Hi all,
I am having an topological defect error while running few of subjects. I have gone through the freesurfer correcting topological defects wikipage. But I was trying understand the log file. For an example, I got the following error for one subject:
Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 13 iterations marking ambiguous vertices... 70557 ambiguous faces found in tessellation segmenting defects... 78 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 19 into 0 -merging segment 22 into 0 -merging segment 68 into 49 -merging segment 61 into 55 74 defects to be corrected 0 vertices coincident reading input surface /work/02510/sray2/Free_Sub/DATA/50011/50011/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.4264 (-4.2132) -vertex loglikelihood: -5.7733 (-2.8866) -normal dot loglikelihood: -3.6047 (-3.6047) -quad curv loglikelihood: -6.1117 (-3.0559) Total Loglikelihood : -23.9161
CORRECTING DEFECT 0 (vertices=27967, convex hull=5893) Segmentation fault
mris_euler_number ../surf/lh.orig
mris_fix_topology failed! (euler number != 2) Trying mris_topo_fixer...
cp ../surf/lh.orig.nofix ../surf/lh.orig
euler # = v-e+f = 2g-2: 116732 - 351516 + 234344 = -440 --> 221 holes F =2V-4: 234344 != 233464-4 (-884) 2E=3F: 703032 = 703032 (0)
total defect index = 442
cp ../surf/lh.qsphere.nofix ../surf/lh.qsphere
cp ../surf/lh.smoothwm.nofix ../surf/lh.smoothwm
/work/02510/sray2/Free_Sub/DATA/50011/50011/scripts
mris_topo_fixer -mgz -warnings -seed 1234 50011 lh
verbose mode on (medium mode): printing warnings setting seed for random number genererator to 1234 Before topology correction, eno=-440 (nv=116732, nf=234344, ne=351516, g=221) Surface Diagnostics: eno=-440 (nv=116732, nf=234344, ne=351516) # of border vertices [ #v ~ #f ] 0 # of edges with single face 0 # of edges with more than 2 faces 0 # of corner configurations 0 The original surface is a valid manifold Counting the number of connected components The original surface has one component The original surface does not self-intersect
The surface has 221 loops (X=-440)
Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations identify defects... marking ambiguous vertices... 68425 ambiguous faces found in tessellation segmenting defects... analyzing defects for overlaps... INFO: assuming .mgz format reading input surface /work/02510/sray2/Free_Sub/DATA/50011/50011/surf/lh.orig... reading brain volume from brain... reading wm segmentation from wm... Detecting contrast direction: right direction [ GM (86.66) < WM (96.03) ] Computing Initial Surface Statistics -face loglikelihood: -5.8578 (-2.9289) -vertex loglikelihood: -5.7524 (-2.8762) -normal dot loglikelihood: -3.6033 (-3.6033) -quad curv loglikelihood: -5.8101 (-2.9050) Total Loglikelihood : -21.0236
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX Correcting Topology of defect 1 with euler number -257 (129 loops) computing statistics for defect 1: 33364 vertices location: [ (156,125,84) - average intensity = 92.126 ] -gray ( 86.57 , 6.29 ) -white ( 95.91 , 6.08 ) -gray ( 89.98 , 24.95 ) -white ( 98.58 , 24.03 ) -intensity (86.574921 [log = -2.404119 ]- 95.914825 [log = -2.517448 ]) -curv (k1=-0.162 (0.730) , r1 = 6.179 | k2=-0.060 (0.191), r2 = 16.806 ) -curv (k1=-0.124 (0.768) , r1 = 8.076 | k2=-0.032 (0.282), r2 = 31.306 ) MRISalloc(8654176, 520): could not allocate vertices Cannot allocate memory
And In some of my subjects the log file stop writing after: "CORRECTING DEFECT 0 (vertices=53786, convex hull=13985)"
My question is what exactly these highlighted number means? Do I have an estimation of number of slices that are to be treated manually?
Thanks, -Siddharth
Hi Siddharth
it means you have a huge defect that we are unable to automatically correct. If you look at the ?h.inflated.nofix it should be obvious what it is
cheers Bruce
On Tue, 25 Feb 2014, Ray, Siddharth wrote:
Hi all,
I am having an topological defect error while running few of subjects. I have gone through the freesurfer correcting topological defects wikipage. But I was trying understand the log file. For an example, I got the following error for one subject:
Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 13 iterations
marking ambiguous vertices...
