Hi Joon
the last defect is pretty big. Did you check the filled.mgz to make sure that nothing is drastically wrong such as the skull or cerebellum being attached to cortex?
cheers Bruce On Mon, 22 Feb 2010, Joonkoo Park wrote:
Dear FreeSurfers,
I got an error during Fix Topology step (seems like from the right hemisphere) in the recon-all process (see below for more information).
I searched the ListServ and learned from other email threads that this may be due to incorrect segmentation of WM or Cerebellum, or possibly from skull stripping. I tried to follow the tutorial on manually fixing topological defects (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect). However, I wasn't sure what to look for because my current result does not yet have rh.white which allows to view WM segmentation in tkmedit window (or am I right?).
What shall I do at this point? I'm very new to FreeSurfer, so it'd be great if anyone can give me some step-by-step approaches to troubleshoot this.
Thanks.
Joon
##### RELEVANT ERROR MESSAGE ######
#@# Fix Topology rh Sun Feb 21 12:55:08 EST 2010
cp ../surf/rh.orig.nofix ../surf/rh.orig
cp ../surf/rh.inflated.nofix ../surf/rh.inflated
/net/raid/FSsubjdir/f06/scripts
mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 f06 rh
reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234
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 1.557.2.19 2009/08/05 22:10:21 nicks Exp $ before topology correction, eno=-198 (nv=92924, nf=186244, ne=279366, g=100) 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 10 iterations marking ambiguous vertices... 46227 ambiguous faces found in tessellation segmenting defects... 82 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 66 into 61 -merging segment 75 into 73 80 defects to be corrected 0 vertices coincident reading input surface /net/raid/FSsubjdir/f06/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -7.8224 (-3.9112) -vertex loglikelihood: -6.6098 (-3.3049) -normal dot loglikelihood: -3.5417 (-3.5417) -quad curv loglikelihood: -5.7498 (-2.8749) Total Loglikelihood : -23.7237
CORRECTING DEFECT 0 (vertices=1720, convex hull=297) After retessellation of defect 0, euler #=-75 (68065,200835,132695) : difference with theory (-77) = -2
CORRECTING DEFECT 1 (vertices=103, convex hull=30) After retessellation of defect 1, euler #=-74 (68071,200866,132721) : difference with theory (-76) = -2
CORRECTING DEFECT 2 (vertices=282, convex hull=188) After retessellation of defect 2, euler #=-73 (68153,201199,132973) : difference with theory (-75) = -2
CORRECTING DEFECT 3 (vertices=19, convex hull=22) After retessellation of defect 3, euler #=-72 (68155,201211,132984) : difference with theory (-74) = -2
CORRECTING DEFECT 4 (vertices=775, convex hull=174) After retessellation of defect 4, euler #=-71 (68194,201406,133141) : difference with theory (-73) = -2
CORRECTING DEFECT 5 (vertices=40, convex hull=28) After retessellation of defect 5, euler #=-70 (68197,201426,133159) : difference with theory (-72) = -2
CORRECTING DEFECT 6 (vertices=30, convex hull=83) After retessellation of defect 6, euler #=-69 (68211,201499,133219) : difference with theory (-71) = -2
CORRECTING DEFECT 7 (vertices=140, convex hull=98) After retessellation of defect 7, euler #=-68 (68225,201587,133294) : difference with theory (-70) = -2
CORRECTING DEFECT 8 (vertices=52, convex hull=67) After retessellation of defect 8, euler #=-67 (68245,201674,133362) : difference with theory (-69) = -2
CORRECTING DEFECT 9 (vertices=25, convex hull=60) After retessellation of defect 9, euler #=-66 (68258,201740,133416) : difference with theory (-68) = -2
CORRECTING DEFECT 10 (vertices=38, convex hull=25) After retessellation of defect 10, euler #=-65 (68261,201758,133432) : difference with theory (-67) = -2
CORRECTING DEFECT 11 (vertices=21, convex hull=28) After retessellation of defect 11, euler #=-64 (68265,201780,133451) : difference with theory (-66) = -2
CORRECTING DEFECT 12 (vertices=103, convex hull=112) After retessellation of defect 12, euler #=-63 (68314,201983,133606) : difference with theory (-65) = -2
CORRECTING DEFECT 13 (vertices=78, convex hull=78) After retessellation of defect 13, euler #=-62 (68346,202110,133702) : difference with theory (-64) = -2
CORRECTING DEFECT 14 (vertices=13, convex hull=20) After retessellation of defect 14, euler #=-61 (68347,202118,133710) : difference with theory (-63) = -2
CORRECTING DEFECT 15 (vertices=20, convex hull=39) After retessellation of defect 15, euler #=-60 (68359,202164,133745) : difference with theory (-62) = -2
CORRECTING DEFECT 16 (vertices=20, convex hull=28) After retessellation of defect 16, euler #=-59 (68360,202177,133758) : difference with theory (-61) = -2
CORRECTING DEFECT 17 (vertices=71, convex hull=37) After retessellation of defect 17, euler #=-58 (68363,202198,133777) : difference with theory (-60) = -2
CORRECTING DEFECT 18 (vertices=37, convex hull=24) After retessellation of defect 18, euler #=-57 (68367,202217,133793) : difference with theory (-59) = -2
CORRECTING DEFECT 19 (vertices=56, convex hull=89) After retessellation of defect 19, euler #=-56 (68376,202281,133849) : difference with theory (-58) = -2
CORRECTING DEFECT 20 (vertices=132, convex hull=25) After retessellation of defect 20, euler #=-55 (68385,202313,133873) : difference with theory (-57) = -2
CORRECTING DEFECT 21 (vertices=90, convex hull=37) After retessellation of defect 21, euler #=-54 (68392,202347,133901) : difference with theory (-56) = -2
CORRECTING DEFECT 22 (vertices=432, convex hull=137) After retessellation of defect 22, euler #=-53 (68486,202692,134153) : difference with theory (-55) = -2
CORRECTING DEFECT 23 (vertices=505, convex hull=86) After retessellation of defect 23, euler #=-52 (68512,202807,134243) : difference with theory (-54) = -2
CORRECTING DEFECT 24 (vertices=479, convex hull=166) After retessellation of defect 24, euler #=-51 (68584,203106,134471) : difference with theory (-53) = -2
CORRECTING DEFECT 25 (vertices=531, convex hull=71) After retessellation of defect 25, euler #=-50 (68614,203224,134560) : difference with theory (-52) = -2
CORRECTING DEFECT 26 (vertices=12, convex hull=30) After retessellation of defect 26, euler #=-49 (68615,203234,134570) : difference with theory (-51) = -2
CORRECTING DEFECT 27 (vertices=35, convex hull=29) After retessellation of defect 27, euler #=-48 (68619,203253,134586) : difference with theory (-50) = -2
CORRECTING DEFECT 28 (vertices=32, convex hull=23) After retessellation of defect 28, euler #=-47 (68620,203263,134596) : difference with theory (-49) = -2
CORRECTING DEFECT 29 (vertices=39, convex hull=31) After retessellation of defect 29, euler #=-46 (68622,203285,134617) : difference with theory (-48) = -2
CORRECTING DEFECT 30 (vertices=8943, convex hull=1769) normal vector of length zero at vertex 73856 with 0 faces vertex 73856 has 0 face Numerical result out of range Linux ***** 2.6.18-164.6.1.el5 #1 SMP Tue Oct 27 11:28:30 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Sun Feb 21 13:38:23 EST 2010 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer