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nipreps / fmriprep

fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.
https://fmriprep.org
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Error with-- cannot run freesurfer #1545

Closed BolinCao closed 5 years ago

BolinCao commented 5 years ago

Hello, I'm confused on the freesurfer running for the last three subjects, all time run this step: resume recon-all : recon-all -autorecon-hemi lh -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nohyporelabel -noaparc2aseg -noapas2aseg -nosegstats -nowmparc -nobalabels -openmp 8 -subjid sub-055 -sd /out/freesurfer

sometime reported this crash.

Node: _autorecon_surfs0 Working directory: /tmp/work/fmriprep_wf/single_subject_082_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs0

Node inputs:

FLAIR_file = T1_files = T2_file = args = big_ventricles = brainstem = directive = autorecon-hemi environ = {} expert = flags = ['-noparcstats', '-nocortparc2', '-noparcstats2', '-nocortparc3', '-noparcstats3', '-nopctsurfcon', '-nohyporelabel', '-noaparc2aseg', '-noapas2aseg', '-nosegstats', '-nowmparc', '-nobalabels'] hemi = lh hippocampal_subfields_T1 = hippocampal_subfields_T2 = hires = mprage = mri_aparc2aseg = mri_ca_label = mri_ca_normalize = mri_ca_register = mri_edit_wm_with_aseg = mri_em_register = mri_fill = mri_mask = mri_normalize = mri_pretess = mri_remove_neck = mri_segment = mri_segstats = mri_tessellate = mri_watershed = mris_anatomical_stats = mris_ca_label = mris_fix_topology = mris_inflate = mris_make_surfaces = mris_register = mris_smooth = mris_sphere = mris_surf2vol = mrisp_paint = openmp = 8 parallel = subject_id = sub-082 subjects_dir = /out/freesurfer talairach = use_FLAIR = use_T2 = xopts =

Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node result['result'] = node.run(updatehash=updatehash) File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 471, in run result = self._run_interface(execute=True) File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 555, in _run_interface return self._run_command(execute) File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_command result = self._interface.run(cwd=outdir) File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 522, in run runtime = self._run_interface(runtime) File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 1038, in _run_interface self.raise_exception(runtime) File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 975, in raise_exception ).format(**runtime.dictcopy())) RuntimeError: Command: recon-all -autorecon-hemi lh -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nohyporelabel -noaparc2aseg -noapas2aseg -nosegstats -nowmparc -nobalabels -openmp 8 -subjid sub-082 -sd /out/freesurfer Standard output: Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a INFO: SUBJECTS_DIR is /out/freesurfer Actual FREESURFER_HOME /opt/freesurfer Linux b16d469ba965 4.4.0-141-generic #167~14.04.1-Ubuntu SMP Mon Dec 10 13:20:24 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux '/opt/freesurfer/bin/recon-all' -> '/out/freesurfer/sub-082/scripts/recon-all.local-copy'

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@# Tessellate lh Wed Mar 13 00:45:54 UTC 2019

/out/freesurfer/sub-082/scripts

mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz

Iteration Number : 1 pass 1 (xy+): 5 found - 5 modified | TOTAL: 5 pass 2 (xy+): 0 found - 5 modified | TOTAL: 5 pass 1 (xy-): 2 found - 2 modified | TOTAL: 7 pass 2 (xy-): 0 found - 2 modified | TOTAL: 7 pass 1 (yz+): 3 found - 3 modified | TOTAL: 10 pass 2 (yz+): 0 found - 3 modified | TOTAL: 10 pass 1 (yz-): 2 found - 2 modified | TOTAL: 12 pass 2 (yz-): 0 found - 2 modified | TOTAL: 12 pass 1 (xz+): 1 found - 1 modified | TOTAL: 13 pass 2 (xz+): 0 found - 1 modified | TOTAL: 13 pass 1 (xz-): 3 found - 3 modified | TOTAL: 16 pass 2 (xz-): 0 found - 3 modified | TOTAL: 16 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 (+-): 2 found - 2 modified | TOTAL: 2 pass 2 (+-): 0 found - 2 modified | TOTAL: 2 pass 1 (--): 4 found - 4 modified | TOTAL: 6 pass 2 (--): 0 found - 4 modified | TOTAL: 6 pass 1 (-+): 1 found - 1 modified | TOTAL: 7 pass 2 (-+): 0 found - 1 modified | TOTAL: 7 Iteration Number : 2 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 : 2 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 : 2 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 = 23 (out of 326350: 0.007048) Ambiguous edge configurations...

mri_pretess done

mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix

$Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 50: 62 vertices, 80 faces slice 60: 3767 vertices, 3991 faces slice 70: 12903 vertices, 13302 faces slice 80: 23047 vertices, 23511 faces slice 90: 33113 vertices, 33588 faces slice 100: 44483 vertices, 45100 faces slice 110: 57268 vertices, 57889 faces slice 120: 69266 vertices, 69901 faces slice 130: 80948 vertices, 81672 faces slice 140: 92777 vertices, 93507 faces slice 150: 103049 vertices, 103825 faces slice 160: 113567 vertices, 114382 faces slice 170: 124012 vertices, 124947 faces slice 180: 133377 vertices, 134284 faces slice 190: 140405 vertices, 141245 faces slice 200: 142300 vertices, 142948 faces slice 210: 142300 vertices, 142948 faces slice 220: 142300 vertices, 142948 faces slice 230: 142300 vertices, 142948 faces slice 240: 142300 vertices, 142948 faces slice 250: 142300 vertices, 142948 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000;

rm -f ../mri/filled-pretess255.mgz

mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix

counting number of connected components... 142300 voxel in cpt #1: X=-648 [v=142300,e=428844,f=285896] located at (-34.191639, -6.548222, 19.964750) For the whole surface: X=-648 [v=142300,e=428844,f=285896] One single component has been found nothing to do done

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@# Smooth1 lh Wed Mar 13 00:45:58 UTC 2019

/out/freesurfer/sub-082/scripts

mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix

setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms...