70557 ambiguous faces found in tessellation
segmenting defects...
78 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
-merging segment 19 into 0
-merging segment 22 into 0
-merging segment 68 into 49
-merging segment 61 into 55
74 defects to be corrected
0 vertices coincident
reading input surface /work/02510/sray2/Free_Sub/DATA/50011/50011/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
-face loglikelihood: -8.4264 (-4.2132)
-vertex loglikelihood: -5.7733 (-2.8866)
-normal dot loglikelihood: -3.6047 (-3.6047)
-quad curv loglikelihood: -6.1117 (-3.0559)
Total Loglikelihood : -23.9161
CORRECTING DEFECT 0 (vertices=27967, convex hull=5893)
Segmentation fault
mris_euler_number ../surf/lh.orig
mris_fix_topology failed! (euler number != 2)
Trying mris_topo_fixer...
cp ../surf/lh.orig.nofix ../surf/lh.orig
euler # = v-e+f = 2g-2: 116732 - 351516 + 234344 = -440 --> 221 holes
F =2V-4: 234344 != 233464-4 (-884)
2E=3F: 703032 = 703032 (0)
total defect index = 442
cp ../surf/lh.qsphere.nofix ../surf/lh.qsphere
cp ../surf/lh.smoothwm.nofix ../surf/lh.smoothwm
/work/02510/sray2/Free_Sub/DATA/50011/50011/scripts
mris_topo_fixer -mgz -warnings -seed 1234 50011 lh
verbose mode on (medium mode): printing warnings
setting seed for random number genererator to 1234
Before topology correction, eno=-440 (nv=116732, nf=234344, ne=351516, g=221)
Surface Diagnostics:
eno=-440 (nv=116732, nf=234344, ne=351516)
# of border vertices [ #v ~ #f ] 0
# of edges with single face 0
# of edges with more than 2 faces 0
# of corner configurations 0
The original surface is a valid manifold
Counting the number of connected components
The original surface has one component
The original surface does not self-intersect
The surface has 221 loops (X=-440)
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 9 iterations
identify defects...
marking ambiguous vertices...
68425 ambiguous faces found in tessellation
segmenting defects...
analyzing defects for overlaps...
INFO: assuming .mgz format
reading input surface /work/02510/sray2/Free_Sub/DATA/50011/50011/surf/lh.orig...
reading brain volume from brain...
reading wm segmentation from wm...
Detecting contrast direction: right direction [ GM (86.66) < WM (96.03) ]
Computing Initial Surface Statistics
-face loglikelihood: -5.8578 (-2.9289)
-vertex loglikelihood: -5.7524 (-2.8762)
-normal dot loglikelihood: -3.6033 (-3.6033)
-quad curv loglikelihood: -5.8101 (-2.9050)
Total Loglikelihood : -21.0236
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
Correcting Topology of defect 1 with euler number -257 (129 loops)
computing statistics for defect 1: 33364 vertices
location: [ (156,125,84) - average intensity = 92.126 ]
-gray ( 86.57 , 6.29 ) -white ( 95.91 , 6.08 )
-gray ( 89.98 , 24.95 ) -white ( 98.58 , 24.03 )
-intensity (86.574921 [log = -2.404119 ]- 95.914825 [log = -2.517448 ])
-curv (k1=-0.162 (0.730) , r1 = 6.179 | k2=-0.060 (0.191), r2 = 16.806 )
-curv (k1=-0.124 (0.768) , r1 = 8.076 | k2=-0.032 (0.282), r2 = 31.306 )
MRISalloc(8654176, 520): could not allocate vertices
Cannot allocate memory
And In some of my subjects the log file stop writing after: “CORRECTING DEFECT 0 (vertices=53786, convex hull=13985)”
My question is what exactly these highlighted number means? Do I have an estimation of number of slices that are to be treated manually?
