Definitely, I will repost this on Monday.
Thanks, -Siddharth
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Thursday, February 20, 2014 1:46 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Topological defect
Hi Siddharth, Bruce will have to answer this one. He's on vacation until next week. Can you repost on monday? doug
On 02/20/2014 11:21 AM, Ray, Siddharth wrote:
Hi all,
I am having an topological defect error while running few of subjects. I have gone through the freesurfer correcting topological defects wikipage. But I was trying understand the log file. For an example, I got the following error for one subject:
Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 13 iterations
marking ambiguous vertices...
70557 ambiguous faces found in tessellation
segmenting defects...
78 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
-merging segment 19 into 0
-merging segment 22 into 0
-merging segment 68 into 49
-merging segment 61 into 55
74 defects to be corrected
0 vertices coincident
reading input surface /work/02510/sray2/Free_Sub/DATA/50011/50011/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
-face loglikelihood: -8.4264 (-4.2132)
-vertex loglikelihood: -5.7733 (-2.8866)
-normal dot loglikelihood: -3.6047 (-3.6047)
-quad curv loglikelihood: -6.1117 (-3.0559)
Total Loglikelihood : -23.9161
CORRECTING DEFECT 0 (vertices=27967, convex hull=5893)
Segmentation fault
mris_euler_number ../surf/lh.orig
mris_fix_topology failed! (euler number != 2)
Trying mris_topo_fixer...
cp ../surf/lh.orig.nofix ../surf/lh.orig
euler # = v-e+f = 2g-2: 116732 - 351516 + 234344 = -440 --> 221 holes
F =2V-4: 234344 != 233464-4 (-884)
2E=3F: 703032 = 703032 (0)
total defect index = 442
cp ../surf/lh.qsphere.nofix ../surf/lh.qsphere
cp ../surf/lh.smoothwm.nofix ../surf/lh.smoothwm
/work/02510/sray2/Free_Sub/DATA/50011/50011/scripts
mris_topo_fixer -mgz -warnings -seed 1234 50011 lh
verbose mode on (medium mode): printing warnings
setting seed for random number genererator to 1234
Before topology correction, eno=-440 (nv=116732, nf=234344, ne=351516, g=221)
Surface Diagnostics:
eno=-440 (nv=116732, nf=234344, ne=351516)
# of border vertices [ #v ~ #f ] 0
# of edges with single face 0
# of edges with more than 2 faces 0
# of corner configurations 0
The original surface is a valid manifold
Counting the number of connected components
The original surface has one component
The original surface does not self-intersect
The surface has 221 loops (X=-440)
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 9 iterations
identify defects...
marking ambiguous vertices...
68425 ambiguous faces found in tessellation
segmenting defects...
analyzing defects for overlaps...
INFO: assuming .mgz format
reading input surface /work/02510/sray2/Free_Sub/DATA/50011/50011/surf/lh.orig...
reading brain volume from brain...
reading wm segmentation from wm...
Detecting contrast direction: right direction [ GM (86.66) < WM (96.03) ]
Computing Initial Surface Statistics
-face loglikelihood: -5.8578 (-2.9289)
-vertex loglikelihood: -5.7524 (-2.8762)
-normal dot loglikelihood: -3.6033 (-3.6033)
-quad curv loglikelihood: -5.8101 (-2.9050)
Total Loglikelihood : -21.0236
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
Correcting Topology of defect 1 with euler number -257 (129 loops)
computing statistics for defect 1: 33364 vertices
location: [ (156,125,84) - average intensity = 92.126 ]
-gray ( 86.57 , 6.29 ) -white ( 95.91 , 6.08 )
-gray ( 89.98 , 24.95 ) -white ( 98.58 , 24.03 )
-intensity (86.574921 [log = -2.404119 ]- 95.914825 [log = -2.517448 ])
-curv (k1=-0.162 (0.730) , r1 = 6.179 | k2=-0.060 (0.191), r2 = 16.806 )
-curv (k1=-0.124 (0.768) , r1 = 8.076 | k2=-0.032 (0.282), r2 = 31.306 )
MRISalloc(8654176, 520): could not allocate vertices
Cannot allocate memory
And In some of my subjects the log file stop writing after: "CORRECTING DEFECT 0 (vertices=53786, convex hull=13985)"
My question is what exactly these highlighted number means? Do I have an estimation of number of slices that are to be treated manually?
Thanks,
-Siddharth
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