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@# Inflation1 lh Wed Mar 13 00:46:02 UTC 2019

/out/freesurfer/sub-082/scripts

mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix

Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 46.6 mm, total surface area = 69974 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.2 minutes

step 000: RMS=0.203 (target=0.015)
step 005: RMS=0.162 (target=0.015)
step 010: RMS=0.142 (target=0.015)
step 015: RMS=0.134 (target=0.015)
step 020: RMS=0.128 (target=0.015)
step 025: RMS=0.124 (target=0.015)
step 030: RMS=0.120 (target=0.015)
step 035: RMS=0.117 (target=0.015)
step 040: RMS=0.116 (target=0.015)
step 045: RMS=0.116 (target=0.015)
step 050: RMS=0.115 (target=0.015)
step 055: RMS=0.115 (target=0.015)
step 060: RMS=0.115 (target=0.015)
inflation complete. Not saving sulc mris_inflate utimesec 61.348000 mris_inflate stimesec 0.532000 mris_inflate ru_maxrss 233440 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 57094 mris_inflate ru_majflt 8 mris_inflate ru_nswap 0 mris_inflate ru_inblock 1504 mris_inflate ru_oublock 10040 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 67501 mris_inflate ru_nivcsw 6493

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@# QSphere lh Wed Mar 13 00:46:16 UTC 2019

/out/freesurfer/sub-082/scripts

mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix

doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.99 +- 0.67 (0.00-->9.62) (max @ vno 86197 --> 86209) face area 0.03 +- 0.05 (-0.71-->1.12)

== Number of threads available to mris_sphere for OpenMP = 8 == scaling brain by 0.371... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=174.333, avgs=0 005/300: dt: 0.9000, rms radial error=174.076, avgs=0 010/300: dt: 0.9000, rms radial error=173.524, avgs=0 015/300: dt: 0.9000, rms radial error=172.800, avgs=0 020/300: dt: 0.9000, rms radial error=171.976, avgs=0 025/300: dt: 0.9000, rms radial error=171.095, avgs=0 030/300: dt: 0.9000, rms radial error=170.182, avgs=0 035/300: dt: 0.9000, rms radial error=169.251, avgs=0 040/300: dt: 0.9000, rms radial error=168.312, avgs=0 045/300: dt: 0.9000, rms radial error=167.369, avgs=0 050/300: dt: 0.9000, rms radial error=166.427, avgs=0 055/300: dt: 0.9000, rms radial error=165.488, avgs=0 060/300: dt: 0.9000, rms radial error=164.551, avgs=0 065/300: dt: 0.9000, rms radial error=163.618, avgs=0 070/300: dt: 0.9000, rms radial error=162.690, avgs=0 075/300: dt: 0.9000, rms radial error=161.767, avgs=0 080/300: dt: 0.9000, rms radial error=160.848, avgs=0 085/300: dt: 0.9000, rms radial error=159.933, avgs=0 090/300: dt: 0.9000, rms radial error=159.026, avgs=0 095/300: dt: 0.9000, rms radial error=158.123, avgs=0 100/300: dt: 0.9000, rms radial error=157.225, avgs=0 105/300: dt: 0.9000, rms radial error=156.333, avgs=0 110/300: dt: 0.9000, rms radial error=155.450, avgs=0 115/300: dt: 0.9000, rms radial error=154.572, avgs=0 120/300: dt: 0.9000, rms radial error=153.698, avgs=0 125/300: dt: 0.9000, rms radial error=152.830, avgs=0 130/300: dt: 0.9000, rms radial error=151.966, avgs=0 135/300: dt: 0.9000, rms radial error=151.106, avgs=0 140/300: dt: 0.9000, rms radial error=150.252, avgs=0 145/300: dt: 0.9000, rms radial error=149.402, avgs=0 150/300: dt: 0.9000, rms radial error=148.557, avgs=0 155/300: dt: 0.9000, rms radial error=147.716, avgs=0 160/300: dt: 0.9000, rms radial error=146.881, avgs=0 165/300: dt: 0.9000, rms radial error=146.049, avgs=0 170/300: dt: 0.9000, rms radial error=145.223, avgs=0 175/300: dt: 0.9000, rms radial error=144.401, avgs=0 180/300: dt: 0.9000, rms radial error=143.584, avgs=0 185/300: dt: 0.9000, rms radial error=142.772, avgs=0 190/300: dt: 0.9000, rms radial error=141.965, avgs=0 195/300: dt: 0.9000, rms radial error=141.162, avgs=0 200/300: dt: 0.9000, rms radial error=140.363, avgs=0 205/300: dt: 0.9000, rms radial error=139.569, avgs=0 210/300: dt: 0.9000, rms radial error=138.779, avgs=0 215/300: dt: 0.9000, rms radial error=137.994, avgs=0 220/300: dt: 0.9000, rms radial error=137.213, avgs=0 225/300: dt: 0.9000, rms radial error=136.437, avgs=0 230/300: dt: 0.9000, rms radial error=135.665, avgs=0 235/300: dt: 0.9000, rms radial error=134.897, avgs=0 240/300: dt: 0.9000, rms radial error=134.134, avgs=0 245/300: dt: 0.9000, rms radial error=133.375, avgs=0 250/300: dt: 0.9000, rms radial error=132.620, avgs=0 255/300: dt: 0.9000, rms radial error=131.870, avgs=0 260/300: dt: 0.9000, rms radial error=131.123, avgs=0 265/300: dt: 0.9000, rms radial error=130.381, avgs=0 270/300: dt: 0.9000, rms radial error=129.644, avgs=0 275/300: dt: 0.9000, rms radial error=128.910, avgs=0 280/300: dt: 0.9000, rms radial error=128.181, avgs=0 285/300: dt: 0.9000, rms radial error=127.456, avgs=0 290/300: dt: 0.9000, rms radial error=126.734, avgs=0 295/300: dt: 0.9000, rms radial error=126.017, avgs=0 300/300: dt: 0.9000, rms radial error=125.304, avgs=0

spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 16172.49 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00014 epoch 2 (K=40.0), pass 1, starting sse = 2927.15 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/10 = 0.00065 epoch 3 (K=160.0), pass 1, starting sse = 564.35 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/11 = 0.00626 epoch 4 (K=640.0), pass 1, starting sse = 167.70 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.19/15 = 0.01271 final distance error %24.49 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.02 hours mris_sphere utimesec 321.468000 mris_sphere stimesec 0.712000 mris_sphere ru_maxrss 233752 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 57134 mris_sphere ru_majflt 16 mris_sphere ru_nswap 0 mris_sphere ru_inblock 1792 mris_sphere ru_oublock 10040 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 82973 mris_sphere ru_nivcsw 33307 FSRUNTIME@ mris_sphere 0.0226 hours 1 threads

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@# Fix Topology Copy lh Wed Mar 13 00:47:37 UTC 2019

/out/freesurfer/sub-082/scripts

cp ../surf/lh.orig.nofix ../surf/lh.orig

cp ../surf/lh.inflated.nofix ../surf/lh.inflated

@# Fix Topology lh Wed Mar 13 00:47:37 UTC 2019

mris_fix_topology -rusage /out/freesurfer/sub-082/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 sub-082 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=-648 (nv=142300, nf=285896, ne=428844, g=325) 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 8 iterations marking ambiguous vertices... 93579 ambiguous faces found in tessellation segmenting defects... 138 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 40 into 12 -merging segment 48 into 47 -merging segment 69 into 47 -merging segment 80 into 47 -merging segment 47 into 60 -merging segment 89 into 88 -merging segment 115 into 111 -merging segment 121 into 120 -merging segment 131 into 122 129 defects to be corrected 0 vertices coincident reading input surface /out/freesurfer/sub-082/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.4188 (-4.7094) -vertex loglikelihood: -7.4598 (-3.7299) -normal dot loglikelihood: -3.5471 (-3.5471) -quad curv loglikelihood: -6.1984 (-3.0992) Total Loglikelihood : -26.6240

CORRECTING DEFECT 0 (vertices=24, convex hull=41, v0=258) After retessellation of defect 0 (v0=258), euler #=-106 (90956,263189,172127) : difference with theory (-126) = -20

CORRECTING DEFECT 1 (vertices=63, convex hull=107, v0=276) After retessellation of defect 1 (v0=276), euler #=-105 (90987,263329,172237) : difference with theory (-125) = -20

CORRECTING DEFECT 2 (vertices=53, convex hull=91, v0=473) After retessellation of defect 2 (v0=473), euler #=-104 (91011,263443,172328) : difference with theory (-124) = -20

CORRECTING DEFECT 3 (vertices=246, convex hull=302, v0=706) After retessellation of defect 3 (v0=706), euler #=-104 (91063,263750,172583) : difference with theory (-123) = -19

CORRECTING DEFECT 4 (vertices=88, convex hull=37, v0=742) After retessellation of defect 4 (v0=742), euler #=-103 (91070,263786,172613) : difference with theory (-122) = -19

CORRECTING DEFECT 5 (vertices=41, convex hull=52, v0=808) After retessellation of defect 5 (v0=808), euler #=-102 (91090,263870,172678) : difference with theory (-121) = -19

CORRECTING DEFECT 6 (vertices=26, convex hull=66, v0=1694) After retessellation of defect 6 (v0=1694), euler #=-101 (91100,263923,172722) : difference with theory (-120) = -19

CORRECTING DEFECT 7 (vertices=52, convex hull=96, v0=2680) After retessellation of defect 7 (v0=2680), euler #=-100 (91113,263999,172786) : difference with theory (-119) = -19

CORRECTING DEFECT 8 (vertices=183, convex hull=85, v0=3440) After retessellation of defect 8 (v0=3440), euler #=-99 (91141,264124,172884) : difference with theory (-118) = -19

CORRECTING DEFECT 9 (vertices=96, convex hull=118, v0=3454) After retessellation of defect 9 (v0=3454), euler #=-98 (91185,264306,173023) : difference with theory (-117) = -19

CORRECTING DEFECT 10 (vertices=58, convex hull=67, v0=3767) After retessellation of defect 10 (v0=3767), euler #=-97 (91201,264382,173084) : difference with theory (-116) = -19

CORRECTING DEFECT 11 (vertices=36, convex hull=70, v0=5638) After retessellation of defect 11 (v0=5638), euler #=-96 (91221,264471,173154) : difference with theory (-115) = -19

CORRECTING DEFECT 12 (vertices=471, convex hull=208, v0=5850) After retessellation of defect 12 (v0=5850), euler #=-94 (91281,264751,173376) : difference with theory (-114) = -20

CORRECTING DEFECT 13 (vertices=35, convex hull=52, v0=6153) After retessellation of defect 13 (v0=6153), euler #=-93 (91294,264808,173421) : difference with theory (-113) = -20

CORRECTING DEFECT 14 (vertices=41, convex hull=55, v0=6604) After retessellation of defect 14 (v0=6604), euler #=-92 (91308,264869,173469) : difference with theory (-112) = -20

CORRECTING DEFECT 15 (vertices=454, convex hull=234, v0=6650) After retessellation of defect 15 (v0=6650), euler #=-91 (91511,265597,173995) : difference with theory (-111) = -20

