Sorry, the screenshots are attached now.
Pradeep
---------- Forwarded message ---------- From: Pradeep Reddy Ramana pkr1@sfu.ca Date: Sun, Mar 1, 2009 at 8:23 PM Subject: Normal vector of length zero To: freesurfer@nmr.mgh.harvard.edu Cc: Faisal Beg mfbeg@ensc.sfu.ca
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
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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
