Hello, Doug,
Yeah, I think so. Please see the attached figs. How can I fix the problem?
Thanks! Guang
Date: Thu, 18 Feb 2010 10:38:35 -0500 From: greve@nmr.mgh.harvard.edu To: freesurfer_zg@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] cross-sectional analyis error
Sorry, not the skull strip, but the filled.mgz
Douglas N Greve wrote:
Check the skull strip to see if the cerebellum is still attached.
doug
Guang Zeng wrote:
Hi, there,
I am testing two subjects using cross-sectional FS. Both of they have being processed for almost four days. Both of them are stuck at the mris_fix_topology step, but there is no error message pops up.
Subject#1
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=-132 (nv=182824, nf=365912, ne=548868, g=67) 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 11 iterations marking ambiguous vertices... 71554 ambiguous faces found in tessellation segmenting defects... 39 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 22 into 9 -merging segment 29 into 27 37 defects to be corrected 0 vertices coincident reading input surface /data1/radiology/m047599/subjects/027_S_0408_20060510/surf/lh.qsphere.nofix...
reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2222 (-4.6111) -vertex loglikelihood: -6.1352 (-3.0676) -normal dot loglikelihood: -3.5992 (-3.5992) -quad curv loglikelihood: -5.8849 (-2.9424) Total Loglikelihood : -24.8415
CORRECTING DEFECT 0 (vertices=30671, convex hull=1376)
Subject#2
Correcting Topology of defect 2 with euler number 1 (0 loops) Nothing to correct for defect 2!! AFTER CORRECTION, EULER IS -262 Surface Diagnostics: eno=-262 (nv=157710, nf=315944, ne=473916) # of border vertices [ #v ~ #f ] 0 # of edges with single face 0 # of edges with more than 2 faces 0 # of corner configurations 0
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX Correcting Topology of defect 3 with euler number -219 (110 loops) computing statistics for defect 3: 23911 vertices location: [ (168,58,111) - average intensity = 83.612 ] -gray ( 77.29 , 6.14 ) -white ( 93.87 , 3.59 ) -gray ( 79.92 , 20.78 ) -white ( 95.75 , 18.72 ) -intensity (77.286301 [log = -2.730186 ]- 93.865768 [log = -2.235836 ]) -curv (k1=-0.170 (0.615) , r1 = 5.894 | k2=-0.052 (0.142), r2 = 19.402 ) -curv (k1=-0.138 (0.656) , r1 = 7.230 | k2=-0.024 (0.219), r2 = 41.547 ) max face = 47468(47468) - loop = 1 (110) - ntries = [18,18997]
BEST FITNESS (o)is -9.95545 mri =0.000 curv = 0.865 unmri = 6.496 ( f=0.00 , v=0.00 , c=0.86 , q= 1.73 ) ( f=0.00 , v=0.00 , c=0.86 , q= 1.73 )
BEST FITNESS (M) is 14.81362 mri =0.000 curv = 0.886 unmri = -18.358 ( f=0.00 , v=0.00 , c=0.89 , q= 1.77 ) ( f=0.00 , v=0.00 , c=0.89 , q= 1.77 )Could any one tell me how to fix this problem, is there a method to ignore this fix_topology step?
Thanks! Guang
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