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... > > #-------------------------------------------- > > [EMAIL PROTECTED] 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