CORRECTING DEFECT 16 (vertices=5, convex hull=23, v0=6887) After retessellation of defect 16 (v0=6887), euler #=-90 (91511,265604,174003) : difference with theory (-110) = -20

CORRECTING DEFECT 17 (vertices=462, convex hull=169, v0=7787) After retessellation of defect 17 (v0=7787), euler #=-89 (91530,265738,174119) : difference with theory (-109) = -20

CORRECTING DEFECT 18 (vertices=26, convex hull=71, v0=8010) After retessellation of defect 18 (v0=8010), euler #=-88 (91540,265796,174168) : difference with theory (-108) = -20

CORRECTING DEFECT 19 (vertices=110, convex hull=143, v0=8286) After retessellation of defect 19 (v0=8286), euler #=-87 (91549,265894,174258) : difference with theory (-107) = -20

CORRECTING DEFECT 20 (vertices=73, convex hull=78, v0=8607) After retessellation of defect 20 (v0=8607), euler #=-87 (91568,265991,174336) : difference with theory (-106) = -19

CORRECTING DEFECT 21 (vertices=39, convex hull=36, v0=8687) After retessellation of defect 21 (v0=8687), euler #=-86 (91570,266007,174351) : difference with theory (-105) = -19

CORRECTING DEFECT 22 (vertices=219, convex hull=99, v0=9209) After retessellation of defect 22 (v0=9209), euler #=-85 (91591,266118,174442) : difference with theory (-104) = -19

CORRECTING DEFECT 23 (vertices=23, convex hull=23, v0=9562) After retessellation of defect 23 (v0=9562), euler #=-84 (91595,266136,174457) : difference with theory (-103) = -19

CORRECTING DEFECT 24 (vertices=160, convex hull=105, v0=9768) After retessellation of defect 24 (v0=9768), euler #=-83 (91631,266290,174576) : difference with theory (-102) = -19

CORRECTING DEFECT 25 (vertices=45, convex hull=17, v0=9886) After retessellation of defect 25 (v0=9886), euler #=-82 (91633,266298,174583) : difference with theory (-101) = -19

CORRECTING DEFECT 26 (vertices=6, convex hull=17, v0=10250) After retessellation of defect 26 (v0=10250), euler #=-81 (91634,266307,174592) : difference with theory (-100) = -19

CORRECTING DEFECT 27 (vertices=16, convex hull=40, v0=10345) After retessellation of defect 27 (v0=10345), euler #=-80 (91638,266331,174613) : difference with theory (-99) = -19

CORRECTING DEFECT 28 (vertices=40, convex hull=27, v0=10411) After retessellation of defect 28 (v0=10411), euler #=-79 (91643,266351,174629) : difference with theory (-98) = -19

CORRECTING DEFECT 29 (vertices=378, convex hull=154, v0=12440) After retessellation of defect 29 (v0=12440), euler #=-78 (91702,266603,174823) : difference with theory (-97) = -19

CORRECTING DEFECT 30 (vertices=104, convex hull=45, v0=13644) After retessellation of defect 30 (v0=13644), euler #=-77 (91709,266640,174854) : difference with theory (-96) = -19

CORRECTING DEFECT 31 (vertices=15, convex hull=31, v0=13991) After retessellation of defect 31 (v0=13991), euler #=-76 (91711,266660,174873) : difference with theory (-95) = -19

CORRECTING DEFECT 32 (vertices=56, convex hull=88, v0=14123) After retessellation of defect 32 (v0=14123), euler #=-75 (91750,266820,174995) : difference with theory (-94) = -19

CORRECTING DEFECT 33 (vertices=173, convex hull=181, v0=14317) After retessellation of defect 33 (v0=14317), euler #=-74 (91822,267121,175225) : difference with theory (-93) = -19

CORRECTING DEFECT 34 (vertices=24, convex hull=65, v0=14489) After retessellation of defect 34 (v0=14489), euler #=-73 (91836,267187,175278) : difference with theory (-92) = -19

CORRECTING DEFECT 35 (vertices=5, convex hull=20, v0=14595) After retessellation of defect 35 (v0=14595), euler #=-72 (91836,267196,175288) : difference with theory (-91) = -19

CORRECTING DEFECT 36 (vertices=77, convex hull=124, v0=14954) After retessellation of defect 36 (v0=14954), euler #=-71 (91856,267306,175379) : difference with theory (-90) = -19

CORRECTING DEFECT 37 (vertices=18, convex hull=16, v0=15106) After retessellation of defect 37 (v0=15106), euler #=-70 (91857,267315,175388) : difference with theory (-89) = -19

CORRECTING DEFECT 38 (vertices=309, convex hull=190, v0=15605) After retessellation of defect 38 (v0=15605), euler #=-69 (91963,267725,175693) : difference with theory (-88) = -19

CORRECTING DEFECT 39 (vertices=65, convex hull=100, v0=16317) After retessellation of defect 39 (v0=16317), euler #=-68 (91977,267809,175764) : difference with theory (-87) = -19

CORRECTING DEFECT 40 (vertices=138, convex hull=128, v0=17513) After retessellation of defect 40 (v0=17513), euler #=-67 (92041,268058,175950) : difference with theory (-86) = -19

CORRECTING DEFECT 41 (vertices=40, convex hull=26, v0=17833) After retessellation of defect 41 (v0=17833), euler #=-66 (92045,268077,175966) : difference with theory (-85) = -19

CORRECTING DEFECT 42 (vertices=96, convex hull=37, v0=18837) After retessellation of defect 42 (v0=18837), euler #=-65 (92050,268106,175991) : difference with theory (-84) = -19

CORRECTING DEFECT 43 (vertices=26, convex hull=42, v0=18950) After retessellation of defect 43 (v0=18950), euler #=-64 (92061,268155,176030) : difference with theory (-83) = -19

