Hi,
I'm relatively new to the FreeSurfer program and have mostly worked with processing adult brains. I am currently working on reconstructing images of young children under 5 and am consistently running into the same error for the two subjects I am running during mris_fix_topology. The error is as follows:
153 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 19 into 4 -merging segment 28 into 7 -merging segment 44 into 7 -merging segment 43 into 7 -merging segment 59 into 7 -merging segment 63 into 7 -merging segment 24 into 8 -merging segment 25 into 17 -merging segment 21 into 18 -merging segment 67 into 30 -merging segment 78 into 30 -merging segment 38 into 33 -merging segment 79 into 73 -merging segment 85 into 77 -merging segment 113 into 77 -merging segment 88 into 77 -merging segment 95 into 77 -merging segment 97 into 77 -merging segment 93 into 87 -merging segment 91 into 90 -merging segment 135 into 117 -merging segment 136 into 117 -merging segment 141 into 126 -merging segment 146 into 140 -merging segment 149 into 142 128 defects to be corrected 0 vertices coincident reading input surface /home/local/SOC/kcl388/wong_ lab/labmridata/FreeSurfer/CMH-3305/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.7664 (-4.8832) -vertex loglikelihood: -7.0295 (-3.5147) -normal dot loglikelihood: -3.5134 (-3.5134) -quad curv loglikelihood: -6.0484 (-3.0242) Total Loglikelihood : -26.3577
CORRECTING DEFECT 0 (vertices=281, convex hull=141) After retessellation of defect 0, euler #=-62 (115680,331866,216124) : difference with theory (-125) = -63
CORRECTING DEFECT 1 (vertices=100, convex hull=64) After retessellation of defect 1, euler #=-61 (115689,331920,216170) : difference with theory (-124) = -63
CORRECTING DEFECT 2 (vertices=12, convex hull=20) After retessellation of defect 2, euler #=-60 (115690,331929,216179) : difference with theory (-123) = -63
CORRECTING DEFECT 3 (vertices=395, convex hull=187) After retessellation of defect 3, euler #=-59 (115735,332152,216358) : difference with theory (-122) = -63
CORRECTING DEFECT 4 (vertices=7865, convex hull=2299)
The defects never completely correct, and the program just hangs on correcting one of the defects (in this case 'DEFECT 4'). Do you have any suggestions as to where to go from here? I have checked talairach and done skull stripping edits, none of which seemed to have worked.
Best, Kevin
Hi Kevin
when you say it hangs, how long do you wait? That is a pretty big defect (7785 vertices, probably 5% of the surface). You can look at the inflated.nofix surface and try to manually correct the defect. The time the topology correction takes goes up as the square of the defect size, so big ones can take a long time (i.e. >10 hours). Usually we remove the big ones automatically by ventrical filling and such, but that may not work as well in the kid brains.
Bruce
On Mon, 18 Jul 2011, Kevin Liu wrote:
Hi,
I'm relatively new to the FreeSurfer program and have mostly worked with processing adult brains. I am currently working on reconstructing images of young children under 5 and am consistently running into the same error for the two subjects I am running during mris_fix_topology. The error is as follows:
153 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 19 into 4 -merging segment 28 into 7 -merging segment 44 into 7 -merging segment 43 into 7 -merging segment 59 into 7 -merging segment 63 into 7 -merging segment 24 into 8 -merging segment 25 into 17 -merging segment 21 into 18 -merging segment 67 into 30 -merging segment 78 into 30 -merging segment 38 into 33 -merging segment 79 into 73 -merging segment 85 into 77 -merging segment 113 into 77 -merging segment 88 into 77 -merging segment 95 into 77 -merging segment 97 into 77 -merging segment 93 into 87 -merging segment 91 into 90 -merging segment 135 into 117 -merging segment 136 into 117 -merging segment 141 into 126 -merging segment 146 into 140 -merging segment 149 into 142 128 defects to be corrected 0 vertices coincident reading input surface/home/local/SOC/kcl388/wong_lab/labmridata/FreeSurfer/CMH-3305/surf/lh.qsph ere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.7664 (-4.8832) -vertex loglikelihood: -7.0295 (-3.5147) -normal dot loglikelihood: -3.5134 (-3.5134) -quad curv loglikelihood: -6.0484 (-3.0242) Total Loglikelihood : -26.3577
CORRECTING DEFECT 0 (vertices=281, convex hull=141) After retessellation of defect 0, euler #=-62 (115680,331866,216124) : difference with theory (-125) = -63
CORRECTING DEFECT 1 (vertices=100, convex hull=64) After retessellation of defect 1, euler #=-61 (115689,331920,216170) : difference with theory (-124) = -63
CORRECTING DEFECT 2 (vertices=12, convex hull=20) After retessellation of defect 2, euler #=-60 (115690,331929,216179) : difference with theory (-123) = -63
CORRECTING DEFECT 3 (vertices=395, convex hull=187) After retessellation of defect 3, euler #=-59 (115735,332152,216358) : difference with theory (-122) = -63
CORRECTING DEFECT 4 (vertices=7865, convex hull=2299)
The defects never completely correct, and the program just hangs on correcting one of the defects (in this case 'DEFECT 4'). Do you have any suggestions as to where to go from here? I have checked talairach and done skull stripping edits, none of which seemed to have worked.
