Hi all,
I got the following error while running recon-all on a patient dataset. Kindly let me know how to proceed.
Thanks! Sindhuja
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... 129422 ambiguous faces found in tessellation segmenting defects... 51 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 1 into 0 -merging segment 2 into 0 -merging segment 8 into 0 -merging segment 5 into 7 -merging segment 28 into 12 -merging segment 35 into 31 -merging segment 47 into 43 44 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/mscat/users/caterina/3T/recons-04082011/MS_pt20_recon/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.5482 (-4.7741) -vertex loglikelihood: -6.9824 (-3.4912) -normal dot loglikelihood: -3.5307 (-3.5307) -quad curv loglikelihood: -5.9945 (-2.9973) Total Loglikelihood : -26.0558
CORRECTING DEFECT 0 (vertices=50712, convex hull=8198) Segmentation fault
recon-all -s MS_pt20_recon exited with ERRORS at Wed Oct 26 18:49:31 EDT 2011
Hi
you probably ran out of memory. That's a giant defect so something is badly wrong. Check to make sure that the hemis are separated and that the skull and cerebellum aren't attached Bruce On Wed, 26 Oct 2011, Sindhuja Tirumalai Govindarajan wrote:
Hi all,
I got the following error while running recon-all on a patient dataset. Kindly let me know how to proceed.
Thanks! Sindhuja
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... 129422 ambiguous faces found in tessellation segmenting defects... 51 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 1 into 0 -merging segment 2 into 0 -merging segment 8 into 0 -merging segment 5 into 7 -merging segment 28 into 12 -merging segment 35 into 31 -merging segment 47 into 43 44 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/mscat/users/caterina/3T/recons-04082011/MS_pt20_recon/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.5482 (-4.7741) -vertex loglikelihood: -6.9824 (-3.4912) -normal dot loglikelihood: -3.5307 (-3.5307) -quad curv loglikelihood: -5.9945 (-2.9973) Total Loglikelihood : -26.0558
CORRECTING DEFECT 0 (vertices=50712, convex hull=8198) Segmentation fault
recon-all -s MS_pt20_recon exited with ERRORS at Wed Oct 26 18:49:31 EDT 2011
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Folks
I am using Freesurfer 5.1 and I get the following error: "ERROR: _FindFacePath: could not find path!"
Is this is a memory related issue ? The same case went through smoothly with Freesurfer 5.0. Also I have not seen this error over a large number of subjects and I thought it might be system related, but even when I re-run it, I get the same error.
From the recon-all.error file, the last command is "mris_topo_fixer -mgz
-warnings -seed 1234 ms0709_01 rh"
Here is a small snippet from the recon-all.log file (just before the error)
Correcting Topology of defect 28 with euler number -1 (1 loops) computing statistics for defect 28: 288 vertices location: [ (106,175,134) - average intensity = 89.717 ] -gray ( 85.29 , 6.61 ) -white ( 95.96 , 3.49 ) -gray ( 83.95 , 18.89 ) -white ( 98.95 , 17.00 ) -intensity (85.286896 [log = -2.118856 ]- 95.961853 [log = -2.118159 ]) -curv (k1=-0.131 (0.556) , r1 = 7.623 | k2=-0.051 (0.131), r2 = 19.605 ) -curv (k1=-0.105 (0.609) , r1 = 9.520 | k2=-0.023 (0.212), r2 = 42.735 ) max face = 548(548) - loop = 1 (1) - ntries = [83,229]
BEST FITNESS (o)is -6.78736 mri =0.000 curv = 1.594 unmri = 0.410 ( f=0.00 , v=0.00 , c=1.59 , q= 3.19 ) ( f=0.00 , v=0.00 , c=1.59 , q= 3.19 )
BEST FITNESS (M) is -6.40381 mri =0.000 curv = 2.115 unmri = -2.054 ( f=0.00 , v=0.00 , c=2.11 , q= 4.23 ) ( f=0.00 , v=0.00 , c=2.11 , q= 4.23 )
ERROR: _FindFacePath: could not find path!
Thanks Mehul
On Wed, Oct 26, 2011 at 6:03 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi
you probably ran out of memory. That's a giant defect so something is badly wrong. Check to make sure that the hemis are separated and that the skull and cerebellum aren't attached Bruce On Wed, 26 Oct 2011, Sindhuja Tirumalai Govindarajan wrote:
Hi all,
I got the following error while running recon-all on a patient dataset. Kindly let me know how to proceed.