CORRECTING DEFECT 44 (vertices=59, convex hull=34, v0=20822) After retessellation of defect 44 (v0=20822), euler #=-63 (92066,268183,176054) : difference with theory (-82) = -19

CORRECTING DEFECT 45 (vertices=12, convex hull=23, v0=20962) After retessellation of defect 45 (v0=20962), euler #=-62 (92067,268193,176064) : difference with theory (-81) = -19

CORRECTING DEFECT 46 (vertices=16, convex hull=17, v0=21848) After retessellation of defect 46 (v0=21848), euler #=-61 (92069,268202,176072) : difference with theory (-80) = -19

CORRECTING DEFECT 47 (vertices=79, convex hull=74, v0=22047) After retessellation of defect 47 (v0=22047), euler #=-60 (92098,268325,176167) : difference with theory (-79) = -19

CORRECTING DEFECT 48 (vertices=179, convex hull=134, v0=22512) After retessellation of defect 48 (v0=22512), euler #=-59 (92169,268596,176368) : difference with theory (-78) = -19

CORRECTING DEFECT 49 (vertices=28, convex hull=39, v0=23908) After retessellation of defect 49 (v0=23908), euler #=-58 (92173,268620,176389) : difference with theory (-77) = -19

CORRECTING DEFECT 50 (vertices=7, convex hull=19, v0=23968) After retessellation of defect 50 (v0=23968), euler #=-57 (92174,268625,176394) : difference with theory (-76) = -19

CORRECTING DEFECT 51 (vertices=26, convex hull=24, v0=24023) After retessellation of defect 51 (v0=24023), euler #=-56 (92176,268643,176411) : difference with theory (-75) = -19

CORRECTING DEFECT 52 (vertices=119, convex hull=130, v0=25659) After retessellation of defect 52 (v0=25659), euler #=-55 (92224,268848,176569) : difference with theory (-74) = -19

CORRECTING DEFECT 53 (vertices=29, convex hull=53, v0=26879) After retessellation of defect 53 (v0=26879), euler #=-54 (92241,268921,176626) : difference with theory (-73) = -19

CORRECTING DEFECT 54 (vertices=35, convex hull=70, v0=27714) After retessellation of defect 54 (v0=27714), euler #=-53 (92252,268979,176674) : difference with theory (-72) = -19

CORRECTING DEFECT 55 (vertices=17, convex hull=27, v0=27804) After retessellation of defect 55 (v0=27804), euler #=-52 (92253,268992,176687) : difference with theory (-71) = -19

CORRECTING DEFECT 56 (vertices=37, convex hull=30, v0=28972) After retessellation of defect 56 (v0=28972), euler #=-51 (92257,269014,176706) : difference with theory (-70) = -19

CORRECTING DEFECT 57 (vertices=9216, convex hull=2162, v0=29043) XL defect detected... After retessellation of defect 57 (v0=29043), euler #=-52 (94054,275609,181503) : difference with theory (-69) = -17

CORRECTING DEFECT 58 (vertices=48, convex hull=42, v0=29215) After retessellation of defect 58 (v0=29215), euler #=-51 (94060,275643,181532) : difference with theory (-68) = -17

CORRECTING DEFECT 59 (vertices=27, convex hull=49, v0=29469) After retessellation of defect 59 (v0=29469), euler #=-50 (94069,275691,181572) : difference with theory (-67) = -17

CORRECTING DEFECT 60 (vertices=33, convex hull=36, v0=29574) After retessellation of defect 60 (v0=29574), euler #=-49 (94072,275712,181591) : difference with theory (-66) = -17

CORRECTING DEFECT 61 (vertices=31, convex hull=51, v0=30292) After retessellation of defect 61 (v0=30292), euler #=-48 (94085,275773,181640) : difference with theory (-65) = -17

CORRECTING DEFECT 62 (vertices=27, convex hull=56, v0=31967) After retessellation of defect 62 (v0=31967), euler #=-47 (94094,275824,181683) : difference with theory (-64) = -17

CORRECTING DEFECT 63 (vertices=485, convex hull=96, v0=32539) After retessellation of defect 63 (v0=32539), euler #=-46 (94110,275917,181761) : difference with theory (-63) = -17

CORRECTING DEFECT 64 (vertices=17, convex hull=16, v0=32619) After retessellation of defect 64 (v0=32619), euler #=-45 (94111,275926,181770) : difference with theory (-62) = -17

CORRECTING DEFECT 65 (vertices=32, convex hull=71, v0=33389) After retessellation of defect 65 (v0=33389), euler #=-44 (94131,276016,181841) : difference with theory (-61) = -17

CORRECTING DEFECT 66 (vertices=50, convex hull=100, v0=37554) After retessellation of defect 66 (v0=37554), euler #=-43 (94164,276155,181948) : difference with theory (-60) = -17

CORRECTING DEFECT 67 (vertices=93, convex hull=138, v0=38621) After retessellation of defect 67 (v0=38621), euler #=-42 (94195,276306,182069) : difference with theory (-59) = -17

CORRECTING DEFECT 68 (vertices=4806, convex hull=741, v0=39136) XL defect detected... After retessellation of defect 68 (v0=39136), euler #=-41 (94526,277712,183145) : difference with theory (-58) = -17

CORRECTING DEFECT 69 (vertices=57, convex hull=33, v0=40900) After retessellation of defect 69 (v0=40900), euler #=-40 (94534,277747,183173) : difference with theory (-57) = -17

CORRECTING DEFECT 70 (vertices=1434, convex hull=643, v0=41048) XL defect detected... After retessellation of defect 70 (v0=41048), euler #=-42 (94956,279387,184389) : difference with theory (-56) = -14

CORRECTING DEFECT 71 (vertices=20, convex hull=22, v0=44873) After retessellation of defect 71 (v0=44873), euler #=-41 (94957,279397,184399) : difference with theory (-55) = -14

