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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
Apache License 2.0
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[BUG] ``_autorecon31`` failed with ERROR: loading mri/aseg.mgz #1352

Closed oesteban closed 5 years ago

oesteban commented 5 years ago

Crashfile contents:

Node: _autorecon31
Working directory: /scratch/users/oesteban/bsnip2-friprep/work/fmriprep_wf/single_subject_S0563CCB1_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon3/mapflow/_autorecon31

Node inputs:

FLAIR_file = <undefined>
T1_files = <undefined>
T2_file = <undefined>
args = <undefined>
big_ventricles = <undefined>
brainstem = <undefined>
directive = autorecon3
environ = {}
expert = <undefined>
flags = <undefined>
hemi = rh
hippocampal_subfields_T1 = <undefined>
hippocampal_subfields_T2 = <undefined>
hires = <undefined>
mprage = <undefined>
mri_aparc2aseg = <undefined>
mri_ca_label = <undefined>
mri_ca_normalize = <undefined>
mri_ca_register = <undefined>
mri_edit_wm_with_aseg = <undefined>
mri_em_register = <undefined>
mri_fill = <undefined>
mri_mask = <undefined>
mri_normalize = <undefined>
mri_pretess = <undefined>
mri_remove_neck = <undefined>
mri_segment = <undefined>
mri_segstats = <undefined>
mri_tessellate = <undefined>
mri_watershed = <undefined>
mris_anatomical_stats = <undefined>
mris_ca_label = <undefined>
mris_fix_topology = <undefined>
mris_inflate = <undefined>
mris_make_surfaces = <undefined>
mris_register = <undefined>
mris_smooth = <undefined>
mris_sphere = <undefined>
mris_surf2vol = <undefined>
mrisp_paint = <undefined>
openmp = 8
parallel = <undefined>
subject_id = sub-S0563CCB1
subjects_dir = /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer
talairach = <undefined>
use_FLAIR = False
use_T2 = False
xopts = <undefined>

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 -autorecon3 -hemi rh -openmp 8 -subjid sub-S0563CCB1 -sd /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial
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 /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer
Actual FREESURFER_HOME /opt/freesurfer
-rw-rw----+ 1 oesteban russpold 156689 Oct 13 05:30 /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/scripts/recon-all.log
Linux sh-102-16.int 3.10.0-862.14.4.el7.x86_64 #1 SMP Wed Sep 26 15:12:11 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
'/opt/freesurfer/bin/recon-all' -> '/oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/scripts/recon-all.local-copy'
#--------------------------------------------
#@# Cortical ribbon mask Sat Oct 13 05:30:15 UTC 2018
/oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/mri

 mris_volmask --aseg_name aseg.presurf --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon sub-S0563CCB1 

SUBJECTS_DIR is /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer
loading input data...
computing distance to left white surface 
computing distance to left pial surface 
computing distance to right white surface 
computing distance to right pial surface 
 hemi masks overlap voxels = 72
writing volume /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/mri/ribbon.mgz
mris_volmask took 4.72 minutes
 writing ribbon files
#-----------------------------------------
#@# Parcellation Stats rh Sat Oct 13 05:34:59 UTC 2018
/oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/scripts

 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab sub-S0563CCB1 rh white 

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/mri/wm.mgz...
reading input surface /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/surf/rh.white...
reading input pial surface /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/surf/rh.pial...
reading input white surface /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total face volume 197110
Total vertex volume 193600 (mask=0)
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Saving annotation colortable ../label/aparc.annot.ctab

table columns are:
    number of vertices
    total surface area (mm^2)
    total gray matter volume (mm^3)
    average cortical thickness +- standard deviation (mm)
    integrated rectified mean curvature
    integrated rectified Gaussian curvature
    folding index
    intrinsic curvature index
    structure name

