External Email - Use Caution
Hi,
I got the following error running mris_topo_fixer:
~$ mris_topo_fixer -mgz -warnings ANTS6-0Months3T lh INFO: assuming .mgz format verbose mode on (medium mode): printing warnings reading input surface /usr/local/freesurfer/subjects/ANTS6-0Months3T/work/ANTS6-0Months3T/surf/lh.orig... Before topology correction, eno=0 (nv=43656, nf=87312, ne=130968, g=1) Surface Diagnostics: eno=0 (nv=43656, nf=87312, ne=130968) # of border vertices [ #v ~ #f ] 0 # of edges with single face 0 # of edges with more than 2 faces 0 # of corner configurations 0 The original surface is a valid manifold Counting the number of connected components The original surface has one component The original surface does not self-intersect
The surface has 1 loops (X=0)
Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations identify defects... marking ambiguous vertices... 1527 ambiguous faces found in tessellation segmenting defects... analyzing defects for overlaps... reading brain volume from brain... reading wm segmentation from wm... Detecting contrast direction: right direction [ GM (129.46) < WM (134.73) ] ASSERTION FAILED: /local_mount/space/terrier/2/terrier_nightly_build/trunk/ah221-infant/utils/mrisurf_topology.c:1002 vt->nsizeMax > 0 ASSERTION FAILED: /local_mount/space/terrier/2/terrier_nightly_build/trunk/ah221-infant/utils/mrisurf_topology.c:1002 vt->nsizeMax > 0 Segmentation fault (core dumped)
Any idea what in the data file could cause the assert "vt->nsizeMax > 0" to be triggered? Any idea how to go around it?
Thank you,
Christian
Hi Christian, if you send me that surface, I can take a look at what's going wrong.
best Andrew
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Christian O'Reilly, Dr christian.oreilly@mcgill.ca Sent: Thursday, January 16, 2020 9:57 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Segfault in mris_topo_fixer
External Email - Use Caution
Hi,
I got the following error running mris_topo_fixer:
~$ mris_topo_fixer -mgz -warnings ANTS6-0Months3T lh INFO: assuming .mgz format verbose mode on (medium mode): printing warnings reading input surface /usr/local/freesurfer/subjects/ANTS6-0Months3T/work/ANTS6-0Months3T/surf/lh.orig... Before topology correction, eno=0 (nv=43656, nf=87312, ne=130968, g=1) Surface Diagnostics: eno=0 (nv=43656, nf=87312, ne=130968) # of border vertices [ #v ~ #f ] 0 # of edges with single face 0 # of edges with more than 2 faces 0 # of corner configurations 0 The original surface is a valid manifold Counting the number of connected components The original surface has one component The original surface does not self-intersect
The surface has 1 loops (X=0)
Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations identify defects... marking ambiguous vertices... 1527 ambiguous faces found in tessellation segmenting defects... analyzing defects for overlaps... reading brain volume from brain... reading wm segmentation from wm... Detecting contrast direction: right direction [ GM (129.46) < WM (134.73) ] ASSERTION FAILED: /local_mount/space/terrier/2/terrier_nightly_build/trunk/ah221-infant/utils/mrisurf_topology.c:1002 vt->nsizeMax > 0 ASSERTION FAILED: /local_mount/space/terrier/2/terrier_nightly_build/trunk/ah221-infant/utils/mrisurf_topology.c:1002 vt->nsizeMax > 0 Segmentation fault (core dumped)
Any idea what in the data file could cause the assert "vt->nsizeMax > 0" to be triggered? Any idea how to go around it?
Thank you,
Christian
freesurfer@nmr.mgh.harvard.edu
-
Christian O'Reilly, Dr -
Hoopes, Andrew