CORRECTING DEFECT 72 (vertices=300, convex hull=51, v0=46288) After retessellation of defect 72 (v0=46288), euler #=-40 (94995,279531,184496) : difference with theory (-54) = -14

CORRECTING DEFECT 73 (vertices=71, convex hull=86, v0=47177) After retessellation of defect 73 (v0=47177), euler #=-39 (95026,279658,184593) : difference with theory (-53) = -14

CORRECTING DEFECT 74 (vertices=55, convex hull=74, v0=47526) After retessellation of defect 74 (v0=47526), euler #=-38 (95053,279770,184679) : difference with theory (-52) = -14

CORRECTING DEFECT 75 (vertices=44, convex hull=35, v0=48035) After retessellation of defect 75 (v0=48035), euler #=-37 (95058,279799,184704) : difference with theory (-51) = -14

CORRECTING DEFECT 76 (vertices=7, convex hull=10, v0=52174) After retessellation of defect 76 (v0=52174), euler #=-36 (95059,279803,184708) : difference with theory (-50) = -14

CORRECTING DEFECT 77 (vertices=102, convex hull=134, v0=55294) After retessellation of defect 77 (v0=55294), euler #=-35 (95115,280025,184875) : difference with theory (-49) = -14

CORRECTING DEFECT 78 (vertices=23, convex hull=34, v0=59013) After retessellation of defect 78 (v0=59013), euler #=-34 (95120,280053,184899) : difference with theory (-48) = -14

CORRECTING DEFECT 79 (vertices=9, convex hull=24, v0=59499) After retessellation of defect 79 (v0=59499), euler #=-33 (95121,280063,184909) : difference with theory (-47) = -14

CORRECTING DEFECT 80 (vertices=169, convex hull=87, v0=60059) After retessellation of defect 80 (v0=60059), euler #=-32 (95157,280217,185028) : difference with theory (-46) = -14

CORRECTING DEFECT 81 (vertices=72, convex hull=90, v0=62039) After retessellation of defect 81 (v0=62039), euler #=-31 (95202,280394,185161) : difference with theory (-45) = -14

CORRECTING DEFECT 82 (vertices=79, convex hull=104, v0=66191) After retessellation of defect 82 (v0=66191), euler #=-30 (95235,280538,185273) : difference with theory (-44) = -14

CORRECTING DEFECT 83 (vertices=230, convex hull=200, v0=67494) After retessellation of defect 83 (v0=67494), euler #=-28 (95325,280903,185550) : difference with theory (-43) = -15

CORRECTING DEFECT 84 (vertices=1901, convex hull=1206, v0=69852) XL defect detected... After retessellation of defect 84 (v0=69852), euler #=-31 (96202,284211,187978) : difference with theory (-42) = -11

CORRECTING DEFECT 85 (vertices=27, convex hull=34, v0=70403) After retessellation of defect 85 (v0=70403), euler #=-30 (96204,284229,187995) : difference with theory (-41) = -11

CORRECTING DEFECT 86 (vertices=72, convex hull=79, v0=71987) After retessellation of defect 86 (v0=71987), euler #=-30 (96238,284366,188098) : difference with theory (-40) = -10

CORRECTING DEFECT 87 (vertices=135, convex hull=143, v0=72089) After retessellation of defect 87 (v0=72089), euler #=-29 (96303,284625,188293) : difference with theory (-39) = -10

CORRECTING DEFECT 88 (vertices=29, convex hull=18, v0=74068) After retessellation of defect 88 (v0=74068), euler #=-28 (96306,284639,188305) : difference with theory (-38) = -10

CORRECTING DEFECT 89 (vertices=32, convex hull=29, v0=75647) After retessellation of defect 89 (v0=75647), euler #=-27 (96308,284651,188316) : difference with theory (-37) = -10

CORRECTING DEFECT 90 (vertices=32, convex hull=57, v0=75906) After retessellation of defect 90 (v0=75906), euler #=-26 (96322,284716,188368) : difference with theory (-36) = -10

CORRECTING DEFECT 91 (vertices=8, convex hull=20, v0=76970) After retessellation of defect 91 (v0=76970), euler #=-25 (96322,284722,188375) : difference with theory (-35) = -10

CORRECTING DEFECT 92 (vertices=85, convex hull=91, v0=78508) After retessellation of defect 92 (v0=78508), euler #=-24 (96353,284860,188483) : difference with theory (-34) = -10

CORRECTING DEFECT 93 (vertices=44, convex hull=99, v0=79855) After retessellation of defect 93 (v0=79855), euler #=-23 (96385,285001,188593) : difference with theory (-33) = -10

CORRECTING DEFECT 94 (vertices=15, convex hull=30, v0=80389) After retessellation of defect 94 (v0=80389), euler #=-22 (96386,285015,188607) : difference with theory (-32) = -10

CORRECTING DEFECT 95 (vertices=47, convex hull=87, v0=81228) After retessellation of defect 95 (v0=81228), euler #=-21 (96404,285107,188682) : difference with theory (-31) = -10

CORRECTING DEFECT 96 (vertices=7, convex hull=26, v0=81300) After retessellation of defect 96 (v0=81300), euler #=-20 (96405,285122,188697) : difference with theory (-30) = -10

CORRECTING DEFECT 97 (vertices=12, convex hull=24, v0=82642) After retessellation of defect 97 (v0=82642), euler #=-19 (96407,285135,188709) : difference with theory (-29) = -10

CORRECTING DEFECT 98 (vertices=48, convex hull=66, v0=83044) After retessellation of defect 98 (v0=83044), euler #=-18 (96429,285231,188784) : difference with theory (-28) = -10

