Ran recon-all autorecon1 without a problem.
Ran recon-all autorecon2 with the following error being produced with mris_fix_topology. Any suggestions on proceeding?
Cliff
Fix Topology rh Wed Aug 31 19:49:23 CDT 2005 /Users/Shared/freesurfer/subjects/00139/scripts mris_fix_topology -ga -mgz 00139 rh
************************************************************* Setting options
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
************************************************************* reading input surface /Users/Shared/freesurfer/subjects/00139/surf/rh.qsphere... INFO: Volume /tmp/mritotal_10838/nu_8_dxyz.mnc cannot be found. before topology correction, eno=-116 (nv=134843, nf=269928, ne=404887, g=59) 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 10 iterations marking ambiguous vertices... 8916 ambiguous faces found in tessellation segmenting defects... 57 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 6 into 4 -merging segment 24 into 21 55 defects to be corrected 0 vertices coincident Computing Initial Surface Statistics -face loglikelihood: -8.5791 (-4.2896) -vertex loglikelihood: -5.5509 (-2.7754) -normal dot loglikelihood: -3.5429 (-3.5429) -quad curv loglikelihood: -6.4438 (-3.2219) Total Loglikelihood : -24.1167
CORRECTING DEFECT 0 Computing statistics for defect 0 [ (128,159,42) - 91.055 ] -white ( 95.29 , 2.78 ) -gray ( 85.38 , 4.30 ) -gray ( 89.45 , 18.92 ) - white ( 99.58 , 17.72 ) -intensity (85.375229 [log = -2.390182 ]- 95.286507 [log = -1.957521 ]) -curvature(kmax=-0.093632 : rmin = 10.680127 | kmin=-0.036819 : rmax = 27.159932 ) - k1 ( -0.06 , 0.70 ) - k2 ( -0.02 , 0.26 ) retessellating defect 0 with 55 vertices (convex hull=80). 125 of 1360 overlapping edges discarded Defect size : 16 by 15 by 13 (scale = 2) Edge Clustering: 3 segments were found (1 were discarded ) cluster 0 has 29 edges cluster 1 has 13 edges cluster 2 has 13 edges l_mri = 1.00 l_unmri = 10.00 l_curv = 1.00 l_qcurv = 1.00 new optimal fitness found at 4: -68.6645 Initial population for defect 0: best fitness at 4: -68.6645 (-70.9431 +- 2.5561) Segmentation fault recon-all exited with errors at Wed Aug 31 19:50:44 CDT 2005
------------------ Clifford Smith, PhD Assistant Professor of Behavioral Sciences Rush University Medical Center 312.942.2893
Cliff,
This was executed on the Mac, right? I presume so from one of your prior emails.
If so, we have seen this segfault occur on a Mac (but not on any of the Linux platforms), and are currently chasing it down.
Nick
On Thu, 2005-09-01 at 16:15 -0500, Clifford A. Smith, PhD wrote:
Ran recon-all –autorecon1 without a problem.
Ran recon-all –autorecon2 with the following error being produced with mris_fix_topology. Any suggestions on proceeding?
Cliff
Fix Topology rh Wed Aug 31 19:49:23 CDT 2005 /Users/Shared/freesurfer/subjects/00139/scripts mris_fix_topology -ga -mgz 00139 rh
Setting options
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
reading input surface /Users/Shared/freesurfer/subjects/00139/surf/rh.qsphere... INFO: Volume /tmp/mritotal_10838/nu_8_dxyz.mnc cannot be found. before topology correction, eno=-116 (nv=134843, nf=269928, ne=404887, g=59) 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 10 iterations marking ambiguous vertices... 8916 ambiguous faces found in tessellation segmenting defects... 57 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 6 into 4 -merging segment 24 into 21 55 defects to be corrected 0 vertices coincident Computing Initial Surface Statistics -face loglikelihood: -8.5791 (-4.2896) -vertex loglikelihood: -5.5509 (-2.7754) -normal dot loglikelihood: -3.5429 (-3.5429) -quad curv loglikelihood: -6.4438 (-3.2219) Total Loglikelihood : -24.1167
CORRECTING DEFECT 0 Computing statistics for defect 0 [ (128,159,42) - 91.055 ] -white ( 95.29 , 2.78 ) -gray ( 85.38 , 4.30 ) -gray ( 89.45 , 18.92 ) - white ( 99.58 , 17.72 ) -intensity (85.375229 [log = -2.390182 ]- 95.286507 [log = -1.957521 ]) -curvature(kmax=-0.093632 : rmin = 10.680127 | kmin=-0.036819 : rmax = 27.159932 ) - k1 ( -0.06 , 0.70 ) - k2 ( -0.02 , 0.26 ) retessellating defect 0 with 55 vertices (convex hull=80). 125 of 1360 overlapping edges discarded Defect size : 16 by 15 by 13 (scale = 2) Edge Clustering: 3 segments were found (1 were discarded ) cluster 0 has 29 edges cluster 1 has 13 edges cluster 2 has 13 edges l_mri = 1.00 l_unmri = 10.00 l_curv = 1.00 l_qcurv = 1.00 new optimal fitness found at 4: -68.6645 Initial population for defect 0: best fitness at 4: -68.6645 (-70.9431 +- 2.5561) Segmentation fault recon-all exited with errors at Wed Aug 31 19:50:44 CDT 2005
Clifford Smith, PhD Assistant Professor of Behavioral Sciences Rush University Medical Center 312.942.2893
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks, Nick. You are correct about the Mac.
