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
===========================================================================
=====
mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
threshold mask volume at 5 writing masked volume to brain.finalsurfs.mgz... #-------------------------------------------- #@# WM Segmentation Sat Feb 4 03:52:43 CST 2006
cp wm.mgz wm.seg.mgz
cp: cannot stat `wm.mgz': No such file or directory
mri_segment -keep brain.mgz wm.seg.mgz
preserving editing changes in output volume... doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM: 105.7 +- 6.0 [80.0 --> 125.0] GM: 74.1 +- 15.7 [30.0 --> 96.0] setting bottom of white matter range to 89.8 setting top of gray matter range to 99.7 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels...
reclassifying voxels using Gaussian border classifier...
removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 11549 sparsely connected voxels removed... thickening thin strands.... 20 segments, 3117 filled 33169 bright non-wm voxels segmented. 4836 diagonally connected voxels added... white matter segmentation took 9.5 minutes writing output to wm.seg.mgz... zcat:
/data/brewster2/tjarvis/thesis_data/software/freesurfer/subjects/icbm/mri/w
m.seg.mgz.gz: No such file or directory
mghRead(/data/brewster2/tjarvis/thesis_data/software/freesurfer/subjects/ic
bm/mri/wm.seg.mgz, -1): read error mri_segment: could not read file wm.seg.mgz to preserve edits
[.....]
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... 19500 ambiguous faces found in tessellation segmenting defects... 75 defects found, arbitrating ambiguous regions... vertex 4982: degenerate normal analyzing neighboring defects... -merging segment 8 into 1 -merging segment 25 into 24 -merging segment 40 into 39 -merging segment 43 into 41 -merging segment 59 into 54 70 defects to be corrected 0 vertices coincident SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations
[.....]
SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations SVDCMP: No convergence in 20 iterations vertex 68123: degenerate normal vertex 68123: degenerate normal vertex 68123: degenerate normal Computing Initial Surface Statistics -face loglikelihood: -8.5636 (-4.2818) -vertex loglikelihood: -5.4447 (-2.7224) -normal dot loglikelihood: -3.5627 (-3.5627) -quad curv loglikelihood: -5.1011 (-2.5506) Total Loglikelihood : -22.6721
CORRECTING DEFECT 0 (vertices=336, convex hull=171) l_mri = 1.00 l_unmri = 10.00 l_curv = 1.00 l_qcurv = 1.00 After retessellation of defect 0, euler #=-64 (187142,557809,370603) : difference with theory (-67) = -3
CORRECTING DEFECT 1 (vertices=1450, convex hull=530) After retessellation of defect 1, euler #=-64 (187528,559270,371678) : difference with theory (-66) = -2
CORRECTING DEFECT 2 (vertices=18, convex hull=45) After retessellation of defect 2, euler #=-63 (187538,559315,371714) : difference with theory (-65) = -2
CORRECTING DEFECT 3 (vertices=181, convex hull=154) After retessellation of defect 3, euler #=-62 (187572,559490,371856) : difference with theory (-64) = -2
CORRECTING DEFECT 4 (vertices=265, convex hull=151) After retessellation of defect 4, euler #=-61 (187594,559630,371975) : difference with theory (-63) = -2
CORRECTING DEFECT 5 (vertices=18, convex hull=41) After retessellation of defect 5, euler #=-60 (187602,559669,372007) : difference with theory (-62) = -2
CORRECTING DEFECT 6 (vertices=46, convex hull=30) After retessellation of defect 6, euler #=-59 (187606,559689,372024) : difference with theory (-61) = -2
CORRECTING DEFECT 7 (vertices=39, convex hull=66) After retessellation of defect 7, euler #=-58 (187619,559757,372080) : difference with theory (-60) = -2
CORRECTING DEFECT 8 (vertices=7, convex hull=36) After retessellation of defect 8, euler #=-57 (187623,559782,372102) : difference with theory (-59) = -2
CORRECTING DEFECT 9 (vertices=52, convex hull=57) After retessellation of defect 9, euler #=-56 (187638,559844,372150) : difference with theory (-58) = -2
CORRECTING DEFECT 10 (vertices=34, convex hull=25) normal vector of length zero at vertex 37101 with 0 faces vertex 37101 has 0 face reading input surface
/data/brewster2/tjarvis/thesis_data/software/freesurfer/subjects/icbm/surf/
lh.qsphere.nofix... INFO: Fixing vertex area reading brain volume from brain... reading wm segmentation from wm... Linux brewster 2.4.20-8smp #1 SMP Thu Mar 13 16:43:01 EST 2003 i686
athlon
i386 GNU/Linux
recon-all exited with ERRORS at Sat Feb 4 05:34:26 CST 2006
Timothy R. Jarvis
Graduate Research Assistant International Neuroimaging Consortium VA Medical Center 612-467-2619 http://www.neurovia.umn.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--------------------------------------- Timothy R. Jarvis --------------------------------------- Graduate Research Assistant International Neuroimaging Consortium VA Medical Center 612-467-2619 http://www.neurovia.umn.edu ---------------------------------------
freesurfer@nmr.mgh.harvard.edu
-
Tim Jarvis