CORRECTING DEFECT 99 (vertices=2763, convex hull=868, v0=83269) XL defect detected... After retessellation of defect 99 (v0=83269), euler #=-19 (96613,286287,189655) : difference with theory (-27) = -8

CORRECTING DEFECT 100 (vertices=1362, convex hull=647, v0=83865) XL defect detected... After retessellation of defect 100 (v0=83865), euler #=-18 (97020,287864,190826) : difference with theory (-26) = -8

CORRECTING DEFECT 101 (vertices=23, convex hull=19, v0=83888) After retessellation of defect 101 (v0=83888), euler #=-17 (97023,287878,190838) : difference with theory (-25) = -8

CORRECTING DEFECT 102 (vertices=56, convex hull=80, v0=90952) After retessellation of defect 102 (v0=90952), euler #=-16 (97059,288019,190944) : difference with theory (-24) = -8

CORRECTING DEFECT 103 (vertices=41, convex hull=33, v0=91717) After retessellation of defect 103 (v0=91717), euler #=-15 (97063,288041,190963) : difference with theory (-23) = -8

CORRECTING DEFECT 104 (vertices=6, convex hull=24, v0=93579) After retessellation of defect 104 (v0=93579), euler #=-14 (97064,288051,190973) : difference with theory (-22) = -8

CORRECTING DEFECT 105 (vertices=139, convex hull=154, v0=94691) After retessellation of defect 105 (v0=94691), euler #=-12 (97094,288220,191114) : difference with theory (-21) = -9

CORRECTING DEFECT 106 (vertices=6, convex hull=9, v0=94885) After retessellation of defect 106 (v0=94885), euler #=-11 (97094,288222,191117) : difference with theory (-20) = -9

CORRECTING DEFECT 107 (vertices=116, convex hull=122, v0=96030) After retessellation of defect 107 (v0=96030), euler #=-10 (97116,288345,191219) : difference with theory (-19) = -9

CORRECTING DEFECT 108 (vertices=20, convex hull=64, v0=96112) After retessellation of defect 108 (v0=96112), euler #=-9 (97125,288397,191263) : difference with theory (-18) = -9

CORRECTING DEFECT 109 (vertices=75, convex hull=85, v0=97088) After retessellation of defect 109 (v0=97088), euler #=-8 (97174,288581,191399) : difference with theory (-17) = -9

CORRECTING DEFECT 110 (vertices=11060, convex hull=2620, v0=100742) XL defect detected... After retessellation of defect 110 (v0=100742), euler #=-17 (98292,293485,195176) : difference with theory (-16) = 1

CORRECTING DEFECT 111 (vertices=28, convex hull=18, v0=101328) After retessellation of defect 111 (v0=101328), euler #=-16 (98293,293495,195186) : difference with theory (-15) = 1

CORRECTING DEFECT 112 (vertices=43, convex hull=63, v0=102767) After retessellation of defect 112 (v0=102767), euler #=-15 (98305,293557,195237) : difference with theory (-14) = 1

CORRECTING DEFECT 113 (vertices=121, convex hull=102, v0=102977) After retessellation of defect 113 (v0=102977), euler #=-13 (98333,293696,195350) : difference with theory (-13) = 0

CORRECTING DEFECT 114 (vertices=9172, convex hull=1599, v0=104289) XL defect detected... After retessellation of defect 114 (v0=104289), euler #=-12 (99286,297422,198124) : difference with theory (-12) = 0

CORRECTING DEFECT 115 (vertices=68, convex hull=35, v0=105976) After retessellation of defect 115 (v0=105976), euler #=-11 (99293,297456,198152) : difference with theory (-11) = 0

CORRECTING DEFECT 116 (vertices=133, convex hull=141, v0=106462) After retessellation of defect 116 (v0=106462), euler #=-10 (99334,297641,198297) : difference with theory (-10) = 0

CORRECTING DEFECT 117 (vertices=31, convex hull=25, v0=106584) After retessellation of defect 117 (v0=106584), euler #=-9 (99336,297662,198317) : difference with theory (-9) = 0

CORRECTING DEFECT 118 (vertices=34, convex hull=75, v0=106846) After retessellation of defect 118 (v0=106846), euler #=-8 (99358,297759,198393) : difference with theory (-8) = 0

CORRECTING DEFECT 119 (vertices=154, convex hull=121, v0=107325) After retessellation of defect 119 (v0=107325), euler #=-7 (99416,297987,198564) : difference with theory (-7) = 0

CORRECTING DEFECT 120 (vertices=90, convex hull=116, v0=111922) After retessellation of defect 120 (v0=111922), euler #=-6 (99474,298207,198727) : difference with theory (-6) = 0

CORRECTING DEFECT 121 (vertices=153, convex hull=126, v0=112812) After retessellation of defect 121 (v0=112812), euler #=-5 (99511,298375,198859) : difference with theory (-5) = 0

CORRECTING DEFECT 122 (vertices=11, convex hull=20, v0=112945) After retessellation of defect 122 (v0=112945), euler #=-4 (99512,298384,198868) : difference with theory (-4) = 0

CORRECTING DEFECT 123 (vertices=93, convex hull=153, v0=117579) After retessellation of defect 123 (v0=117579), euler #=-3 (99571,298636,199062) : difference with theory (-3) = 0

CORRECTING DEFECT 124 (vertices=22, convex hull=21, v0=124719) After retessellation of defect 124 (v0=124719), euler #=-2 (99574,298650,199074) : difference with theory (-2) = 0

CORRECTING DEFECT 125 (vertices=9, convex hull=19, v0=124934) After retessellation of defect 125 (v0=124934), euler #=-1 (99575,298659,199083) : difference with theory (-1) = 0

CORRECTING DEFECT 126 (vertices=6, convex hull=24, v0=129847) After retessellation of defect 126 (v0=129847), euler #=0 (99576,298671,199095) : difference with theory (0) = 0