Thanks,
-Siddharth
Hi Bruce,
Do I have any estimation of how many slices are need to be corrected using these numbers? “CORRECTING DEFECT 0 (vertices=53786, convex hull=13985)”
Thanks, -Siddharth
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tuesday, February 25, 2014 10:03 AM To: Ray, Siddharth Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: Topological defect
Hi Siddharth
it means you have a huge defect that we are unable to automatically correct. If you look at the ?h.inflated.nofix it should be obvious what it is
cheers Bruce
On Tue, 25 Feb 2014, Ray, Siddharth wrote:
Hi all,
I am having an topological defect error while running few of subjects. I have gone through the freesurfer correcting topological defects wikipage. But I was trying understand the log file. For an example, I got the following error for one subject:
Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 13 iterations
marking ambiguous vertices...
70557 ambiguous faces found in tessellation
segmenting defects...
78 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
-merging segment 19 into 0
-merging segment 22 into 0
-merging segment 68 into 49
-merging segment 61 into 55
74 defects to be corrected
0 vertices coincident
reading input surface /work/02510/sray2/Free_Sub/DATA/50011/50011/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
-face loglikelihood: -8.4264 (-4.2132)
-vertex loglikelihood: -5.7733 (-2.8866)
-normal dot loglikelihood: -3.6047 (-3.6047)
-quad curv loglikelihood: -6.1117 (-3.0559)
Total Loglikelihood : -23.9161
CORRECTING DEFECT 0 (vertices=27967, convex hull=5893)
Segmentation fault
mris_euler_number ../surf/lh.orig
mris_fix_topology failed! (euler number != 2)
Trying mris_topo_fixer...
cp ../surf/lh.orig.nofix ../surf/lh.orig
euler # = v-e+f = 2g-2: 116732 - 351516 + 234344 = -440 --> 221 holes
F =2V-4: 234344 != 233464-4 (-884)
2E=3F: 703032 = 703032 (0)
total defect index = 442
cp ../surf/lh.qsphere.nofix ../surf/lh.qsphere
cp ../surf/lh.smoothwm.nofix ../surf/lh.smoothwm
/work/02510/sray2/Free_Sub/DATA/50011/50011/scripts
mris_topo_fixer -mgz -warnings -seed 1234 50011 lh
verbose mode on (medium mode): printing warnings
setting seed for random number genererator to 1234
Before topology correction, eno=-440 (nv=116732, nf=234344, ne=351516, g=221)
Surface Diagnostics:
eno=-440 (nv=116732, nf=234344, ne=351516)
# of border vertices [ #v ~ #f ] 0
# of edges with single face 0
# of edges with more than 2 faces 0
# of corner configurations 0
The original surface is a valid manifold
Counting the number of connected components
The original surface has one component
The original surface does not self-intersect
The surface has 221 loops (X=-440)
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 9 iterations
identify defects...
marking ambiguous vertices...
68425 ambiguous faces found in tessellation
segmenting defects...
analyzing defects for overlaps...
INFO: assuming .mgz format
reading input surface /work/02510/sray2/Free_Sub/DATA/50011/50011/surf/lh.orig...
reading brain volume from brain...
reading wm segmentation from wm...
Detecting contrast direction: right direction [ GM (86.66) < WM (96.03) ]
Computing Initial Surface Statistics
-face loglikelihood: -5.8578 (-2.9289)
-vertex loglikelihood: -5.7524 (-2.8762)
-normal dot loglikelihood: -3.6033 (-3.6033)
-quad curv loglikelihood: -5.8101 (-2.9050)
Total Loglikelihood : -21.0236
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
Correcting Topology of defect 1 with euler number -257 (129 loops)
computing statistics for defect 1: 33364 vertices
location: [ (156,125,84) - average intensity = 92.126 ]
-gray ( 86.57 , 6.29 ) -white ( 95.91 , 6.08 )
-gray ( 89.98 , 24.95 ) -white ( 98.58 , 24.03 )
-intensity (86.574921 [log = -2.404119 ]- 95.914825 [log = -2.517448 ])
-curv (k1=-0.162 (0.730) , r1 = 6.179 | k2=-0.060 (0.191), r2 = 16.806 )
-curv (k1=-0.124 (0.768) , r1 = 8.076 | k2=-0.032 (0.282), r2 = 31.306 )
MRISalloc(8654176, 520): could not allocate vertices
Cannot allocate memory
And In some of my subjects the log file stop writing after: “CORRECTING DEFECT 0 (vertices=53786, convex hull=13985)”
My question is what exactly these highlighted number means? Do I have an estimation of number of slices that are to be treated manually?
