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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> >> <http://clk.atdmt.com/GBL/go/201469230/direct/01/>
> >> ------------------------------------------------------------------------
> >>
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> >
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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>
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