External Email - Use Caution
I would like to follow-up this thread. I've encountered similar problem about the recon-all process is stuck at fix topology for a long time (10+ hours) [Centos 6, Freesurfer 6.0.0] I can't see any problem from log files, just as follows 1.
#@# Fix Topology Copy rh Fri Feb 15 00:34:11 CST 2019
/home/yfc/subjects/BK036/scripts
cp ../surf/rh.orig.nofix ../surf/rh.orig
cp ../surf/rh.inflated.nofix ../surf/rh.inflated
#@# Fix Topology lh Fri Feb 15 00:34:11 CST 2019
mris_fix_topology -rusage /home/yfc/subjects/BK036/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 BK036 lh
#@# Fix Topology rh Fri Feb 15 00:34:11 CST 2019
mris_fix_topology -rusage /home/yfc/subjects/BK036/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 BK036 rh
Waiting for PID 15635 of (15635 15638) to complete...
2.
#@# Fix Topology Copy rh Fri Feb 15 21:23:50 CST 2019
/home/yfc/subjects/BK151/scripts
cp ../surf/rh.orig.nofix ../surf/rh.orig
cp ../surf/rh.inflated.nofix ../surf/rh.inflated
#@# Fix Topology lh Fri Feb 15 21:23:50 CST 2019
mris_fix_topology -rusage /home/yfc/subjects/BK151/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 BK151 lh
#@# Fix Topology rh Fri Feb 15 21:23:50 CST 2019
mris_fix_topology -rusage /home/yfc/subjects/BK151/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 BK151 rh
Waiting for PID 16471 of (16471 16474) to complete...
Intriguingly, I've run through these subjects before on MacOS, Freesurfer 5.3.0 without error or being stuck.
What's the problem here?
Yi-Fang
Bruce Fischl fischl@nmr.mgh.harvard.edu 於 2019年2月15日 週五 下午11:13寫道：
Hi Milène
did you edit in freeview? Or something else? If you load the wm.mgz on top of the norm.mgz, does is still look to be in the same space? If so, feel free to tar and gzip the entire subject dir and upload it and we will take a look
cheers Bruce
On Fri, 15 Feb 2019, Milene Buerger wrote:
External Email - Use CautionThank you Bruce for your answer! I figured out how to edit the wm.mgz. Indeed some parts of the skull
were not properly removed from the
brainmask and therefor considered as white matter. I manually removed
voxels from the wm.mgz and then I
tried to reintegrate the wm.mgz to the recon-all command by doing the
mri_fill <inputvol> <outputvol>.
Unfortunately I got this error:
mbuerger@beo-05:
/data/projects/pediatric_mr_myelin/Evaluation_Milene/processed_with_freesurfer/FJ_2017042
5_T1/mri $ mri_fill wm.mgz filled.mgz reading input volume...done. searching for cutting planes...talairach transform 1.18336 0.13264 0.04891 10.53902; -0.11077 0.95044 0.09947 -11.50818; -0.00953 -0.18656 1.07681 -50.07034; 0.00000 0.00000 0.00000 1.00000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 voxel to talairach voxel transform 1.18336 0.04891 -0.13264 -14.02849; -0.00953 1.07681 0.18656 15.85732; 0.11077 -0.09947 0.95044 6.22865; 0.00000 0.00000 0.00000 1.00000; mri_fill: could not find valid seed for the cc Looking for area (min, max) = (350, 1400) area[0] = 9142 (min = 350, max = 1400), aspect = 0.54 (min = 0.10, max
= 0.75)
need search nearby using +/- offset search region where offset is 3..... using +/- offset search region where offset is 6..... using +/- offset search region where offset is 9..... using +/- offset search region where offset is 12..... area[0] = 597 (min = 350, max = 1400), aspect = 0.56 (min = 0.10, max =
0.75)
min_slice = -1, min_area = 65536 Looking for area (min, max) = (350, 1400) area[0] = 1874 (min = 350, max = 1400), aspect = 0.53 (min = 0.10, max
= 0.75)
need search nearby using +/- offset search region where offset is 3..... using +/- offset search region where offset is 6..... using +/- offset search region where offset is 9..... using +/- offset search region where offset is 12..... using +/- offset search region where offset is 15..... using +/- offset search region where offset is 18..... using +/- offset search region where offset is 21..... using +/- offset search region where offset is 24..... using +/- offset search region where offset is 27..... using +/- offset search region where offset is 30..... using +/- offset search region where offset is 33..... using +/- offset search region where offset is 36..... using +/- offset search region where offset is 39..... using +/- offset search region where offset is 42..... using +/- offset search region where offset is 45..... using +/- offset search region where offset is 48..... mri_fill: could not find corpus callosum
Do you have any ideas?
Milène
Gesendet: Mittwoch, 13. Februar 2019 um 16:01 Uhr Von: "Bruce Fischl" fischl@nmr.mgh.harvard.edu An: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Fix topology correcting defect Hi Milène
a couple of things. First, to view a surface in freeview you have to specify that it is a surface with -f before the surface file name. So, from the mri dir you could do:
freeview -v norm.mgz -f ../surf/lh.orig.nofix ../surf/lh.inflated.nofix
Second, how long did you wait? Big defects take a long time. You should definitely look at your inflated and orig surfaces though to make sure
that
some dramatic isn't wrong (like skull attached, or hemispheres not separated) as your defect is probably too large to be an ordinary one
that
the topo fixer will correct successfully.
cheers Bruce
On Wed, 13 Feb 2019, "Milene Bürger" wrote:
External Email - Use CautionHi Freesurfers, I tried to run the recon-all command for several subjects of my
study. It worked out for all of them
except for one. This one froze at fixing topology „Correcting defect“
11 out of 140 defects.