atlas_icv (eTIV) = 1251282 mm^3    (det: 1.556888 )
lhCtxGM: 196348.285 196060.000  diff=  288.3  pctdiff= 0.147
rhCtxGM: 193469.206 193128.000  diff=  341.2  pctdiff= 0.176
lhCtxWM: 206427.664 206465.000  diff=  -37.3  pctdiff=-0.018
rhCtxWM: 205105.042 205904.000  diff= -799.0  pctdiff=-0.390
SubCortGMVol  52132.000
SupraTentVol  867948.197 (866254.000) diff=1694.197 pctdiff=0.195
SupraTentVolNotVent  855413.197 (853719.000) diff=1694.197 pctdiff=0.198
BrainSegVol  985826.000 (983934.000) diff=1892.000 pctdiff=0.192
BrainSegVolNotVent  970372.000 (970091.197) diff=280.803 pctdiff=0.029
BrainSegVolNotVent  970372.000
CerebellumVol 116579.000
VentChorVol   12535.000
3rd4th5thCSF   2919.000
CSFVol  1027.000, OptChiasmVol    74.000
MaskVol 1279518.000
  979    690   1607  2.463 0.533     0.110     0.018        7     0.7  bankssts
 1084    671   1855  2.736 0.530     0.118     0.014       12     0.6  caudalanteriorcingulate
 2510   1636   4447  2.551 0.478     0.113     0.025       21     2.8  caudalmiddlefrontal
 2398   1508   3054  1.946 0.449     0.162     0.035       40     3.5  cuneus
  572    385   2222  3.674 0.771     0.115     0.034        5     0.6  entorhinal
 3800   2564   8296  2.796 0.623     0.136     0.028       55     4.3  fusiform
 5757   3864  10028  2.356 0.488     0.137     0.028       81     6.3  inferiorparietal
 4177   2731   8391  2.719 0.702     0.133     0.031       59     5.3  inferiortemporal
 1186    746   1888  2.372 0.750     0.140     0.030       22     1.2  isthmuscingulate
 6301   3992   9054  2.095 0.554     0.136     0.029       79     7.6  lateraloccipital
 2675   1871   5528  2.644 0.733     0.133     0.037       31     4.0  lateralorbitofrontal
 3931   2660   5523  2.008 0.576     0.147     0.033       56     5.1  lingual
 2030   1393   4181  2.565 0.637     0.129     0.032       35     2.6  medialorbitofrontal
 4289   2864   8812  2.753 0.632     0.134     0.030       61     5.1  middletemporal
  852    543   1477  2.431 0.683     0.092     0.015        6     0.4  parahippocampal
 2069   1265   3134  2.394 0.570     0.104     0.017       15     1.4  paracentral
 1683   1156   3198  2.533 0.418     0.110     0.019       15     1.3  parsopercularis
  990    720   2156  2.352 0.601     0.168     0.046       22     2.0  parsorbitalis
 1961   1295   3640  2.474 0.592     0.119     0.027       21     2.0  parstriangularis
 2369   1570   2151  1.561 0.452     0.128     0.029       25     2.6  pericalcarine
 5525   3525   7276  1.938 0.552     0.100     0.018       41     4.1  postcentral
 1334    920   2634  2.583 0.660     0.140     0.024       19     1.3  posteriorcingulate
 6566   4052  10968  2.525 0.535     0.105     0.021       51     5.6  precentral
 5367   3510   8826  2.393 0.507     0.129     0.029       63     6.1  precuneus
  850    548   1632  2.425 0.603     0.140     0.030       15     1.1  rostralanteriorcingulate
 7258   5029  13183  2.300 0.586     0.146     0.038      109    11.4  rostralmiddlefrontal
 8562   5647  17656  2.775 0.538     0.118     0.025       76     8.6  superiorfrontal
 7246   4758  11151  2.165 0.485     0.135     0.026       88     7.7  superiorparietal
 4603   3175   9772  2.720 0.588     0.121     0.027       59     5.0  superiortemporal
 4886   3233   8770  2.546 0.515     0.130     0.028       61     5.5  supramarginal
  481    303   1077  2.502 0.660     0.176     0.048       11     1.0  frontalpole
  828    554   2842  3.490 0.946     0.150     0.059       13     2.0  temporalpole
  513    273    812  2.585 0.383     0.098     0.020        4     0.3  transversetemporal
 3327   2225   6295  2.803 0.798     0.112     0.029       30     3.5  insula