Thanks! Sindhuja
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... 129422 ambiguous faces found in tessellation segmenting defects... 51 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 1 into 0 -merging segment 2 into 0 -merging segment 8 into 0 -merging segment 5 into 7 -merging segment 28 into 12 -merging segment 35 into 31 -merging segment 47 into 43 44 defects to be corrected 0 vertices coincident reading input surface
/autofs/cluster/mscat/users/caterina/3T/recons-04082011/MS_pt20_recon/surf/lh.qsphere.nofix...
reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.5482 (-4.7741) -vertex loglikelihood: -6.9824 (-3.4912) -normal dot loglikelihood: -3.5307 (-3.5307) -quad curv loglikelihood: -5.9945 (-2.9973) Total Loglikelihood : -26.0558
CORRECTING DEFECT 0 (vertices=50712, convex hull=8198) Segmentation fault
recon-all -s MS_pt20_recon exited with ERRORS at Wed Oct 26 18:49:31 EDT
2011
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 http://www.partners.org/complianceline . 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.
Hi Mehul
this is a bug in the topology correction that we haven't been able to track down, mainly because the person who wrote this piece is long gone. If you edit the wm to remove a defect it usually goes away
Bruce On Mon, 31 Oct 2011, Mehul Sampat wrote:
Hi Folks
I am using Freesurfer 5.1 and I get the following error: "ERROR: _FindFacePath: could not find path!"
Is this is a memory related issue ? The same case went through smoothly with Freesurfer 5.0. Also I have not seen this error over a large number of subjects and I thought it might be system related, but even when I re-run it, I get the same error.
From the recon-all.error file, the last command is "mris_topo_fixer -mgz -warnings -seed 1234 ms0709_01 rh" Here is a small snippet from the recon-all.log file (just before the error)
Correcting Topology of defect 28 with euler number -1 (1 loops) computing statistics for defect 28: 288 vertices location: [ (106,175,134) - average intensity = 89.717 ] -gray ( 85.29 , 6.61 ) -white ( 95.96 , 3.49 ) -gray ( 83.95 , 18.89 ) -white ( 98.95 , 17.00 ) -intensity (85.286896 [log = -2.118856 ]- 95.961853 [log = -2.118159 ]) -curv (k1=-0.131 (0.556) , r1 = 7.623 | k2=-0.051 (0.131), r2 = 19.605 ) -curv (k1=-0.105 (0.609) , r1 = 9.520 | k2=-0.023 (0.212), r2 = 42.735 ) max face = 548(548) - loop = 1 (1) - ntries = [83,229]
BEST FITNESS (o)is -6.78736 mri =0.000 curv = 1.594 unmri = 0.410 ( f=0.00 , v=0.00 , c=1.59 , q= 3.19 ) ( f=0.00 , v=0.00 , c=1.59 , q= 3.19 )
BEST FITNESS (M) is -6.40381 mri =0.000 curv = 2.115 unmri = -2.054 ( f=0.00 , v=0.00 , c=2.11 , q= 4.23 ) ( f=0.00 , v=0.00 , c=2.11 , q= 4.23 )
ERROR: _FindFacePath: could not find path!
Thanks Mehul
On Wed, Oct 26, 2011 at 6:03 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi
you probably ran out of memory. That's a giant defect so something is badly wrong. Check to make sure that the hemis are separated and that the skull and cerebellum aren't attached BruceOn Wed, 26 Oct 2011, Sindhuja Tirumalai Govindarajan wrote:
Hi all,
I got the following error while running recon-all on a patient
dataset.
Kindly let me know how to proceed.
Thanks! Sindhuja
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... 129422 ambiguous faces found in tessellation segmenting defects... 51 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 1 into 0 -merging segment 2 into 0 -merging segment 8 into 0 -merging segment 5 into 7 -merging segment 28 into 12 -merging segment 35 into 31 -merging segment 47 into 43 44 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/mscat/users/caterina/3T/recons-04082011/MS_pt20_recon/surf/
lh.qsphere.nofix...
reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.5482 (-4.7741) -vertex loglikelihood: -6.9824 (-3.4912) -normal dot loglikelihood: -3.5307 (-3.5307) -quad curv loglikelihood: -5.9945 (-2.9973) Total Loglikelihood : -26.0558
CORRECTING DEFECT 0 (vertices=50712, convex hull=8198) Segmentation fault
recon-all -s MS_pt20_recon exited with ERRORS at Wed Oct 26 18:49:31
EDT 2011
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 http://www.partners.org/complianceline . 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.
