... reading wm segmentation from wm...
Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 14 iterations marking ambiguous vertices... ERROR: mris_fix_topology exited with non-zero status
Filesystem 1K-blocks Used Available Use% Mounted on /dev/sdb7 136908624 11451328 118388296 9% /data
recon-all exited with errors at Wed Nov 9 23:55:36 EST 2005
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