Thanks,
-Siddharth
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at https://urldefense.proofpoint.com/v1/url?u=http://www.partners.org/complianc... . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
no, there's no way to tell. It could be caused by a single voxel On Thu, 27 Feb 2014, Ray, Siddharth wrote:
Hi Bruce,
Do I have any estimation of how many slices are need to be corrected using these numbers? “CORRECTING DEFECT 0 (vertices=53786, convex hull=13985)”
Thanks, -Siddharth
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tuesday, February 25, 2014 10:03 AM To: Ray, Siddharth Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: Topological defect
Hi Siddharth
it means you have a huge defect that we are unable to automatically correct. If you look at the ?h.inflated.nofix it should be obvious what it is
cheers Bruce
On Tue, 25 Feb 2014, Ray, Siddharth wrote:
Hi all,
I am having an topological defect error while running few of subjects. I have gone through the freesurfer correcting topological defects wikipage. But I was trying understand the log file. For an example, I got the following error for one subject:
Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 13 iterations
marking ambiguous vertices...
70557 ambiguous faces found in tessellation
segmenting defects...
78 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
-merging segment 19 into 0
-merging segment 22 into 0
-merging segment 68 into 49
-merging segment 61 into 55
74 defects to be corrected
0 vertices coincident
reading input surface /work/02510/sray2/Free_Sub/DATA/50011/50011/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
-face loglikelihood: -8.4264 (-4.2132)
-vertex loglikelihood: -5.7733 (-2.8866)
-normal dot loglikelihood: -3.6047 (-3.6047)
-quad curv loglikelihood: -6.1117 (-3.0559)
Total Loglikelihood : -23.9161
CORRECTING DEFECT 0 (vertices=27967, convex hull=5893)
Segmentation fault
mris_euler_number ../surf/lh.orig
mris_fix_topology failed! (euler number != 2)
Trying mris_topo_fixer...
cp ../surf/lh.orig.nofix ../surf/lh.orig
euler # = v-e+f = 2g-2: 116732 - 351516 + 234344 = -440 --> 221 holes
F =2V-4: 234344 != 233464-4 (-884)
2E=3F: 703032 = 703032 (0)
total defect index = 442
cp ../surf/lh.qsphere.nofix ../surf/lh.qsphere
cp ../surf/lh.smoothwm.nofix ../surf/lh.smoothwm
/work/02510/sray2/Free_Sub/DATA/50011/50011/scripts
mris_topo_fixer -mgz -warnings -seed 1234 50011 lh
verbose mode on (medium mode): printing warnings
setting seed for random number genererator to 1234
Before topology correction, eno=-440 (nv=116732, nf=234344, ne=351516, g=221)
Surface Diagnostics:
eno=-440 (nv=116732, nf=234344, ne=351516)
# of border vertices [ #v ~ #f ] 0
# of edges with single face 0
# of edges with more than 2 faces 0
# of corner configurations 0
The original surface is a valid manifold
Counting the number of connected components
The original surface has one component
The original surface does not self-intersect
The surface has 221 loops (X=-440)
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 9 iterations
identify defects...
marking ambiguous vertices...
68425 ambiguous faces found in tessellation
segmenting defects...
analyzing defects for overlaps...
INFO: assuming .mgz format
reading input surface /work/02510/sray2/Free_Sub/DATA/50011/50011/surf/lh.orig...
reading brain volume from brain...
reading wm segmentation from wm...