 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab sub-S0563CCB1 rh pial 

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/mri/wm.mgz...
reading input surface /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/surf/rh.pial...
reading input pial surface /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/surf/rh.pial...
reading input white surface /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total face volume 197110
Total vertex volume 193600 (mask=0)
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Saving annotation colortable ../label/aparc.annot.ctab

table columns are:
    number of vertices
    total surface area (mm^2)
    total gray matter volume (mm^3)
    average cortical thickness +- standard deviation (mm)
    integrated rectified mean curvature
    integrated rectified Gaussian curvature
    folding index
    intrinsic curvature index
    structure name

atlas_icv (eTIV) = 1251282 mm^3    (det: 1.556888 )
lhCtxGM: 196348.285 196060.000  diff=  288.3  pctdiff= 0.147
rhCtxGM: 193469.206 193128.000  diff=  341.2  pctdiff= 0.176
lhCtxWM: 206427.664 206465.000  diff=  -37.3  pctdiff=-0.018
rhCtxWM: 205105.042 205904.000  diff= -799.0  pctdiff=-0.390
SubCortGMVol  52132.000
SupraTentVol  867948.197 (866254.000) diff=1694.197 pctdiff=0.195
SupraTentVolNotVent  855413.197 (853719.000) diff=1694.197 pctdiff=0.198
BrainSegVol  985826.000 (983934.000) diff=1892.000 pctdiff=0.192
BrainSegVolNotVent  970372.000 (970091.197) diff=280.803 pctdiff=0.029
BrainSegVolNotVent  970372.000
CerebellumVol 116579.000
VentChorVol   12535.000
3rd4th5thCSF   2919.000
CSFVol  1027.000, OptChiasmVol    74.000
MaskVol 1279518.000
  979    638   1607  2.463 0.533     0.132     0.035       15     1.4  bankssts
 1084    747   1855  2.736 0.530     0.134     0.028       19     1.2  caudalanteriorcingulate
 2510   1833   4447  2.551 0.478     0.113     0.022       25     2.2  caudalmiddlefrontal
 2398   1748   3054  1.946 0.449     0.133     0.031       38     3.4  cuneus
  572    786   2222  3.674 0.771     0.210     0.044        8     1.2  entorhinal
 3800   3335   8296  2.796 0.623     0.145     0.035       54     5.9  fusiform
 5757   4608  10028  2.356 0.488     0.150     0.033      110     7.7  inferiorparietal
 4177   3340   8391  2.719 0.702     0.132     0.033       73     5.9  inferiortemporal
 1186    851   1888  2.372 0.750     0.125     0.027       24     1.2  isthmuscingulate
 6301   4611   9054  2.095 0.554     0.127     0.032       95     7.9  lateraloccipital
 2675   2291   5528  2.644 0.733     0.169     0.045       45     5.4  lateralorbitofrontal
 3931   2985   5523  2.008 0.576     0.131     0.031       46     5.6  lingual
 2030   1908   4181  2.565 0.637     0.163     0.036       47     3.5  medialorbitofrontal
 4289   3474   8812  2.753 0.632     0.132     0.029       52     5.3  middletemporal
  852    666   1477  2.431 0.683     0.116     0.025        9     0.9  parahippocampal
 2069   1384   3134  2.394 0.570     0.104     0.018       20     1.6  paracentral
 1683   1388   3198  2.533 0.418     0.129     0.026       19     2.0  parsopercularis
  990   1062   2156  2.352 0.601     0.189     0.040       12     1.9  parsorbitalis
 1961   1605   3640  2.474 0.592     0.142     0.031       22     2.8  parstriangularis
 2369   1381   2151  1.561 0.452     0.104     0.027       34     2.5  pericalcarine
 5525   4104   7276  1.938 0.552     0.110     0.019       39     4.5  postcentral
 1334   1094   2634  2.583 0.660     0.144     0.033       27     1.6  posteriorcingulate
 6566   4558  10968  2.525 0.535     0.103     0.020       60     5.4  precentral
 5367   3837   8826  2.393 0.507     0.131     0.029       75     6.7  precuneus
  850    749   1632  2.425 0.603     0.165     0.032       17     1.2  rostralanteriorcingulate
 7258   6303  13183  2.300 0.586     0.168     0.038      103    13.7  rostralmiddlefrontal
 8562   6956  17656  2.775 0.538     0.126     0.027       80     9.7  superiorfrontal
 7246   5529  11151  2.165 0.485     0.135     0.027       84     8.0  superiorparietal
 4603   3987   9772  2.720 0.588     0.139     0.027       51     5.8  superiortemporal
 4886   3596   8770  2.546 0.515     0.126     0.027       50     5.5  supramarginal
  481    502   1077  2.502 0.660     0.194     0.038        7     0.9  frontalpole
  828   1024   2842  3.490 0.946     0.212     0.051       13     2.0  temporalpole
  513    369    812  2.585 0.383     0.107     0.021        3     0.5  transversetemporal
 3327   2166   6295  2.803 0.798     0.129     0.038       76     5.5  insula
#-----------------------------------------
#@# Cortical Parc 2 rh Sat Oct 13 05:35:43 UTC 2018
/oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-S0563CCB1 rh ../surf/rh.sphere.reg /opt/freesurfer/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.a2009s.annot 