CORRECTING DEFECT 127 (vertices=58, convex hull=107, v0=133275) After retessellation of defect 127 (v0=133275), euler #=1 (99591,298759,199169) : difference with theory (1) = 0

CORRECTING DEFECT 128 (vertices=20, convex hull=25, v0=135771) After retessellation of defect 128 (v0=135771), euler #=2 (99592,298770,199180) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.93 +- 0.50 (0.02-->19.57) (max @ vno 81424 --> 88580) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.93 +- 0.50 (0.02-->19.57) (max @ vno 81424 --> 88580) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 438 mutations (36.0%), 777 crossovers (64.0%), 6957 vertices were eliminated building final representation... 42708 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=99592, nf=199180, ne=298770, g=0) writing corrected surface to /out/freesurfer/sub-082/surf/lh.orig... MRISwrite(/out/freesurfer/sub-082/surf/lh.orig): can't create file

0 defective edges removing intersecting faces 000: 4042 intersecting 001: 306 intersecting 002: 140 intersecting 003: 123 intersecting 004: 87 intersecting 005: 68 intersecting 006: 62 intersecting 007: 45 intersecting 008: 20 intersecting No such file or directory

0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 1112.6 minutes mris_fix_topology utimesec 66722.916000 mris_fix_topology stimesec 17.384000 mris_fix_topology ru_maxrss 1589096 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 12333608 mris_fix_topology ru_majflt 25687 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 428464 mris_fix_topology ru_oublock 3344 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 33822 mris_fix_topology ru_nivcsw 5602139 FSRUNTIME@ mris_fix_topology lh 18.5441 hours 1 threads tee: /out/freesurfer/sub-082/scripts/recon-all-lh.log: No such file or directory

mris_euler_number ../surf/lh.orig

Abort (core dumped) Linux b16d469ba965 4.4.0-141-generic #167~14.04.1-Ubuntu SMP Mon Dec 10 13:20:24 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux tee: /out/freesurfer/sub-082/scripts/recon-all-lh.log: No such file or directory

tee: /out/freesurfer/sub-082/scripts/recon-all-lh.log: No such file or directory recon-all -s sub-082 exited with ERRORS at Wed Mar 13 19:20:18 UTC 2019 tee: /out/freesurfer/sub-082/scripts/recon-all-lh.log: No such file or directory

For more details, see the log file /out/freesurfer/sub-082/scripts/recon-all-lh.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Standard error: tee: /out/freesurfer/sub-082/scripts/recon-all-lh.cmd: No such file or directory tee: /out/freesurfer/sub-082/scripts/recon-all-lh.log: No such file or directory tee: /out/freesurfer/sub-082/scripts/recon-all-status-lh.log: No such file or directory tee: /out/freesurfer/sub-082/scripts/recon-all-status-lh.log: No such file or directory tee: /out/freesurfer/sub-082/scripts/recon-all-status-lh.log: No such file or directory tee: /out/freesurfer/sub-082/scripts/recon-all-status-lh.log: No such file or directory tee: /out/freesurfer/sub-082/scripts/recon-all-lh.log: No such file or directory /out/freesurfer/sub-082/scripts/recon-all.error: No such file or directory. Return code: 1

effigies commented 5 years ago

This looks like a filesystem issue. Did you run out of space or hit a quota during your run? It also looks like you're running in Docker. Could you give your full command that you ran? And what OS are you running from?

BolinCao commented 5 years ago

Yes, I run it using ubuntu docker on 128G workstation.
sudo docker run -ti --rm -v /home/Data/doc_data/bids:/data:ro -v /home/Data/doc_data/out:/out -v /home/Desktop/script/license.txt:/opt/freesurfer/license.txt poldracklab/fmriprep:latest /data /out participant --use-syn-sdc --bold2t1w-dof 12 --template-resampling-grid 2mm --participant_label sub-034

effigies commented 5 years ago

Thanks. So first I'll just note that the following lines make me think it's a filesystem issue:

writing corrected surface to /out/freesurfer/sub-082/surf/lh.orig...
MRISwrite(/out/freesurfer/sub-082/surf/lh.orig): can't create file
...
tee: /out/freesurfer/sub-082/scripts/recon-all-lh.log: No such file or directory
...
/out/freesurfer/sub-082/scripts/recon-all.error: No such file or directory.

The first could be an issue of a full filesystem, but the latter two are unlikely to be missing files, as they should have been written to before, and there's no evidence of that until the very end. This is consistent with a disconnection.

What kind of filesystem is /home/Data/doc_data hosted on? If it's an NFS mount or removal drive, I would guess that what happened is a connection error at an inconvenient time. I would simply make sure it's reconnected and retry. It's also possible that there was some kind of filesystem-related glitch in Docker that would appear to be a disconnection from the perspective of a job running in Docker. Again the solution would probably be to retry.

If it's a typical Linux filesystem, then I would consider whether you hit a quota or filled up the disk. quota and df will be useful tools here. If it's full, then the solution would be to clear up space or increase your quota (for root, the quota issue is very unlikely).

I would check your /home/Data/doc_data/out/freesurfer/sub-082/scripts/ directory and remove any files that have IsRunning in the name. The odds are good that the script was unable to remove them when it was shutting down. If they're still there when you attempt to run again, then recon-all will quit.

As an aside, I would recommend using a specific version, rather than poldracklab/fmriprep:latest. As long as you don't pull a new version, it will be fine, but from the perspective of reproducibility, it's a good habit to specify the exact version. (It also makes it easier for us to associate versions with issues.)

BolinCao commented 5 years ago

Thanks a lot! I resolved this problem by running those subjects on freesurfer rather than on docker. Then putting the results into original place, the docker run Successfully. Thank you for your time.

effigies commented 5 years ago

Great! Glad to hear it.