Best, Kevin
-- Kevin LiuMD Candidate 2014 Feinberg School of Medicine
-- Kevin LiuMD Candidate 2014 Feinberg School of Medicine
Did you check to see whether the cerebellum (or some large bit of skull or brain stem) are still attached? doug
Kevin Liu wrote:
Hi,
I'm relatively new to the FreeSurfer program and have mostly worked with processing adult brains. I am currently working on reconstructing images of young children under 5 and am consistently running into the same error for the two subjects I am running during mris_fix_topology. The error is as follows:
153 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 19 into 4 -merging segment 28 into 7 -merging segment 44 into 7 -merging segment 43 into 7 -merging segment 59 into 7 -merging segment 63 into 7 -merging segment 24 into 8 -merging segment 25 into 17 -merging segment 21 into 18 -merging segment 67 into 30 -merging segment 78 into 30 -merging segment 38 into 33 -merging segment 79 into 73 -merging segment 85 into 77 -merging segment 113 into 77 -merging segment 88 into 77 -merging segment 95 into 77 -merging segment 97 into 77 -merging segment 93 into 87 -merging segment 91 into 90 -merging segment 135 into 117 -merging segment 136 into 117 -merging segment 141 into 126 -merging segment 146 into 140 -merging segment 149 into 142 128 defects to be corrected 0 vertices coincident reading input surface /home/local/SOC/kcl388/wong_ lab/labmridata/FreeSurfer/CMH-3305/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.7664 (-4.8832) -vertex loglikelihood: -7.0295 (-3.5147) -normal dot loglikelihood: -3.5134 (-3.5134) -quad curv loglikelihood: -6.0484 (-3.0242) Total Loglikelihood : -26.3577
CORRECTING DEFECT 0 (vertices=281, convex hull=141) After retessellation of defect 0, euler #=-62 (115680,331866,216124) : difference with theory (-125) = -63
CORRECTING DEFECT 1 (vertices=100, convex hull=64) After retessellation of defect 1, euler #=-61 (115689,331920,216170) : difference with theory (-124) = -63
CORRECTING DEFECT 2 (vertices=12, convex hull=20) After retessellation of defect 2, euler #=-60 (115690,331929,216179) : difference with theory (-123) = -63
CORRECTING DEFECT 3 (vertices=395, convex hull=187) After retessellation of defect 3, euler #=-59 (115735,332152,216358) : difference with theory (-122) = -63
CORRECTING DEFECT 4 (vertices=7865, convex hull=2299)
The defects never completely correct, and the program just hangs on correcting one of the defects (in this case 'DEFECT 4'). Do you have any suggestions as to where to go from here? I have checked talairach and done skull stripping edits, none of which seemed to have worked.
Best, Kevin
-- Kevin Liu MD Candidate 2014 Feinberg School of Medicine
-- Kevin Liu MD Candidate 2014 Feinberg School of Medicine
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
try looking at the ?h.inflated.nofix to see what the big defect is and we can go from there.
cheers Bruce
On Mon, 18 Jul 2011, Kevin Liu wrote:
Hi,
I'm relatively new to the FreeSurfer program and have mostly worked with processing adult brains. I am currently working on reconstructing images of young children under 5 and am consistently running into the same error for the two subjects I am running during mris_fix_topology. The error is as follows:
153 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 19 into 4 -merging segment 28 into 7 -merging segment 44 into 7 -merging segment 43 into 7 -merging segment 59 into 7 -merging segment 63 into 7 -merging segment 24 into 8 -merging segment 25 into 17 -merging segment 21 into 18 -merging segment 67 into 30 -merging segment 78 into 30 -merging segment 38 into 33 -merging segment 79 into 73 -merging segment 85 into 77 -merging segment 113 into 77 -merging segment 88 into 77 -merging segment 95 into 77 -merging segment 97 into 77 -merging segment 93 into 87 -merging segment 91 into 90 -merging segment 135 into 117 -merging segment 136 into 117 -merging segment 141 into 126 -merging segment 146 into 140 -merging segment 149 into 142 128 defects to be corrected 0 vertices coincident reading input surface/home/local/SOC/kcl388/wong_lab/labmridata/FreeSurfer/CMH-3305/surf/lh.qsph ere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.7664 (-4.8832) -vertex loglikelihood: -7.0295 (-3.5147) -normal dot loglikelihood: -3.5134 (-3.5134) -quad curv loglikelihood: -6.0484 (-3.0242) Total Loglikelihood : -26.3577
CORRECTING DEFECT 0 (vertices=281, convex hull=141) After retessellation of defect 0, euler #=-62 (115680,331866,216124) : difference with theory (-125) = -63
CORRECTING DEFECT 1 (vertices=100, convex hull=64) After retessellation of defect 1, euler #=-61 (115689,331920,216170) : difference with theory (-124) = -63
CORRECTING DEFECT 2 (vertices=12, convex hull=20) After retessellation of defect 2, euler #=-60 (115690,331929,216179) : difference with theory (-123) = -63
CORRECTING DEFECT 3 (vertices=395, convex hull=187) After retessellation of defect 3, euler #=-59 (115735,332152,216358) : difference with theory (-122) = -63
CORRECTING DEFECT 4 (vertices=7865, convex hull=2299)
The defects never completely correct, and the program just hangs on correcting one of the defects (in this case 'DEFECT 4'). Do you have any suggestions as to where to go from here? I have checked talairach and done skull stripping edits, none of which seemed to have worked.
Best, Kevin
-- Kevin LiuMD Candidate 2014 Feinberg School of Medicine
-- Kevin LiuMD Candidate 2014 Feinberg School of Medicine
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas N Greve -
Kevin Liu