Hi,<br><br>I am processing the anatomical monkey brain now. <br>When recon-all runs, it stops at the step of &quot;mris_fix_topology&quot;<br><br>I inserted the last part of my recon-all.log below:<br><br>It stops at  &quot;CORRECTING DEFECT 0 (vertices=65691, convex hull=4296)&quot;<br>
for more than 12 hours. Does this step take that long? Or are there some problems in the data that make freesurfer idling?<br><br>Thanks,<br><br>Yang  <br><br><br><br>#--------------------------------------------<br>#@# Fix Topology lh Sat Dec  4 17:01:16 EST 2010<br>
<br> cp ../surf/lh.orig.nofix ../surf/lh.orig <br><br><br> cp ../surf/lh.inflated.nofix ../surf/lh.inflated <br><br>/home/yang/091017Castor/scripts<br><br> mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 091017Castor lh <br>
<br>reading spherical homeomorphism from &#39;qsphere.nofix&#39;<br>using genetic algorithm with optimized parameters<br>setting seed for random number genererator to 1234<br><br>*************************************************************<br>
Topology Correction Parameters<br>retessellation mode:           genetic search<br>number of patches/generation : 10<br>number of generations :        10<br>surface mri loglikelihood coefficient :         1.0<br>volume mri loglikelihood coefficient :          10.0<br>
normal dot loglikelihood coefficient :          1.0<br>quadratic curvature loglikelihood coefficient : 1.0<br>volume resolution :                             2<br>eliminate vertices during search :              1<br>initial patch selection :                       1<br>
select all defect vertices :                    0<br>ordering dependant retessellation:              0<br>use precomputed edge table :                    0<br>smooth retessellated patch :                    2<br>match retessellated patch :                     1<br>
verbose mode :                                  0<br><br>*************************************************************<br>INFO: assuming .mgz format<br>$Id: mris_fix_topology.c,v 1.43 2007/01/05 16:57:16 nicks Exp $<br>  $Id: mrisurf.c,v 1.557.2.19 2009/08/05 22:10:21 nicks Exp $<br>
before topology correction, eno=-810 (nv=213660, nf=428940, ne=643410, g=406)<br>using quasi-homeomorphic spherical map to tessellate cortical surface...<br><br>Correction of the Topology<br>Finding true center and radius of Spherical Surface...done<br>
Surface centered at (0,0,0) with radius 100.0 in 9 iterations<br>marking ambiguous vertices...<br>156279 ambiguous faces found in tessellation<br>segmenting defects...<br>64 defects found, arbitrating ambiguous regions...<br>
analyzing neighboring defects...<br>      -merging segment 14 into 0<br>      -merging segment 11 into 10<br>      -merging segment 23 into 18<br>      -merging segment 33 into 22<br>      -merging segment 40 into 22<br>      -merging segment 62 into 25<br>
      -merging segment 39 into 34<br>      -merging segment 35 into 46<br>56 defects to be corrected <br>0 vertices coincident<br>reading input surface /home/yang/091017Castor/surf/lh.qsphere.nofix...<br>reading brain volume from brain...<br>
reading wm segmentation from wm...<br>Computing Initial Surface Statistics<br>      -face       loglikelihood: -8.8048  (-4.4024)<br>      -vertex     loglikelihood: -5.5855  (-2.7928)<br>      -normal dot loglikelihood: -3.4654  (-3.4654)<br>
      -quad curv  loglikelihood: -5.6070  (-2.8035)<br>      Total Loglikelihood : -23.4627<br><br>CORRECTING DEFECT 0 (vertices=65691, convex hull=4296)<br><br>