I have run freesurfer 6Beta on the scan with very large CSF spaces With flags: -bigventricles and -notal-check . I used the latter flag per suggestions in the log as the first run failed on a talaraich check. This second run appears to be hung as it has not written anything new into the recon-all.log file for 7 hours. I would like to restart this at a reasonable point rather than at the beginning. Can you recognize where it is and what is are suggested restart flags?
Here are the files which have appeared in the mri directory. aseg.auto.mgz aseg.presurf.mgz brainmask.mgz error.log mri_nu_correct.mni.log.bak nu_noneck.mgz orig_nu.log segment.dat talairach.log transforms wm.mgz aseg.auto_noCCseg.label_intensities.txt brain.finalsurfs.mgz brain.mgz filled.mgz norm.mgz orig orig_nu.mgz T1.mgz talairach_with_skull_2.log v.mgz wm.seg.mgz aseg.auto_noCCseg.mgz brainmask.auto.mgz ctrl_pts.mgz mri_nu_correct.mni.log nu.mgz orig.mgz rawavg.mgz talairach.label_intensities.txt talairach_with_skull.log wm.asegedit.mgz
Here are the last 50 lines or so of the log file: ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2 ion: 3.10.73-1.el6.elrepo.x86_64 CompilerName: GCC CompilerVersion: 40400 ...skipping... mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 201 lh
reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234
************************************************************* 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
************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.767.2.2 2015/07/06 21:59:21 greve Exp $ before topology correction, eno=-510 (nv=99342, nf=199704, ne=299556, g=256) 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... 111330 ambiguous faces found in tessellation segmenting defects... 38 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 13 into 0 -merging segment 23 into 0 -merging segment 29 into 0 -merging segment 32 into 0 -merging segment 36 into 0 -merging segment 16 into 12 -merging segment 15 into 14 31 defects to be corrected 0 vertices coincident reading input surface /oasis/scratch/comet/donkri/temp_project/subjects/201/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2710 (-4.6355) -vertex loglikelihood: -8.2866 (-4.1433) -normal dot loglikelihood: -3.4816 (-3.4816) -quad curv loglikelihood: -6.0138 (-3.0069) Total Loglikelihood : -27.0531
CORRECTING DEFECT 0 (vertices=53053, convex hull=8873)
Thanks for your direction on this. - Don
Hi Don
the defect is too big to fix, and probably means something dramatic is wrong (e.g. skull or cerebellum attached to the brain component of the wm.mgz). Check out the ?h.inflated.nofix and see what is going on and correct it before rerunning
cheers Bruce On Wed, 18 Nov 2015, Krieger, Donald N. wrote:
I have run freesurfer 6Beta on the scan with very large CSF spaces
With flags: -bigventricles and –notal-check .
I used the latter flag per suggestions in the log as the first run failed on a talaraich check.
This second run appears to be hung as it has not written anything new into the recon-all.log file for 7 hours.
I would like to restart this at a reasonable point rather than at the beginning.
Can you recognize where it is and what is are suggested restart flags?
Here are the files which have appeared in the mri directory.
aseg.auto.mgz aseg.presurf.mgz brainmask.mgz error.log mri_nu_correct.mni.log.bak nu_noneck.mgz orig_nu.log segment.dat talairach.log transforms wm.mgz
aseg.auto_noCCseg.label_intensities.txt brain.finalsurfs.mgz brain.mgz filled.mgz norm.mgz orig orig_nu.mgz T1.mgz talairach_with_skull_2.log v.mgz wm.seg.mgz
aseg.auto_noCCseg.mgz brainmask.auto.mgz ctrl_pts.mgz mri_nu_correct.mni.log nu.mgz orig.mgz rawavg.mgz talairach.label_intensities.txt talairach_with_skull.log wm.asegedit.mgz
Here are the last 50 lines or so of the log file:
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2
ion: 3.10.73-1.el6.elrepo.x86_64 CompilerName: GCC CompilerVersion: 40400
...skipping...
mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 201 lh
reading spherical homeomorphism from 'qsphere.nofix'
using genetic algorithm with optimized parameters
setting seed for random number genererator to 1234
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
INFO: assuming .mgz format
$Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $
$Id: mrisurf.c,v 1.767.2.2 2015/07/06 21:59:21 greve Exp $
before topology correction, eno=-510 (nv=99342, nf=199704, ne=299556, g=256)
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...