setting seed for random number generator to 1234
using ../mri/aseg.presurf.mgz aseg volume to correct midline
$Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading atlas from /opt/freesurfer/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs...
reading color table from GCSA file....
average std = 1.4   using min determinant for regularization = 0.020
0 singular and 719 ill-conditioned covariance matrices regularized
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
42 labels changed using aseg
relabeling using gibbs priors...
000:   7720 changed, 116888 examined...
001:   1856 changed, 30621 examined...
002:    561 changed, 9744 examined...
003:    227 changed, 3257 examined...
004:    100 changed, 1311 examined...
005:     40 changed, 566 examined...
006:     29 changed, 233 examined...
007:      6 changed, 141 examined...
008:      5 changed, 35 examined...
009:      2 changed, 25 examined...
010:      2 changed, 16 examined...
011:      1 changed, 14 examined...
012:      0 changed, 7 examined...
27 labels changed using aseg
000: 225 total segments, 139 labels (1812 vertices) changed
001: 90 total segments, 6 labels (14 vertices) changed
002: 84 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 21 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
821 vertices marked for relabeling...
821 labels changed in reclassification.
writing output to ../label/rh.aparc.a2009s.annot...
classification took 0 minutes and 13 seconds.
#-----------------------------------------
#@# Parcellation Stats 2 rh Sat Oct 13 05:35:56 UTC 2018
/oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/scripts

 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab sub-S0563CCB1 rh white 

computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
reading volume /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/mri/wm.mgz...
reading input surface /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/surf/rh.white...
reading input pial surface /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/surf/rh.pial...
reading input white surface /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total face volume 197110
Total vertex volume 193600 (mask=0)
reading colortable from annotation file...
colortable with 76 entries read (originally Simple_surface_labels2008.txt)
Saving annotation colortable ../label/aparc.annot.a2009s.ctab

table columns are:
    number of vertices
    total surface area (mm^2)
    total gray matter volume (mm^3)
    average cortical thickness +- standard deviation (mm)
    integrated rectified mean curvature
    integrated rectified Gaussian curvature
    folding index
    intrinsic curvature index
    structure name

