Hi All,<div>I am  running  recon-all  on a  set of  Diff  images since last  2  days and  it looks like FS stopped  working.It  says correcting defect 0  since  yesterday afternoon.</div><div><div>Any way to  figure whats going on?</div>
<div>Many Thanks</div><div>Chikku</div></div><div><br></div><div><br></div><div><div>#@# Fix Topology lh Tue Apr 16 14:47:22 CEST 2013</div><div>\n cp ../surf/lh.orig.nofix ../surf/lh.orig \n</div><div>\n cp ../surf/lh.inflated.nofix ../surf/lh.inflated \n</div>
<div>/Applications/freesurfer/subjects/Diff1/scripts</div><div>\n mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 Diff1 lh \n</div><div>reading spherical homeomorphism from &#39;qsphere.nofix&#39;</div><div>using genetic algorithm with optimized parameters</div>
<div>setting seed for random number genererator to 1234</div><div><br></div><div>*************************************************************</div><div>Topology Correction Parameters</div><div>retessellation mode:           genetic search</div>
<div>number of patches/generation : 10</div><div>number of generations :        10</div><div>surface mri loglikelihood coefficient :         1.0</div><div>volume mri loglikelihood coefficient :          10.0</div><div>normal dot loglikelihood coefficient :          1.0</div>
<div>quadratic curvature loglikelihood coefficient : 1.0</div><div>volume resolution :                             2</div><div>eliminate vertices during search :              1</div><div>initial patch selection :                       1</div>
<div>select all defect vertices :                    0</div><div>ordering dependant retessellation:              0</div><div>use precomputed edge table :                    0</div><div>smooth retessellated patch :                    2</div>
<div>match retessellated patch :                     1</div><div>verbose mode :                                  0</div><div><br></div><div>*************************************************************</div><div>INFO: assuming .mgz format</div>
<div>$Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $</div><div>  $Id: mrisurf.c,v 1.693.2.4 2012/11/07 22:38:00 nicks Exp $</div><div>before topology correction, eno=-340 (nv=73648, nf=147976, ne=221964, g=171)</div>
<div>using quasi-homeomorphic spherical map to tessellate cortical surface...</div><div><br></div><div>Correction of the Topology</div><div>Finding true center and radius of Spherical Surface...done</div><div>Surface centered at (0,0,0) with radius 100.0 in 12 iterations</div>
<div>marking ambiguous vertices...</div><div>82800 ambiguous faces found in tessellation</div><div>segmenting defects...</div><div>41 defects found, arbitrating ambiguous regions...</div><div>analyzing neighboring defects...</div>
<div>      -merging segment 2 into 0</div><div>      -merging segment 10 into 0</div><div>      -merging segment 32 into 15</div><div>      -merging segment 19 into 16</div><div>      -merging segment 38 into 40</div><div>
36 defects to be corrected </div><div>0 vertices coincident</div><div>reading input surface /Applications/freesurfer/subjects/Diff1/surf/lh.qsphere.nofix...</div><div>reading brain volume from brain...</div><div>reading wm segmentation from wm...</div>
<div>Computing Initial Surface Statistics</div><div>      -face       loglikelihood: -8.8449  (-4.4225)</div><div>      -vertex     loglikelihood: -7.8841  (-3.9420)</div><div>      -normal dot loglikelihood: -3.5035  (-3.5035)</div>
<div>      -quad curv  loglikelihood: -6.1723  (-3.0862)</div><div>      Total Loglikelihood : -26.4048</div><div><br></div><div>CORRECTING DEFECT 0 (vertices=30266, convex hull=4754)</div><div> </div></div><div><br></div>