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-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@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


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