Detecting contrast direction: right direction [ GM (86.66) < WM (96.03) ]
Computing Initial Surface Statistics
-face loglikelihood: -5.8578 (-2.9289)
-vertex loglikelihood: -5.7524 (-2.8762)
-normal dot loglikelihood: -3.6033 (-3.6033)
-quad curv loglikelihood: -5.8101 (-2.9050)
Total Loglikelihood : -21.0236
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
Correcting Topology of defect 1 with euler number -257 (129 loops)
computing statistics for defect 1: 33364 vertices
location: [ (156,125,84) - average intensity = 92.126 ]
-gray ( 86.57 , 6.29 ) -white ( 95.91 , 6.08 )
-gray ( 89.98 , 24.95 ) -white ( 98.58 , 24.03 )
-intensity (86.574921 [log = -2.404119 ]- 95.914825 [log = -2.517448 ])
-curv (k1=-0.162 (0.730) , r1 = 6.179 | k2=-0.060 (0.191), r2 = 16.806 )
-curv (k1=-0.124 (0.768) , r1 = 8.076 | k2=-0.032 (0.282), r2 = 31.306 )
MRISalloc(8654176, 520): could not allocate vertices
Cannot allocate memory
And In some of my subjects the log file stop writing after: “CORRECTING DEFECT 0 (vertices=53786, convex hull=13985)”
My question is what exactly these highlighted number means? Do I have an estimation of number of slices that are to be treated manually?
Thanks,
-Siddharth
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at https://urldefense.proofpoint.com/v1/url?u=http://www.partners.org/complianc... . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Ok, and is there anyway to know the vertex index of these voxels due to which topological defect happened?
Thanks
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thursday, February 27, 2014 11:00 AM To: Ray, Siddharth Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] FW: Topological defect
no, there's no way to tell. It could be caused by a single voxel On Thu, 27 Feb 2014, Ray, Siddharth wrote:
Hi Bruce,
Do I have any estimation of how many slices are need to be corrected using these numbers? “CORRECTING DEFECT 0 (vertices=53786, convex hull=13985)”
Thanks, -Siddharth
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tuesday, February 25, 2014 10:03 AM To: Ray, Siddharth Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: Topological defect
Hi Siddharth
it means you have a huge defect that we are unable to automatically correct. If you look at the ?h.inflated.nofix it should be obvious what it is
cheers Bruce
On Tue, 25 Feb 2014, Ray, Siddharth wrote:
Hi all,
I am having an topological defect error while running few of subjects. I have gone through the freesurfer correcting topological defects wikipage. But I was trying understand the log file. For an example, I got the following error for one subject:
Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 13 iterations
marking ambiguous vertices...
70557 ambiguous faces found in tessellation
segmenting defects...
78 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
-merging segment 19 into 0
-merging segment 22 into 0
-merging segment 68 into 49
-merging segment 61 into 55
74 defects to be corrected
0 vertices coincident
reading input surface /work/02510/sray2/Free_Sub/DATA/50011/50011/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
-face loglikelihood: -8.4264 (-4.2132)
-vertex loglikelihood: -5.7733 (-2.8866)
-normal dot loglikelihood: -3.6047 (-3.6047)
-quad curv loglikelihood: -6.1117 (-3.0559)
Total Loglikelihood : -23.9161
CORRECTING DEFECT 0 (vertices=27967, convex hull=5893)
Segmentation fault
mris_euler_number ../surf/lh.orig
mris_fix_topology failed! (euler number != 2)
Trying mris_topo_fixer...
cp ../surf/lh.orig.nofix ../surf/lh.orig
euler # = v-e+f = 2g-2: 116732 - 351516 + 234344 = -440 --> 221 holes
F =2V-4: 234344 != 233464-4 (-884)
2E=3F: 703032 = 703032 (0)
total defect index = 442
cp ../surf/lh.qsphere.nofix ../surf/lh.qsphere
cp ../surf/lh.smoothwm.nofix ../surf/lh.smoothwm
/work/02510/sray2/Free_Sub/DATA/50011/50011/scripts
mris_topo_fixer -mgz -warnings -seed 1234 50011 lh
verbose mode on (medium mode): printing warnings
setting seed for random number genererator to 1234
Before topology correction, eno=-440 (nv=116732, nf=234344, ne=351516, g=221)
Surface Diagnostics:
eno=-440 (nv=116732, nf=234344, ne=351516)
# of border vertices [ #v ~ #f ] 0
# of edges with single face 0
# of edges with more than 2 faces 0
# of corner configurations 0
The original surface is a valid manifold
Counting the number of connected components
The original surface has one component
The original surface does not self-intersect
The surface has 221 loops (X=-440)
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 9 iterations
identify defects...
marking ambiguous vertices...