atlas_icv (eTIV) = 1251282 mm^3    (det: 1.556888 )
lhCtxGM: 196348.285 196060.000  diff=  288.3  pctdiff= 0.147
rhCtxGM: 193469.206 193128.000  diff=  341.2  pctdiff= 0.176
lhCtxWM: 206427.664 206465.000  diff=  -37.3  pctdiff=-0.018
rhCtxWM: 205105.042 205904.000  diff= -799.0  pctdiff=-0.390
SubCortGMVol  52132.000
SupraTentVol  867948.197 (866254.000) diff=1694.197 pctdiff=0.195
SupraTentVolNotVent  855413.197 (853719.000) diff=1694.197 pctdiff=0.198
BrainSegVol  985826.000 (983934.000) diff=1892.000 pctdiff=0.192
BrainSegVolNotVent  970372.000 (970091.197) diff=280.803 pctdiff=0.029
BrainSegVolNotVent  970372.000
CerebellumVol 116579.000
VentChorVol   12535.000
3rd4th5thCSF   2919.000
CSFVol  1027.000, OptChiasmVol    74.000
MaskVol 1279518.000
  744    518   1289  2.083 0.649     0.171     0.056       17     1.6  G&S_frontomargin
 1031    676   2213  2.612 0.686     0.141     0.029       14     1.2  G&S_occipital_inf
 1390    787   2258  2.365 0.619     0.106     0.021       12     1.3  G&S_paracentral
 1277    811   2380  2.585 0.544     0.120     0.023       13     1.2  G&S_subcentral
 1181    760   2282  2.432 0.563     0.169     0.051       24     2.5  G&S_transv_frontopol
 2596   1722   4599  2.503 0.554     0.124     0.023       30     2.5  G&S_cingul-Ant
 1295    865   2461  2.767 0.427     0.123     0.021       13     1.2  G&S_cingul-Mid-Ant
 1179    806   2193  2.525 0.539     0.113     0.021       10     1.0  G&S_cingul-Mid-Post
  429    277   1146  2.976 0.745     0.169     0.041        9     0.6  G_cingul-Post-dorsal
  358    197    619  2.494 0.611     0.133     0.035        6     0.5  G_cingul-Post-ventral
 2459   1533   3120  1.893 0.471     0.160     0.035       42     3.4  G_cuneus
 1003    670   2247  2.646 0.377     0.120     0.025       12     1.0  G_front_inf-Opercular
  417    278    953  2.440 0.479     0.173     0.045       11     0.9  G_front_inf-Orbital
  777    505   1793  2.815 0.476     0.132     0.032       10     0.9  G_front_inf-Triangul
 3415   2201   7653  2.615 0.542     0.150     0.041       61     6.1  G_front_middle
 5532   3541  12361  2.861 0.566     0.125     0.027       58     6.1  G_front_sup
  468    326   1215  3.421 0.529     0.104     0.022        3     0.3  G_Ins_lg&S_cent_ins
  570    349   1694  3.477 0.658     0.116     0.029        6     0.7  G_insular_short
 1713   1069   3247  2.349 0.508     0.144     0.030       28     2.0  G_occipital_middle
 1350    818   1848  1.957 0.442     0.133     0.032       17     1.7  G_occipital_sup
 1897   1193   4498  2.918 0.551     0.147     0.036       34     2.6  G_oc-temp_lat-fusifor
 2454   1551   3656  2.083 0.637     0.159     0.040       43     3.8  G_oc-temp_med-Lingual
 1029    655   3103  3.179 0.942     0.112     0.027       10     0.9  G_oc-temp_med-Parahip
 1980   1385   5202  2.833 0.653     0.158     0.047       37     3.7  G_orbital
 1987   1305   4242  2.523 0.495     0.155     0.036       40     2.8  G_pariet_inf-Angular
 2420   1559   5235  2.829 0.468     0.140     0.033       37     3.2  G_pariet_inf-Supramar
 2622   1698   4752  2.246 0.496     0.152     0.031       43     3.2  G_parietal_sup
 1981   1148   2696  1.933 0.429     0.104     0.019       18     1.6  G_postcentral
 2298   1307   4747  2.746 0.452     0.105     0.026       21     2.3  G_precentral
 2392   1529   4372  2.373 0.558     0.140     0.031       36     3.1  G_precuneus
  642    445   1610  2.456 0.590     0.150     0.063       18     1.7  G_rectus
   96     89    260  2.619 0.450     0.083     0.017        1     0.0  G_subcallosal
  439    233    729  2.507 0.398     0.104     0.025        5     0.4  G_temp_sup-G_T_transv
 1525   1007   3908  2.912 0.624     0.133     0.037       30     1.9  G_temp_sup-Lateral
 1118    810   2207  2.492 0.935     0.144     0.050       21     2.3  G_temp_sup-Plan_polar
  737    486   1488  2.681 0.391     0.120     0.027        8     0.8  G_temp_sup-Plan_tempo
 2111   1287   4911  2.749 0.783     0.131     0.035       35     3.0  G_temporal_inf
 2602   1669   5967  2.868 0.638     0.151     0.036       53     3.7  G_temporal_middle
  352    233    408  1.943 0.492     0.087     0.018        2     0.2  Lat_Fis-ant-Horizont
  244    174    393  2.577 0.520     0.088     0.012        1     0.1  Lat_Fis-ant-Vertical
 1247    859   1681  2.269 0.520     0.111     0.018        8     0.9  Lat_Fis-post
 3302   2035   3930  1.835 0.458     0.140     0.032       44     4.3  Pole_occipital
 2014   1327   6514  3.436 0.772     0.153     0.052       35     4.3  Pole_temporal
 2363   1651   2525  1.795 0.588     0.119     0.022       19     2.1  S_calcarine
 2856   1910   3013  1.846 0.627     0.099     0.017       17     2.1  S_central
 1008    685   1479  2.239 0.510     0.106     0.015        7     0.6  S_cingul-Marginalis
  507    350    787  2.681 0.593     0.108     0.030        3     0.5  S_circular_insula_ant
 1118    757   1619  2.525 0.425     0.089     0.011        5     0.5  S_circular_insula_inf
 1252    862   1809  2.476 0.463     0.092     0.018        5     0.9  S_circular_insula_sup
  762    536   1245  2.587 0.584     0.121     0.019        7     0.6  S_collat_transv_ant
  393    272    438  1.910 0.356     0.136     0.025        4     0.3  S_collat_transv_post
 1896   1322   2695  2.057 0.432     0.119     0.021       16     1.6  S_front_inf
 1735   1236   2673  2.214 0.528     0.126     0.030       16     2.4  S_front_middle
 2479   1690   4109  2.544 0.479     0.102     0.017       15     1.6  S_front_sup
  281    201    394  2.019 0.373     0.111     0.014        2     0.2  S_interm_prim-Jensen
 3098   2058   4255  2.260 0.458     0.128     0.023       31     3.0  S_intrapariet&P_trans
  845    571    933  2.013 0.358     0.139     0.029        9     0.9  S_oc_middle&Lunatus
  964    645   1133  2.021 0.480     0.116     0.023        7     0.8  S_oc_sup&transversal
  609    435    769  2.069 0.442     0.111     0.023        3     0.5  S_occipital_ant
  866    633   1320  2.458 0.301     0.108     0.012        6     0.5  S_oc-temp_lat
 1697   1244   2502  2.366 0.551     0.103     0.014       10     1.0  S_oc-temp_med&Lingual
  473    332    600  1.924 0.427     0.129     0.032        3     0.6  S_orbital_lateral
  475    364    910  2.668 0.711     0.098     0.018        3     0.2  S_orbital_med-olfact
  955    679   1670  2.303 0.716     0.126     0.036        9     1.4  S_orbital-H_Shaped
 2042   1385   2770  2.252 0.473     0.124     0.024       17     2.0  S_parieto_occipital
 1118    685   1118  2.238 0.755     0.137     0.021       20     0.7  S_pericallosal
 2421   1629   3081  2.170 0.420     0.105     0.018       16     1.7  S_postcentral
 1621   1137   2508  2.428 0.343     0.102     0.015        9     1.0  S_precentral-inf-part
 1075    724   1596  2.505 0.445     0.098     0.015        6     0.7  S_precentral-sup-part
  193    126    301  2.775 0.627     0.141     0.017        3     0.1  S_suborbital
 1086    756   1742  2.408 0.522     0.137     0.032       12     1.4  S_subparietal
 1174    823   1587  2.457 0.412     0.135     0.024       10     1.4  S_temporal_inf
 4696   3321   7581  2.382 0.490     0.113     0.019       37     3.8  S_temporal_sup
  245    179    354  2.798 0.377     0.124     0.014        2     0.1  S_temporal_transverse
#-----------------------------------------
#@# Cortical Parc 3 rh Sat Oct 13 05:36:18 UTC 2018
/oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-S0563CCB1 rh ../surf/rh.sphere.reg /opt/freesurfer/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.DKTatlas.annot 

