Hello Freesurfer Experts,
I ran into the following error when running Freesurfer for one of our
subjects, during:
mris_fix_topology -mgz -sphere qsphere.nofix -ga FirstOrderPoly lh
I could only find a partial answer to a previous post on a similar
problem - pasted at the end. Following that, I looked at lh.orig.nofix
surface - screenshots attached. I am not sure whether its alright. No
rh surfaces were created.
Please let me know how to correct this problem and proceed further.
Quick response will be greatly appreciated,
Pradeep
======= Tail end of scripts/recon-all.log ==========
#--------------------------------------------
#...@# Fix Topology lh Fri Feb 27 19:29:56 PST 2009
cp ../surf/lh.orig.nofix ../surf/lh.orig
cp ../surf/lh.inflated.nofix ../surf/lh.inflated
/ensc/CORTEX/PROJECTS/UNSW/WEIWEN_PARF/PROCESSED_DATA/scanner_differences/FirstOrderPoly/scripts
mris_fix_topology -mgz -sphere qsphere.nofix -ga FirstOrderPoly lh
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 1.43 2007/01/05 16:57:16 nicks Exp $
$Id: mrisurf.c,v 1.557.2.10 2008/03/10 13:59:45 nicks Exp $
before topology correction, eno=-264 (nv=105340, nf=211208, ne=316812, g=133)
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 8 iterations
marking ambiguous vertices...
45195 ambiguous faces found in tessellation
segmenting defects...
81 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
-merging segment 6 into 0
-merging segment 7 into 0
-merging segment 0 into 18
-merging segment 39 into 28
-merging segment 37 into 30
-merging segment 54 into 46
-merging segment 53 into 59
-merging segment 72 into 64
-merging segment 71 into 70
72 defects to be corrected
0 vertices coincident
reading input surface
/ensc/CORTEX/PROJECTS/UNSW/WEIWEN_PARF/PROCESSED_DATA/scanner_differences/FirstOrderPoly/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
-face loglikelihood: -9.2008 (-4.6004)
-vertex loglikelihood: -6.9827 (-3.4913)
-normal dot loglikelihood: -3.5884 (-3.5884)
-quad curv loglikelihood: -6.0560 (-3.0280)
Total Loglikelihood : -25.8279
CORRECTING DEFECT 0 (vertices=73, convex hull=66)
After retessellation of defect 0, euler #=-61 (80515,236855,156279) :
difference with theory (-69) = -8
CORRECTING DEFECT 1 (vertices=212, convex hull=29)
After retessellation of defect 1, euler #=-60 (80531,236912,156321) :
difference with theory (-68) = -8
CORRECTING DEFECT 2 (vertices=14, convex hull=24)
After retessellation of defect 2, euler #=-59 (80534,236928,156335) :
difference with theory (-67) = -8
CORRECTING DEFECT 3 (vertices=10731, convex hull=2557)
normal vector of length zero at vertex 90051 with 0 faces
vertex 90051 has 0 face
No such file or directory
Linux ilpc9.cs.sfu.ca 2.6.18-92.1.22.el5 #1 SMP Tue Dec 16 11:57:43
EST 2008 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Fri Feb 27 21:07:28 PST 2009
========================================
------------------ Previous post with a similar problem -------------------
[Freesurfer] Problem with latest dev version (crashes correcting errors)
Tim Jarvis jarv0075 at umn.edu
Mon Feb 6 12:41:21 EST 2006
* Previous message: [Freesurfer] Problem with latest dev version
(crashes correcting errors)
* Next message: [Freesurfer] Problem with latest dev version
(crashes correctingerrors)
* Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
For the lh, there is no cerebellum and no skull, looks to be correct.
I don't see any rh* files though?
brewster 14%> ls
/data/brewster2/tjarvis/thesis_data/software/freesurfer/subjects/icbm/surf/
lh.defect_borders lh.defect_chull lh.defect_labels lh.inflated
lh.inflated.nofix lh.orig lh.orig.nofix lh.qsphere.nofix
lh.smoothwm.nofix
On 6 Feb 2006, Bruce Fischl wrote:
> yes, mri_ca_register takes a long time. The good news is it works really
> well :>. As for the mris_topology_fixing problem, what does the
> ?h.orig.nofix surface look like? Does it include cerebellum or skull?
Does
> it look approximately correct?
>
> On Mon, 6 Feb 2006, Tim Jarvis wrote:
>
> > Gave the new dev version a spin with autorecon-all, couple of things...
> >
> > For the mri_ca_register step, it took a total of 791 minutes! Is this
> > normal or could this be a hint as to things going wrong early in the
> > pipeline?
> >
> > Also, the program eventually crashed during the error correction, below
are
> > the lines that seem like they may have had some effect:
> >
> > Anyone else experience this problem?
> >
> >
> >
> > Thanks
> >
--
Pradeep Kumar Reddy. Raamana
PhD Student - Biomedical Engg.
Medical Image Analysis Lab,
Simon Fraser University,
Burnaby BC - V5A1S6 - Canada.
Work : +1 778 782 5509
Freedom from the desire for an answer is essential to the
understanding of a problem - Jiddu Krishnamurti
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