On 9/1/05 4:37 PM, "Nick Schmansky" nicks@nmr.mgh.harvard.edu wrote:
Cliff,
This was executed on the Mac, right? I presume so from one of your prior emails.
If so, we have seen this segfault occur on a Mac (but not on any of the Linux platforms), and are currently chasing it down.
Nick
On Thu, 2005-09-01 at 16:15 -0500, Clifford A. Smith, PhD wrote:
Ran recon-all autorecon1 without a problem.
Ran recon-all autorecon2 with the following error being produced with mris_fix_topology. Any suggestions on proceeding?
Cliff
Fix Topology rh Wed Aug 31 19:49:23 CDT 2005 /Users/Shared/freesurfer/subjects/00139/scripts mris_fix_topology -ga -mgz 00139 rh
Setting options
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
reading input surface /Users/Shared/freesurfer/subjects/00139/surf/rh.qsphere... INFO: Volume /tmp/mritotal_10838/nu_8_dxyz.mnc cannot be found. before topology correction, eno=-116 (nv=134843, nf=269928, ne=404887, g=59) 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 10 iterations marking ambiguous vertices... 8916 ambiguous faces found in tessellation segmenting defects... 57 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 6 into 4 -merging segment 24 into 21 55 defects to be corrected 0 vertices coincident Computing Initial Surface Statistics -face loglikelihood: -8.5791 (-4.2896) -vertex loglikelihood: -5.5509 (-2.7754) -normal dot loglikelihood: -3.5429 (-3.5429) -quad curv loglikelihood: -6.4438 (-3.2219) Total Loglikelihood : -24.1167
CORRECTING DEFECT 0 Computing statistics for defect 0 [ (128,159,42) - 91.055 ] -white ( 95.29 , 2.78 ) -gray ( 85.38 , 4.30 ) -gray ( 89.45 , 18.92 ) - white ( 99.58 , 17.72 ) -intensity (85.375229 [log = -2.390182 ]- 95.286507 [log = -1.957521 ]) -curvature(kmax=-0.093632 : rmin = 10.680127 | kmin=-0.036819 : rmax = 27.159932 ) - k1 ( -0.06 , 0.70 ) - k2 ( -0.02 , 0.26 ) retessellating defect 0 with 55 vertices (convex hull=80). 125 of 1360 overlapping edges discarded Defect size : 16 by 15 by 13 (scale = 2) Edge Clustering: 3 segments were found (1 were discarded ) cluster 0 has 29 edges cluster 1 has 13 edges cluster 2 has 13 edges l_mri = 1.00 l_unmri = 10.00 l_curv = 1.00 l_qcurv = 1.00 new optimal fitness found at 4: -68.6645 Initial population for defect 0: best fitness at 4: -68.6645 (-70.9431 +- 2.5561) Segmentation fault recon-all exited with errors at Wed Aug 31 19:50:44 CDT 2005
Clifford Smith, PhD Assistant Professor of Behavioral Sciences Rush University Medical Center 312.942.2893
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
------------------ Clifford Smith, PhD Assistant Professor of Behavioral Sciences Rush University Medical Center 312.942.2893
freesurfer@nmr.mgh.harvard.edu
-
Clifford A. Smith, PhD -
Nick Schmansky