setting seed for random number generator to 1234
using ../mri/aseg.presurf.mgz aseg volume to correct midline
$Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading atlas from /opt/freesurfer/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs...
reading color table from GCSA file....
average std = 0.9   using min determinant for regularization = 0.009
0 singular and 325 ill-conditioned covariance matrices regularized
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
1394 labels changed using aseg
relabeling using gibbs priors...
000:   1766 changed, 116888 examined...
001:    417 changed, 8185 examined...
002:    121 changed, 2308 examined...
003:     59 changed, 743 examined...
004:     41 changed, 360 examined...
005:     17 changed, 219 examined...
006:     11 changed, 92 examined...
007:      7 changed, 52 examined...
008:      6 changed, 38 examined...
009:      6 changed, 29 examined...
010:      5 changed, 29 examined...
011:      6 changed, 30 examined...
012:      3 changed, 32 examined...
013:      4 changed, 18 examined...
014:      4 changed, 23 examined...
015:      3 changed, 22 examined...
016:      4 changed, 20 examined...
017:      5 changed, 21 examined...
018:      5 changed, 25 examined...
019:      3 changed, 27 examined...
020:      2 changed, 16 examined...
021:      0 changed, 13 examined...
267 labels changed using aseg
000: 48 total segments, 15 labels (302 vertices) changed
001: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 5 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
420 vertices marked for relabeling...
420 labels changed in reclassification.
writing output to ../label/rh.aparc.DKTatlas.annot...
classification took 0 minutes and 10 seconds.
#-----------------------------------------
#@# Parcellation Stats 3 rh Sat Oct 13 05:36:28 UTC 2018
/oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/scripts