Hi Mehul, Alternatively you can try rerunning the skullstrip step, sometimes this works as well.
recon-all -skullstrip -autorecon2 -autorecon3 -s [SubjID]
-Louis
On Tue, 1 Nov 2011, Bruce Fischl wrote:
Hi Mehul
this is a bug in the topology correction that we haven't been able to track down, mainly because the person who wrote this piece is long gone. If you edit the wm to remove a defect it usually goes away
Bruce On Mon, 31 Oct 2011, Mehul Sampat wrote:
Hi Folks
I am using Freesurfer 5.1 and I get the following error: "ERROR: _FindFacePath: could not find path!"
Is this is a memory related issue ? The same case went through smoothly with Freesurfer 5.0. Also I have not seen this error over a large number of subjects and I thought it might be system related, but even when I re-run it, I get the same error.
From the recon-all.error file, the last command is "mris_topo_fixer -mgz -warnings -seed 1234 ms0709_01 rh" Here is a small snippet from the recon-all.log file (just before the error)
Correcting Topology of defect 28 with euler number -1 (1 loops) computing statistics for defect 28: 288 vertices location: [ (106,175,134) - average intensity = 89.717 ] -gray ( 85.29 , 6.61 ) -white ( 95.96 , 3.49 ) -gray ( 83.95 , 18.89 ) -white ( 98.95 , 17.00 ) -intensity (85.286896 [log = -2.118856 ]- 95.961853 [log = -2.118159 ] ) -curv (k1=-0.131 (0.556) , r1 = 7.623 | k2=-0.051 (0.131), r2 = 19.605 ) -curv (k1=-0.105 (0.609) , r1 = 9.520 | k2=-0.023 (0.212), r2 = 42.735 ) max face = 548(548) - loop = 1 (1) - ntries = [83,229]
BEST FITNESS (o)is -6.78736 mri =0.000 curv = 1.594 unmri = 0.410 ( f=0.00 , v=0.00 , c=1.59 , q= 3.19 ) ( f=0.00 , v=0.00 , c=1.59 , q= 3.19 )
BEST FITNESS (M) is -6.40381 mri =0.000 curv = 2.115 unmri = -2.054 ( f=0.00 , v=0.00 , c=2.11 , q= 4.23 ) ( f=0.00 , v=0.00 , c=2.11 , q= 4.23 )
ERROR: _FindFacePath: could not find path!
Thanks Mehul
On Wed, Oct 26, 2011 at 6:03 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi
you probably ran out of memory. That's a giant defect so something is badly wrong. Check to make sure that the hemis are separated and that the skull and cerebellum aren't attached BruceOn Wed, 26 Oct 2011, Sindhuja Tirumalai Govindarajan wrote:
Hi all,
I got the following error while running recon-all on a patient
dataset.
Kindly let me know how to proceed.
Thanks! Sindhuja
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... 129422 ambiguous faces found in tessellation segmenting defects... 51 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 1 into 0 -merging segment 2 into 0 -merging segment 8 into 0 -merging segment 5 into 7 -merging segment 28 into 12 -merging segment 35 into 31 -merging segment 47 into 43 44 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/mscat/users/caterina/3T/recons-04082011/MS_pt20_recon/surf/
lh.qsphere.nofix...
reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.5482 (-4.7741) -vertex loglikelihood: -6.9824 (-3.4912) -normal dot loglikelihood: -3.5307 (-3.5307) -quad curv loglikelihood: -5.9945 (-2.9973) Total Loglikelihood : -26.0558
CORRECTING DEFECT 0 (vertices=50712, convex hull=8198) Segmentation fault
recon-all -s MS_pt20_recon exited with ERRORS at Wed Oct 26 18:49:31
EDT 2011
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 http://www.partners.org/complianceline . 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.