I looked for advises in the mailing list but I can’t find any major
problems in the images that
Freesurfer processed so far. The last correct file that I can open in
freeview, is filled.mgz (the
skull and cerebellum are properly removed and it shows the two
hemispheres with 127 for rh and 255
for lh). I can’t find the file "filled-pretess255.mgz“ which should
be the output, but I do have the
files lh.orig.nofix and rh.orig.nofix for example. I tried to look at
these files, but freeview
can't open them (failed to load MRI) so that I can’t see if there are
topological defects to correct
as you described on one of the FsTutorials. I already tried to run
only the autorecon2 command, but
the same freezing problem appeared at one point. I also tried to only
use the mri_pretess command
with different options, but it didn’t work.
I copied you the fix topology and what I tried with mri_pretess. I use
freesurfer version 6.0.1.
Thanks a lot!
Milène
mris_fix_topology-rusage/data/projects/pediatric_mr_myelin/Evaluation_Milene/processed_with_freesurfer/FJ_20170425_T1_Vers
u
ch_Pretess/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.
nofix -g 1234
FJ_20170425_T1_Versuch_Pretess 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 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ before topology correction, eno=-666 (nv=184736, nf=370804,
ne=556206, g=334)
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 11 iterations marking ambiguous vertices... 92297 ambiguous faces found in tessellation segmenting defects... 151 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 3 into 2 -merging segment 32 into 12 -merging segment 94 into 12 -merging segment 45 into 36 -merging segment 53 into 37 -merging segment 62 into 60 -merging segment 81 into 70 -merging segment 88 into 70 -merging segment 144 into 132 -merging segment 141 into 138 -merging segment 150 into 147 140 defects to be corrected 0 vertices coincident reading inputsurface
/data/projects/pediatric_mr_myelin/Evaluation_Milene/processed_with_freesurfer/FJ_20170425_T1_Vers
u
ch_Pretess/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.3516 (-4.6758) -vertex loglikelihood: -6.1930 (-3.0965) -normal dot loglikelihood: -3.5442 (-3.5442) -quad curv loglikelihood: -6.0556 (-3.0278) Total Loglikelihood : -25.1443
CORRECTING DEFECT 0 (vertices=9329, convex hull=1902, v0=235) XL defect detected... After retessellation of defect 0 (v0=235), euler #=-122
(135106,396534,261306) : difference with
theory (-137) = -15 CORRECTING DEFECT 1 (vertices=47, convex hull=87, v0=788) After retessellation of defect 1 (v0=788), euler #=-121
(135129,396640,261390) : difference with
theory (-136) = -15 CORRECTING DEFECT 2 (vertices=1438, convex hull=465, v0=1311) XL defect detected... After retessellation of defect 2 (v0=1311), euler #=-119
(135552,398142,262471) : difference with
theory (-135) = -16 CORRECTING DEFECT 3 (vertices=24, convex hull=64, v0=9358) After retessellation of defect 3 (v0=9358), euler #=-118
(135563,398202,262521) : difference with
theory (-134) = -16 CORRECTING DEFECT 4 (vertices=35, convex hull=54, v0=11845) After retessellation of defect 4 (v0=11845), euler #=-117
(135574,398251,262560) : difference with
theory (-133) = -16 CORRECTING DEFECT 5 (vertices=68, convex hull=94, v0=12131) After retessellation of defect 5 (v0=12131), euler #=-116
(135584,398327,262627) : difference with
theory (-132) = -16 CORRECTING DEFECT 6 (vertices=66, convex hull=29, v0=12470) After retessellation of defect 6 (v0=12470), euler #=-115
(135586,398344,262643) : difference with
theory (-131) = -16 CORRECTING DEFECT 7 (vertices=29, convex hull=34, v0=16888) After retessellation of defect 7 (v0=16888), euler #=-114
(135587,398360,262659) : difference with
theory (-130) = -16 CORRECTING DEFECT 8 (vertices=66, convex hull=79, v0=16899) After retessellation of defect 8 (v0=16899), euler #=-113
(135625,398509,262771) : difference with
theory (-129) = -16 CORRECTING DEFECT 9 (vertices=219, convex hull=64, v0=16932) After retessellation of defect 9 (v0=16932), euler #=-112
(135644,398592,262836) : difference with
theory (-128) = -16 CORRECTING DEFECT 10 (vertices=69, convex hull=58, v0=19570) After retessellation of defect 10 (v0=19570), euler #=-111
(135659,398659,262889) : difference with
theory (-127) = -16 CORRECTING DEFECT 11 (vertices=18978, convex hull=4487, v0=19837)
mri_pretess: mbuerger@beo-05:
/data/projects/pediatric_mr_myelin/Evaluation_Milene/processed_with_freesurfer/FJ_2
0170425_T1/mri $
rm
/data/projects/pediatric_mr_myelin/Evaluation_Milene/processed_with_freesurfer/FJ_20170425_T1_Versu
ch_Pretess/scripts/IsRunning.lh+rh rm: remove regular
file
`/data/projects/pediatric_mr_myelin/Evaluation_Milene/processed_with_freesurfer/FJ_20170425_T1_Vers
uch_Pretess/scripts/IsRunning.lh+rh'? mbuerger@beo-05:
/data/projects/pediatric_mr_myelin/Evaluation_Milene/processed_with_freesurfer/FJ_2
0170425_T1/mri $ mri_pretess -keep wm.mgz wm127 norm.mgz wm.mgz keeping edits Ambiguous edge configurations... Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 0 (out of 16189883: 0.000000) Searching for edits to keep ... kept 0 WM ON voxels kept 0 WM OFF voxels mri_pretess done
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