68425 ambiguous faces found in tessellation
segmenting defects...
analyzing defects for overlaps...
INFO: assuming .mgz format
reading input surface /work/02510/sray2/Free_Sub/DATA/50011/50011/surf/lh.orig...
reading brain volume from brain...
reading wm segmentation from wm...
Detecting contrast direction: right direction [ GM (86.66) < WM (96.03) ]
Computing Initial Surface Statistics
-face loglikelihood: -5.8578 (-2.9289)
-vertex loglikelihood: -5.7524 (-2.8762)
-normal dot loglikelihood: -3.6033 (-3.6033)
-quad curv loglikelihood: -5.8101 (-2.9050)
Total Loglikelihood : -21.0236
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
Correcting Topology of defect 1 with euler number -257 (129 loops)
computing statistics for defect 1: 33364 vertices
location: [ (156,125,84) - average intensity = 92.126 ]
-gray ( 86.57 , 6.29 ) -white ( 95.91 , 6.08 )
-gray ( 89.98 , 24.95 ) -white ( 98.58 , 24.03 )
-intensity (86.574921 [log = -2.404119 ]- 95.914825 [log = -2.517448 ])
-curv (k1=-0.162 (0.730) , r1 = 6.179 | k2=-0.060 (0.191), r2 = 16.806 )
-curv (k1=-0.124 (0.768) , r1 = 8.076 | k2=-0.032 (0.282), r2 = 31.306 )
MRISalloc(8654176, 520): could not allocate vertices
Cannot allocate memory
And In some of my subjects the log file stop writing after: “CORRECTING DEFECT 0 (vertices=53786, convex hull=13985)”
My question is what exactly these highlighted number means? Do I have an estimation of number of slices that are to be treated manually?
Thanks,
-Siddharth
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at https://urldefense.proofpoint.com/v1/url?u=http://www.partners.org/complianc... . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
yes, Doug has some tools, or you can load the ?h.defect_labels in the ?h.inflated.nofix surface (or ?h.orig.nofix)
cheers Bruce On Thu, 27 Feb 2014, Ray, Siddharth wrote:
Ok, and is there anyway to know the vertex index of these voxels due to which topological defect happened?
Thanks
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thursday, February 27, 2014 11:00 AM To: Ray, Siddharth Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] FW: Topological defect
no, there's no way to tell. It could be caused by a single voxel On Thu, 27 Feb 2014, Ray, Siddharth wrote:
Hi Bruce,
Do I have any estimation of how many slices are need to be corrected using these numbers? “CORRECTING DEFECT 0 (vertices=53786, convex hull=13985)”
Thanks, -Siddharth
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tuesday, February 25, 2014 10:03 AM To: Ray, Siddharth Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: Topological defect
Hi Siddharth
it means you have a huge defect that we are unable to automatically correct. If you look at the ?h.inflated.nofix it should be obvious what it is
cheers Bruce
On Tue, 25 Feb 2014, Ray, Siddharth wrote:
Hi all,
I am having an topological defect error while running few of subjects. I have gone through the freesurfer correcting topological defects wikipage. But I was trying understand the log file. For an example, I got the following error for one subject:
Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 13 iterations
marking ambiguous vertices...
70557 ambiguous faces found in tessellation
segmenting defects...
78 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
-merging segment 19 into 0
-merging segment 22 into 0
-merging segment 68 into 49
-merging segment 61 into 55
74 defects to be corrected
0 vertices coincident
reading input surface /work/02510/sray2/Free_Sub/DATA/50011/50011/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
-face loglikelihood: -8.4264 (-4.2132)
-vertex loglikelihood: -5.7733 (-2.8866)
-normal dot loglikelihood: -3.6047 (-3.6047)
-quad curv loglikelihood: -6.1117 (-3.0559)
Total Loglikelihood : -23.9161
CORRECTING DEFECT 0 (vertices=27967, convex hull=5893)
Segmentation fault
mris_euler_number ../surf/lh.orig
mris_fix_topology failed! (euler number != 2)
Trying mris_topo_fixer...
