Hello Freesurfer Experts, I ran into the following error when running Freesurfer for one of our subjects, during:
mris_fix_topology -mgz -sphere qsphere.nofix -ga FirstOrderPoly lh I could only find a partial answer to a previous post on a similar problem - pasted at the end. Following that, I looked at lh.orig.nofix surface - screenshots attached. I am not sure whether its alright. No rh surfaces were created. Please let me know how to correct this problem and proceed further. Quick response will be greatly appreciated, Pradeep ======= Tail end of scripts/recon-all.log ========== #-------------------------------------------- #...@# Fix Topology lh Fri Feb 27 19:29:56 PST 2009 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /ensc/CORTEX/PROJECTS/UNSW/WEIWEN_PARF/PROCESSED_DATA/scanner_differences/FirstOrderPoly/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga FirstOrderPoly lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.43 2007/01/05 16:57:16 nicks Exp $ $Id: mrisurf.c,v 1.557.2.10 2008/03/10 13:59:45 nicks Exp $ before topology correction, eno=-264 (nv=105340, nf=211208, ne=316812, g=133) 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 8 iterations marking ambiguous vertices... 45195 ambiguous faces found in tessellation segmenting defects... 81 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 6 into 0 -merging segment 7 into 0 -merging segment 0 into 18 -merging segment 39 into 28 -merging segment 37 into 30 -merging segment 54 into 46 -merging segment 53 into 59 -merging segment 72 into 64 -merging segment 71 into 70 72 defects to be corrected 0 vertices coincident reading input surface /ensc/CORTEX/PROJECTS/UNSW/WEIWEN_PARF/PROCESSED_DATA/scanner_differences/FirstOrderPoly/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2008 (-4.6004) -vertex loglikelihood: -6.9827 (-3.4913) -normal dot loglikelihood: -3.5884 (-3.5884) -quad curv loglikelihood: -6.0560 (-3.0280) Total Loglikelihood : -25.8279 CORRECTING DEFECT 0 (vertices=73, convex hull=66) After retessellation of defect 0, euler #=-61 (80515,236855,156279) : difference with theory (-69) = -8 CORRECTING DEFECT 1 (vertices=212, convex hull=29) After retessellation of defect 1, euler #=-60 (80531,236912,156321) : difference with theory (-68) = -8 CORRECTING DEFECT 2 (vertices=14, convex hull=24) After retessellation of defect 2, euler #=-59 (80534,236928,156335) : difference with theory (-67) = -8 CORRECTING DEFECT 3 (vertices=10731, convex hull=2557) normal vector of length zero at vertex 90051 with 0 faces vertex 90051 has 0 face No such file or directory Linux ilpc9.cs.sfu.ca 2.6.18-92.1.22.el5 #1 SMP Tue Dec 16 11:57:43 EST 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Fri Feb 27 21:07:28 PST 2009 ======================================== ------------------ Previous post with a similar problem ------------------- [Freesurfer] Problem with latest dev version (crashes correcting errors) Tim Jarvis jarv0075 at umn.edu Mon Feb 6 12:41:21 EST 2006 * Previous message: [Freesurfer] Problem with latest dev version (crashes correcting errors) * Next message: [Freesurfer] Problem with latest dev version (crashes correctingerrors) * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] For the lh, there is no cerebellum and no skull, looks to be correct. I don't see any rh* files though? brewster 14%> ls /data/brewster2/tjarvis/thesis_data/software/freesurfer/subjects/icbm/surf/ lh.defect_borders lh.defect_chull lh.defect_labels lh.inflated lh.inflated.nofix lh.orig lh.orig.nofix lh.qsphere.nofix lh.smoothwm.nofix On 6 Feb 2006, Bruce Fischl wrote: > yes, mri_ca_register takes a long time. The good news is it works really > well :>. As for the mris_topology_fixing problem, what does the > ?h.orig.nofix surface look like? Does it include cerebellum or skull? Does > it look approximately correct? > > On Mon, 6 Feb 2006, Tim Jarvis wrote: > > > Gave the new dev version a spin with autorecon-all, couple of things... > > > > For the mri_ca_register step, it took a total of 791 minutes! Is this > > normal or could this be a hint as to things going wrong early in the > > pipeline? > > > > Also, the program eventually crashed during the error correction, below are > > the lines that seem like they may have had some effect: > > > > Anyone else experience this problem? > > > > > > > > Thanks > > -- Pradeep Kumar Reddy. Raamana PhD Student - Biomedical Engg. Medical Image Analysis Lab, Simon Fraser University, Burnaby BC - V5A1S6 - Canada. Work : +1 778 782 5509 Freedom from the desire for an answer is essential to the understanding of a problem - Jiddu Krishnamurti _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer