Hi Martin
see my response to a similar question just a minute or two ago. This is the same issue (a defect that is too big)
cheers Bruce On Thu, 7 Nov 2013, Martin Luessi wrote:
Hi,
I'm running recon-all on a subject from the human connectome project, and for some reason "mris_fix_topology" seems to be hanging, or at least it has been using 100% of a CPU for more than 24h with no new output. Is this normal or is there a way to fix this problem?
Best,
Martin
PS: I'm using FS 5.3
... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 28 iterations marking ambiguous vertices... 127679 ambiguous faces found in tessellation segmenting defects... 1 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 1 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/fusion/mluessi/hcp_data/subjects/100307/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -10.9679 (-5.4839) -vertex loglikelihood: -10.8878 (-5.4439) -normal dot loglikelihood: -3.6700 (-3.6700) -quad curv loglikelihood: -8.7258 (-4.3629) Total Loglikelihood : -34.2514
CORRECTING DEFECT 0 (vertices=65102, convex hull=346) _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer