Hi freeserver folks,
First time poster here. First off, thanks so much to the folks who work on and make this software available to the public. It seems like pretty incredible tech, from what little I understand of it. :)
My problem is that the freesurfer process appears to be stuck on the recon-all command. It’s been sitting at ”CORRECTING DEFECT 0 (vertices=96285, convex hull=13916)” for about 10 hours now. Any way to cut that number down or should I just let it keep doing its thing? I’ve pasted all of the output pasted at end of the message.
Thanks so much!
Dan
************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-684 (nv=141228, nf=283824, ne=425736, g=343) 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 14 iterations marking ambiguous vertices... 190731 ambiguous faces found in tessellation segmenting defects... 40 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 2 into 0 -merging segment 5 into 0 -merging segment 8 into 0 -merging segment 14 into 0 -merging segment 25 into 0 -merging segment 28 into 0 -merging segment 20 into 17 -merging segment 29 into 17 -merging segment 36 into 35 31 defects to be corrected 0 vertices coincident reading input surface /Applications/freesurfer/subjects/Dan/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.8790 (-4.4395) -vertex loglikelihood: -7.4039 (-3.7020) -normal dot loglikelihood: -3.5029 (-3.5029) -quad curv loglikelihood: -6.1567 (-3.0783) Total Loglikelihood : -25.9425
CORRECTING DEFECT 0 (vertices=96285, convex hull=13916)
Hi Dan
that defect is too big, there must be something wrong. Check to see if the surface is connected to dura or across the hemis or something. You can look at the lh.inflated.nofix and/or the lh.orig.nofix to see where the defects are. Then you'll need to correct something once you've figured out why there is such a huge defect.
cheers Bruce
p.s. if you can't sort this out you can tar and gzip your whole subject dir and we will take a look
On Fri, 24 Jun 2016, Dan Loewenherz wrote:
Hi freeserver folks,
First time poster here. First off, thanks so much to the folks who work on and make this software available to the public. It seems like pretty incredible tech, from what little I understand of it. :)
My problem is that the freesurfer process appears to be stuck on the recon-all command. It’s been sitting at ”CORRECTING DEFECT 0 (vertices=96285, convex hull=13916)” for about 10 hours now. Any way to cut that number down or should I just let it keep doing its thing? I’ve pasted all of the output pasted at end of the message.
Thanks so much!
Dan
INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-684 (nv=141228, nf=283824, ne=425736, g=343) 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 14 iterations marking ambiguous vertices... 190731 ambiguous faces found in tessellation segmenting defects... 40 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 2 into 0 -merging segment 5 into 0 -merging segment 8 into 0 -merging segment 14 into 0 -merging segment 25 into 0 -merging segment 28 into 0 -merging segment 20 into 17 -merging segment 29 into 17 -merging segment 36 into 35 31 defects to be corrected 0 vertices coincident reading input surface /Applications/freesurfer/subjects/Dan/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.8790 (-4.4395) -vertex loglikelihood: -7.4039 (-3.7020) -normal dot loglikelihood: -3.5029 (-3.5029) -quad curv loglikelihood: -6.1567 (-3.0783) Total Loglikelihood : -25.9425
CORRECTING DEFECT 0 (vertices=96285, convex hull=13916)
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce,
Thanks for the tips. I tried playing around with the files for a bit but didn’t make much progress.
Here’s a link to the full tar/gz’ed subject dir: http://gate.nmr.mgh.harvard.edu/filedrop2/?p=4ej948sa49s
Thanks! Dan
On Fri Jun 24 22:22:17 EDT 2016, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Dan
that defect is too big, there must be something wrong. Check to see if the surface is connected to dura or across the hemis or something. You can look at the lh.inflated.nofix and/or the lh.orig.nofix to see where the defects are. Then you'll need to correct something once you've figured out why there is such a huge defect.
cheers Bruce
p.s. if you can't sort this out you can tar and gzip your whole subject dir and we will take a look
On Fri, Jun 24, 2016 at 9:15 PM, Dan Loewenherz daniel.loewenherz@aya.yale.edu wrote:
Hi freeserver folks,
First time poster here. First off, thanks so much to the folks who work on and make this software available to the public. It seems like pretty incredible tech, from what little I understand of it. :)
My problem is that the freesurfer process appears to be stuck on the recon-all command. It’s been sitting at ”CORRECTING DEFECT 0 (vertices=96285, convex hull=13916)” for about 10 hours now. Any way to cut that number down or should I just let it keep doing its thing? I’ve pasted all of the output pasted at end of the message.
Thanks so much!
Dan
************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-684 (nv=141228, nf=283824,ne=425736, g=343) 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 14 iterations marking ambiguous vertices... 190731 ambiguous faces found in tessellation segmenting defects... 40 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 2 into 0 -merging segment 5 into 0 -merging segment 8 into 0 -merging segment 14 into 0 -merging segment 25 into 0 -merging segment 28 into 0 -merging segment 20 into 17 -merging segment 29 into 17 -merging segment 36 into 35 31 defects to be corrected 0 vertices coincident reading input surface/Applications/freesurfer/subjects/Dan/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.8790 (-4.4395) -vertex loglikelihood: -7.4039 (-3.7020) -normal dot loglikelihood: -3.5029 (-3.5029) -quad curv loglikelihood: -6.1567 (-3.0783) Total Loglikelihood : -25.9425
CORRECTING DEFECT 0 (vertices=96285, convex hull=13916)
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Dan Loewenherz