cp ../surf/lh.orig.nofix ../surf/lh.orig
euler # = v-e+f = 2g-2: 116732 - 351516 + 234344 = -440 --> 221 holes
F =2V-4: 234344 != 233464-4 (-884)
2E=3F: 703032 = 703032 (0)
total defect index = 442
cp ../surf/lh.qsphere.nofix ../surf/lh.qsphere
cp ../surf/lh.smoothwm.nofix ../surf/lh.smoothwm
/work/02510/sray2/Free_Sub/DATA/50011/50011/scripts
mris_topo_fixer -mgz -warnings -seed 1234 50011 lh
verbose mode on (medium mode): printing warnings
setting seed for random number genererator to 1234
Before topology correction, eno=-440 (nv=116732, nf=234344, ne=351516, g=221)
Surface Diagnostics:
eno=-440 (nv=116732, nf=234344, ne=351516)
# of border vertices [ #v ~ #f ] 0
# of edges with single face 0
# of edges with more than 2 faces 0
# of corner configurations 0
The original surface is a valid manifold
Counting the number of connected components
The original surface has one component
The original surface does not self-intersect
The surface has 221 loops (X=-440)
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 9 iterations
identify defects...
marking ambiguous vertices...
68425 ambiguous faces found in tessellation
segmenting defects...
analyzing defects for overlaps...
INFO: assuming .mgz format
reading input surface /work/02510/sray2/Free_Sub/DATA/50011/50011/surf/lh.orig...
reading brain volume from brain...
reading wm segmentation from wm...
Detecting contrast direction: right direction [ GM (86.66) < WM (96.03) ]
Computing Initial Surface Statistics
-face loglikelihood: -5.8578 (-2.9289)
-vertex loglikelihood: -5.7524 (-2.8762)
-normal dot loglikelihood: -3.6033 (-3.6033)
-quad curv loglikelihood: -5.8101 (-2.9050)
Total Loglikelihood : -21.0236
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
Correcting Topology of defect 1 with euler number -257 (129 loops)
computing statistics for defect 1: 33364 vertices
location: [ (156,125,84) - average intensity = 92.126 ]
-gray ( 86.57 , 6.29 ) -white ( 95.91 , 6.08 )
-gray ( 89.98 , 24.95 ) -white ( 98.58 , 24.03 )
-intensity (86.574921 [log = -2.404119 ]- 95.914825 [log = -2.517448 ])
-curv (k1=-0.162 (0.730) , r1 = 6.179 | k2=-0.060 (0.191), r2 = 16.806 )
-curv (k1=-0.124 (0.768) , r1 = 8.076 | k2=-0.032 (0.282), r2 = 31.306 )
MRISalloc(8654176, 520): could not allocate vertices
Cannot allocate memory
And In some of my subjects the log file stop writing after: “CORRECTING DEFECT 0 (vertices=53786, convex hull=13985)”
My question is what exactly these highlighted number means? Do I have an estimation of number of slices that are to be treated manually?
Thanks,
-Siddharth
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at https://urldefense.proofpoint.com/v1/url?u=http://www.partners.org/complianc... . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
try the defect-seg script. Run it with --help to get more info doug On 02/27/2014 02:49 PM, Bruce Fischl wrote:
yes, Doug has some tools, or you can load the ?h.defect_labels in the ?h.inflated.nofix surface (or ?h.orig.nofix)
cheers Bruce On Thu, 27 Feb 2014, Ray, Siddharth wrote:
Ok, and is there anyway to know the vertex index of these voxels due to which topological defect happened?
Thanks
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thursday, February 27, 2014 11:00 AM To: Ray, Siddharth Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] FW: Topological defect
no, there's no way to tell. It could be caused by a single voxel On Thu, 27 Feb 2014, Ray, Siddharth wrote:
Hi Bruce,
Do I have any estimation of how many slices are need to be corrected using these numbers? “CORRECTING DEFECT 0 (vertices=53786, convex hull=13985)”
Thanks, -Siddharth
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tuesday, February 25, 2014 10:03 AM To: Ray, Siddharth Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: Topological defect
Hi Siddharth
it means you have a huge defect that we are unable to automatically correct. If you look at the ?h.inflated.nofix it should be obvious what it is
cheers Bruce
On Tue, 25 Feb 2014, Ray, Siddharth wrote:
Hi all,
I am having an topological defect error while running few of subjects. I have gone through the freesurfer correcting topological defects wikipage. But I was trying understand the log file. For an example, I got the following error for one subject:
Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 13 iterations
marking ambiguous vertices...
