Hi Falk
you are almost certainly running into a problem with some MAX number of defects/faces or something. If you upload the subject dir I'll fix it
cheers Bruce On Wed, 12 Oct 2016, Falk Lüsebrink wrote:
Dear all,
using mris_topo_fixer instead of mris_fix_topology also results in a segmentation fault. The command line used was:
mris_topo_fixer -mgz -warning -seed 1234 <subjID> lh
INFO: assuming .mgz format setting seed for random number genererator to 1234 reading input surface /surf/lh.orig... Before topology correction, eno=-2042 (nv=2743306, nf=5490696, ne=8236044, g=1022) Surface Diagnostics: eno=-2042 (nv=2743306, nf=5490696, ne=8236044) # 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 1022 loops (X=-2042)
Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 15 iterations identify defects... marking ambiguous vertices... 1475515 ambiguous faces found in tessellation segmenting defects... Segmentation fault
Any suggestions or tips are highly appreciated.
Best,
Falk
Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Falk Lüsebrink Gesendet: Donnerstag, 6. Oktober 2016 17:51 An: Freesurfer support list Betreff: [Freesurfer] [Dev Build] Processing very high resolution dataset
Dear all,
I am currently trying to process a MPRAGE with an isotropic resolution of 250 µm acquired in vivo. Downsampling the data to .5 and 1 mm resulted in no errors and surfaces look good.
However, while processing the data at native resolution I receive a segmentation fault during topology fixation. May this be related to the number of vertices / faces? Surfaces look okay and not totally corrupted. Memory and disk space are available plentiful.
INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.50 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781 2016/06/13 21:20:50 fischl Exp $ before topology correction, eno=-2042 (nv=2743306, nf=5490696, ne=8236044, g=1022) using quasi-homeomorphic spherical map to tessellate cortical surface...
Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 11 iterations marking ambiguous vertices... 1461809 ambiguous faces found in tessellation segmenting defects... Segmentation fault
Uploading of the dataset is currently not possible.
Best,
Falk