 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab sub-S0563CCB1 rh white 

computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot.
reading volume /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/mri/wm.mgz...
reading input surface /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/surf/rh.white...
reading input pial surface /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/surf/rh.pial...
reading input white surface /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total face volume 197110
Total vertex volume 193600 (mask=0)
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab

table columns are:
    number of vertices
    total surface area (mm^2)
    total gray matter volume (mm^3)
    average cortical thickness +- standard deviation (mm)
    integrated rectified mean curvature
    integrated rectified Gaussian curvature
    folding index
    intrinsic curvature index
    structure name

atlas_icv (eTIV) = 1251282 mm^3    (det: 1.556888 )
lhCtxGM: 196348.285 196060.000  diff=  288.3  pctdiff= 0.147
rhCtxGM: 193469.206 193128.000  diff=  341.2  pctdiff= 0.176
lhCtxWM: 206427.664 206465.000  diff=  -37.3  pctdiff=-0.018
rhCtxWM: 205105.042 205904.000  diff= -799.0  pctdiff=-0.390
SubCortGMVol  52132.000
SupraTentVol  867948.197 (866254.000) diff=1694.197 pctdiff=0.195
SupraTentVolNotVent  855413.197 (853719.000) diff=1694.197 pctdiff=0.198
BrainSegVol  985826.000 (983934.000) diff=1892.000 pctdiff=0.192
BrainSegVolNotVent  970372.000 (970091.197) diff=280.803 pctdiff=0.029
BrainSegVolNotVent  970372.000
CerebellumVol 116579.000
VentChorVol   12535.000
3rd4th5thCSF   2919.000
CSFVol  1027.000, OptChiasmVol    74.000
MaskVol 1279518.000
 1234    770   2203  2.745 0.501     0.121     0.014       15     0.7  caudalanteriorcingulate
 2687   1742   4701  2.550 0.479     0.114     0.025       23     3.0  caudalmiddlefrontal
 2952   1869   3792  1.974 0.446     0.156     0.034       45     4.1  cuneus
  506    338   1987  3.668 0.837     0.121     0.033        5     0.6  entorhinal
 3427   2323   7037  2.749 0.571     0.131     0.026       45     3.5  fusiform
 5731   3824   9925  2.361 0.478     0.137     0.028       81     6.3  inferiorparietal
 4710   3048  10048  2.781 0.731     0.136     0.033       71     6.4  inferiortemporal
 1135    713   1798  2.369 0.733     0.139     0.030       21     1.1  isthmuscingulate
 6259   3966   8861  2.067 0.544     0.137     0.029       80     7.5  lateraloccipital
 3376   2345   6812  2.527 0.804     0.147     0.046       57     6.2  lateralorbitofrontal
 3852   2609   5414  2.006 0.577     0.147     0.033       55     5.1  lingual
 1482   1039   3346  2.619 0.620     0.138     0.039       31     2.4  medialorbitofrontal
 4950   3343   9925  2.728 0.624     0.131     0.028       65     5.7  middletemporal
  916    590   1622  2.456 0.690     0.093     0.015        7     0.4  parahippocampal
 2160   1333   3265  2.378 0.566     0.105     0.017       16     1.5  paracentral
 1938   1332   3605  2.517 0.436     0.111     0.019       17     1.5  parsopercularis
  890    644   1887  2.358 0.577     0.150     0.041       14     1.6  parsorbitalis
 1950   1296   3530  2.393 0.613     0.122     0.028       22     2.1  parstriangularis
 2355   1562   2162  1.562 0.455     0.129     0.028       25     2.7  pericalcarine
 6107   3924   8092  1.962 0.556     0.104     0.019       47     4.8  postcentral
 1427    983   2740  2.542 0.683     0.141     0.024       20     1.4  posteriorcingulate
 6366   3934  10703  2.530 0.532     0.105     0.021       50     5.3  precentral
 5509   3606   9108  2.371 0.517     0.129     0.028       66     6.1  precuneus
 1001    654   1880  2.409 0.581     0.135     0.028       16     1.1  rostralanteriorcingulate
 5099   3540   9365  2.328 0.565     0.145     0.037       74     7.8  rostralmiddlefrontal
10877   7190  21835  2.680 0.591     0.122     0.027      109    12.0  superiorfrontal
 6043   3961   9474  2.202 0.483     0.135     0.026       74     6.4  superiorparietal
 6223   4283  14028  2.792 0.713     0.123     0.030       78     7.4  superiortemporal
 4559   3036   8238  2.544 0.529     0.130     0.028       56     5.3  supramarginal
  519    275    819  2.566 0.391     0.098     0.023        5     0.4  transversetemporal
 2736   1825   5398  2.927 0.690     0.106     0.022       19     2.3  insula
#-----------------------------------------
#@# WM/GM Contrast rh Sat Oct 13 05:36:49 UTC 2018
/oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/scripts