Hi Bruce and Louis,
Thank you for the suggestions. I will try them out.
Just fyi. For our dataset this error is very rare. So far it occured only in 1 out of 525+ scans processed with FS 5.1.
Thank you, Mehul
On Tue, Nov 1, 2011 at 6:50 AM, Louis Nicholas Vinke < vinke@nmr.mgh.harvard.edu> wrote:
Hi Mehul, Alternatively you can try rerunning the skullstrip step, sometimes this works as well.
recon-all -skullstrip -autorecon2 -autorecon3 -s [SubjID]
-Louis
On Tue, 1 Nov 2011, Bruce Fischl wrote:
Hi Mehul
this is a bug in the topology correction that we haven't been able to track down, mainly because the person who wrote this piece is long gone. If you edit the wm to remove a defect it usually goes away
Bruce On Mon, 31 Oct 2011, Mehul Sampat wrote:
Hi Folks
I am using Freesurfer 5.1 and I get the following error: "ERROR: _FindFacePath: could not find path!"
Is this is a memory related issue ? The same case went through smoothly with Freesurfer 5.0. Also I have not seen this error over a large number of subjects and I thought it might be system related, but even when I re-run it, I get the same error.
From the recon-all.error file, the last command is "mris_topo_fixer -mgz -warnings -seed 1234 ms0709_01 rh"
Here is a small snippet from the recon-all.log file (just before the error)
Correcting Topology of defect 28 with euler number -1 (1 loops) computing statistics for defect 28: 288 vertices location: [ (106,175,134) - average intensity = 89.717 ] -gray ( 85.29 , 6.61 ) -white ( 95.96 , 3.49 ) -gray ( 83.95 , 18.89 ) -white ( 98.95 , 17.00 ) -intensity (85.286896 [log = -2.118856 ]- 95.961853 [log = -2.118159 ] ) -curv (k1=-0.131 (0.556) , r1 = 7.623 | k2=-0.051 (0.131), r2 = 19.605 ) -curv (k1=-0.105 (0.609) , r1 = 9.520 | k2=-0.023 (0.212), r2 = 42.735 ) max face = 548(548) - loop = 1 (1) - ntries = [83,229]
BEST FITNESS (o)is -6.78736 mri =0.000 curv = 1.594 unmri = 0.410 ( f=0.00 , v=0.00 , c=1.59 , q= 3.19 ) ( f=0.00 , v=0.00 , c=1.59 , q= 3.19 ) BEST FITNESS (M) is -6.40381 mri =0.000 curv = 2.115 unmri = -2.054 ( f=0.00 , v=0.00 , c=2.11 , q= 4.23 ) ( f=0.00 , v=0.00 , c=2.11 , q= 4.23 )ERROR: _FindFacePath: could not find path!
Thanks Mehul
On Wed, Oct 26, 2011 at 6:03 PM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote: Hi
you probably ran out of memory. That's a giant defect so something is badly wrong. Check to make sure that the hemis are separated and that the skull and cerebellum aren't attached BruceOn Wed, 26 Oct 2011, Sindhuja Tirumalai Govindarajan wrote:
Hi all,
I got the following error while running recon-all on a patient
dataset.
Kindly let me know how to proceed.
Thanks!
Sindhuja
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... 129422 ambiguous faces found in tessellation segmenting defects... 51 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 1 into 0 -merging segment 2 into 0 -merging segment 8 into 0 -merging segment 5 into 7 -merging segment 28 into 12 -merging segment 35 into 31 -merging segment 47 into 43 44 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/mscat/users/**caterina/3T/recons-04082011/**
MS_pt20_recon/surf/ lh.qsphere.nofix...
reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.5482 (-4.7741) -vertex loglikelihood: -6.9824 (-3.4912) -normal dot loglikelihood: -3.5307 (-3.5307) -quad curv loglikelihood: -5.9945 (-2.9973) Total Loglikelihood : -26.0558
CORRECTING DEFECT 0 (vertices=50712, convex hull=8198)
Segmentation fault
recon-all -s MS_pt20_recon exited with ERRORS at Wed Oct 26 18:49:31
EDT 2011
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______________________________**_________________
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. 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.
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Louis Nicholas Vinke -
Mehul Sampat -
Sindhuja Tirumalai Govindarajan