111330 ambiguous faces found in tessellation
segmenting defects...
38 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
-merging segment 13 into 0
-merging segment 23 into 0
-merging segment 29 into 0
-merging segment 32 into 0
-merging segment 36 into 0
-merging segment 16 into 12
-merging segment 15 into 14
31 defects to be corrected
0 vertices coincident
reading input surface/oasis/scratch/comet/donkri/temp_project/subjects/201/surf/lh.qsphere.nofix ...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
-face loglikelihood: -9.2710 (-4.6355)
-vertex loglikelihood: -8.2866 (-4.1433)
-normal dot loglikelihood: -3.4816 (-3.4816)
-quad curv loglikelihood: -6.0138 (-3.0069)
Total Loglikelihood : -27.0531
CORRECTING DEFECT 0 (vertices=53053, convex hull=8873)
Thanks for your direction on this. - Don
Thanks, Bruce. - Don
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer- bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Wednesday, November 18, 2015 8:55 AM To: Freesurfer support list Subject: Re: [Freesurfer] direction for restart in the middle
Hi Don
the defect is too big to fix, and probably means something dramatic is wrong (e.g. skull or cerebellum attached to the brain component of the wm.mgz). Check out the ?h.inflated.nofix and see what is going on and correct it before rerunning
cheers Bruce On Wed, 18 Nov 2015, Krieger, Donald N. wrote:
I have run freesurfer 6Beta on the scan with very large CSF spaces
With flags: -bigventricles and –notal-check .
I used the latter flag per suggestions in the log as the first run failed on a talaraich check.
This second run appears to be hung as it has not written anything new into the recon-all.log file for 7 hours.
I would like to restart this at a reasonable point rather than at the beginning.
Can you recognize where it is and what is are suggested restart flags?
Here are the files which have appeared in the mri directory.
aseg.auto.mgz aseg.presurf.mgz brainmask.mgz error.log mri_nu_correct.mni.log.bak nu_noneck.mgz orig_nu.log segment.dat talairach.log transforms wm.mgz
aseg.auto_noCCseg.label_intensities.txt brain.finalsurfs.mgz brain.mgz filled.mgz norm.mgz orig orig_nu.mgz T1.mgz talairach_with_skull_2.log v.mgz wm.seg.mgz
aseg.auto_noCCseg.mgz brainmask.auto.mgz ctrl_pts.mgz mri_nu_correct.mni.log nu.mgz orig.mgz rawavg.mgz talairach.label_intensities.txt talairach_with_skull.log wm.asegedit.mgz
Here are the last 50 lines or so of the log file:
ProgramName: mri_ca_normalize ProgramArguments: -all-
info ProgramVersion:
$Name: stable5 $ TimeStamp: 2
ion: 3.10.73-1.el6.elrepo.x86_64 CompilerName: GCC CompilerVersion: 40400
...skipping...
mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 201 lh
reading spherical homeomorphism from 'qsphere.nofix'
using genetic algorithm with optimized parameters
setting seed for random number genererator to 1234
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
INFO: assuming .mgz format
$Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $
$Id: mrisurf.c,v 1.767.2.2 2015/07/06 21:59:21 greve Exp $
before topology correction, eno=-510 (nv=99342, nf=199704, ne=299556, g=256)
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...
111330 ambiguous faces found in tessellation
segmenting defects...
38 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
-merging segment 13 into 0
-merging segment 23 into 0
-merging segment 29 into 0
-merging segment 32 into 0
-merging segment 36 into 0
-merging segment 16 into 12
-merging segment 15 into 14
31 defects to be corrected
0 vertices coincident
reading input surface/oasis/scratch/comet/donkri/temp_project/subjects/201/surf/lh.q sphere.nofix ...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
-face loglikelihood: -9.2710 (-4.6355)
-vertex loglikelihood: -8.2866 (-4.1433)
-normal dot loglikelihood: -3.4816 (-3.4816)
-quad curv loglikelihood: -6.0138 (-3.0069)
Total Loglikelihood : -27.0531
CORRECTING DEFECT 0 (vertices=53053, convex hull=8873)
Thanks for your direction on this. - Don
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Krieger, Donald N.