Hi everyone,
I'm using recon-all to flatten a number of scans from patients and
controls. Most of them work fine, but there are 3 that do not
reconstruct correctly. They all seem to share the same problem:
Recon-all aborts during the automatic topology correction step, and
there's a line in the log saying mrisDefectAnalysis : defect XXX overlap
defect YYY.
I've checked registration to talairach, skull strip and initial
surfaces, the only thing I could see was that in some cases, bits of the
superior sagittal sinus were wrongly included in the lh.orig.nofix, or
small bits of dura, but nothing major.
I'm attaching the relevant output from the topology fixer for two
different cases. I would be grateful if someone could point me at other
things to try. Is it possible to visualise the defects' locations, so I
could find out which defect is actually causing the overlap message?
Thanks for your help everyone,
Johannes
----------
CASE 1
#@# Fix Topology lh Wed Jun 14 04:04:29 BST 2006
\n cp ../surf/lh.orig.nofix ../surf/lh.orig \n
\n cp ../surf/lh.inflated.nofix ../surf/lh.inflated \n
/Volumes/JalapenoSAN/Scratch/natalie/schizophrenia/fs/PAT_2280/scripts
\n mris_fix_topology -mgz -sphere qsphere.nofix -ga PAT_2280 lh \n
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 1.41 2006/02/06 19:41:59 nicks Exp $
$Id: mrisurf.c,v 1.441.2.1 2006/03/06 21:12:31 greve Exp $
before topology correction, eno=-656 (nv=197397, nf=396220, ne=594273,
g=329)
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 9 iterations
marking ambiguous vertices...
30743 ambiguous faces found in tessellation
segmenting defects...
defect 6 : 7 vertices have been added to the surface
[ ... ]
defect 314 : 2 vertices have been added to the surface
total of 95 vertices has been added to the surface
analyzing defects...
mrisDefectAnalysis : defect 277 overlap defect 272
reading input surface
/Volumes/JalapenoSAN/Scratch/natalie/schizophrenia/fs/PAT_2280/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Darwin jalapeno6.fmrib.ox.ac.uk 8.6.0 Darwin Kernel Version 8.6.0: Tue
Mar 7 16:58:48 PST 2006; root:xnu-792.6.70.obj~1/RELEASE_PPC Power
Macintosh powerpc
recon-all exited with ERRORS at Wed Jun 14 04:08:10 BST 2006
CASE 2
#@# Fix Topology rh Thu Jun 15 12:13:05 BST 2006
\n cp ../surf/rh.orig.nofix ../surf/rh.orig \n
\n cp ../surf/rh.inflated.nofix ../surf/rh.inflated \n
/Volumes/JalapenoSAN/Scratch/natalie/schizophrenia/fs/PAT_3509/scripts
\n mris_fix_topology -mgz -sphere qsphere.nofix -ga PAT_3509 rh \n
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 1.41 2006/02/06 19:41:59 nicks Exp $
$Id: mrisurf.c,v 1.441.2.1 2006/03/06 21:12:31 greve Exp $
before topology correction, eno=-2025 (nv=252518, nf=509180, ne=763723,
g=1013)
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 13 iterations
marking ambiguous vertices...
137391 ambiguous faces found in tessellation
segmenting defects...
defect 12 : 4 vertices have been added to the surface
[ ... ]
defect 440 : 4 vertices have been added to the surface
total of 340 vertices has been added to the surface
analyzing defects...
mrisDefectAnalysis : defect 395 overlap defect 393
reading input surface
/Volumes/JalapenoSAN/Scratch/natalie/schizophrenia/fs/PAT_3509/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Darwin jalapeno4.fmrib.ox.ac.uk 8.6.0 Darwin Kernel Version 8.6.0: Tue
Mar 7 16:58:48 PST 2006; root:xnu-792.6.70.obj~1/RELEASE_PPC Power
Macintosh powerpc
recon-all exited with ERRORS at Thu Jun 15 12:19:26 BST 2006