70557 ambiguous faces found in tessellation
segmenting defects...
78 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
-merging segment 19 into 0
-merging segment 22 into 0
-merging segment 68 into 49
-merging segment 61 into 55
74 defects to be corrected
0 vertices coincident
reading input surface /work/02510/sray2/Free_Sub/DATA/50011/50011/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
-face loglikelihood: -8.4264 (-4.2132)
-vertex loglikelihood: -5.7733 (-2.8866)
-normal dot loglikelihood: -3.6047 (-3.6047)
-quad curv loglikelihood: -6.1117 (-3.0559)
Total Loglikelihood : -23.9161
CORRECTING DEFECT 0 (vertices=27967, convex hull=5893)
Segmentation fault
mris_euler_number ../surf/lh.orig
mris_fix_topology failed! (euler number != 2)
Trying mris_topo_fixer...
cp ../surf/lh.orig.nofix ../surf/lh.orig
euler # = v-e+f = 2g-2: 116732 - 351516 + 234344 = -440 --> 221 holes
F =2V-4: 234344 != 233464-4 (-884)
2E=3F: 703032 = 703032 (0)
total defect index = 442
cp ../surf/lh.qsphere.nofix ../surf/lh.qsphere
cp ../surf/lh.smoothwm.nofix ../surf/lh.smoothwm
/work/02510/sray2/Free_Sub/DATA/50011/50011/scripts
mris_topo_fixer -mgz -warnings -seed 1234 50011 lh
verbose mode on (medium mode): printing warnings
setting seed for random number genererator to 1234
Before topology correction, eno=-440 (nv=116732, nf=234344, ne=351516, g=221)
Surface Diagnostics:
eno=-440 (nv=116732, nf=234344, ne=351516)
# of border vertices [ #v ~ #f ] 0
# of edges with single face 0
# of edges with more than 2 faces 0
# of corner configurations 0
The original surface is a valid manifold
Counting the number of connected components
The original surface has one component
The original surface does not self-intersect
The surface has 221 loops (X=-440)
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 9 iterations
identify defects...
marking ambiguous vertices...
68425 ambiguous faces found in tessellation
segmenting defects...
analyzing defects for overlaps...
INFO: assuming .mgz format
reading input surface /work/02510/sray2/Free_Sub/DATA/50011/50011/surf/lh.orig...
reading brain volume from brain...
reading wm segmentation from wm...
Detecting contrast direction: right direction [ GM (86.66) < WM (96.03) ]
Computing Initial Surface Statistics
-face loglikelihood: -5.8578 (-2.9289)
-vertex loglikelihood: -5.7524 (-2.8762)
-normal dot loglikelihood: -3.6033 (-3.6033)
-quad curv loglikelihood: -5.8101 (-2.9050)
Total Loglikelihood : -21.0236
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
Correcting Topology of defect 1 with euler number -257 (129 loops)
computing statistics for defect 1: 33364 vertices
location: [ (156,125,84) - average intensity = 92.126 ]
-gray ( 86.57 , 6.29 ) -white ( 95.91 , 6.08 )
-gray ( 89.98 , 24.95 ) -white ( 98.58 , 24.03 )
-intensity (86.574921 [log = -2.404119 ]- 95.914825 [log = -2.517448 ])
-curv (k1=-0.162 (0.730) , r1 = 6.179 | k2=-0.060 (0.191), r2 = 16.806 )
-curv (k1=-0.124 (0.768) , r1 = 8.076 | k2=-0.032 (0.282), r2 = 31.306 )
MRISalloc(8654176, 520): could not allocate vertices
Cannot allocate memory
And In some of my subjects the log file stop writing after: “CORRECTING DEFECT 0 (vertices=53786, convex hull=13985)”
My question is what exactly these highlighted number means? Do I have an estimation of number of slices that are to be treated manually?
Thanks,
-Siddharth
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at https://urldefense.proofpoint.com/v1/url?u=http://www.partners.org/complianc... . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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Ray, Siddharth