 pctsurfcon --s sub-S0563CCB1 --rh-only 

Log file is /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/scripts/pctsurfcon.log
Sat Oct 13 05:36:49 UTC 2018
setenv SUBJECTS_DIR /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer
cd /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/scripts
/opt/freesurfer/bin/pctsurfcon
$Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $
Linux sh-102-16.int 3.10.0-862.14.4.el7.x86_64 #1 SMP Wed Sep 26 15:12:11 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
FREESURFER_HOME /opt/freesurfer
mri_vol2surf --mov /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/surf/tmp.pctsurfcon.26767/rh.wm.mgh --regheader sub-S0563CCB1 --cortex
srcvol = /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/mri/rawavg.mgz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = rh
ProjDist = -1
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Computing registration from header.
  Using /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/mri/orig.mgz as target reference.
-------- original matrix -----------
-1.00000   0.00000   0.00000  -0.00002;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000  -0.00002;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/label/rh.cortex.label
Reading surface /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/surf/rh.white
Done reading source surface
Mapping Source Volume onto Source Subject Surface
 1 -1 -1 -1
using old
Done mapping volume to surface
Number of source voxels hit = 56967
Masking with /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/label/rh.cortex.label
Writing to /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/surf/tmp.pctsurfcon.26767/rh.wm.mgh
Dim: 116888 1 1
mri_vol2surf --mov /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/surf/tmp.pctsurfcon.26767/rh.gm.mgh --projfrac 0.3 --regheader sub-S0563CCB1 --cortex
srcvol = /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/mri/rawavg.mgz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = rh
ProjFrac = 0.3
thickness = thickness
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Computing registration from header.
  Using /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/mri/orig.mgz as target reference.
-------- original matrix -----------
-1.00000   0.00000   0.00000  -0.00002;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000  -0.00002;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/label/rh.cortex.label
Reading surface /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/surf/rh.white
Done reading source surface
Reading thickness /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/surf/rh.thickness
Done
Mapping Source Volume onto Source Subject Surface
 1 0.3 0.3 0.3
using old
Done mapping volume to surface
Number of source voxels hit = 67640
Masking with /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/label/rh.cortex.label
Writing to /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/surf/tmp.pctsurfcon.26767/rh.gm.mgh
Dim: 116888 1 1
mri_concat /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/surf/tmp.pctsurfcon.26767/rh.wm.mgh /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/surf/tmp.pctsurfcon.26767/rh.gm.mgh --paired-diff-norm --mul 100 --o /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/surf/rh.w-g.pct.mgh
ninputs = 2
Checking inputs
nframestot = 2
Allocing output
Done allocing
Combining pairs
nframes = 1
Multiplying by 100.000000
Writing to /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/surf/rh.w-g.pct.mgh
mri_segstats --in /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/surf/rh.w-g.pct.mgh --annot sub-S0563CCB1 rh aparc --sum /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/stats/rh.w-g.pct.stats --snr

$Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
cwd 
cmdline mri_segstats --in /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/surf/rh.w-g.pct.mgh --annot sub-S0563CCB1 rh aparc --sum /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/stats/rh.w-g.pct.stats --snr 
sysname  Linux
hostname sh-102-16.int
machine  x86_64
user     oesteban
UseRobust  0
Constructing seg from annotation

Reading annotation /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/label/rh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Seg base 2000
Loading /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/surf/rh.w-g.pct.mgh
Vertex Area is 0.659664 mm^3
Generating list of segmentation ids
Found  36 segmentations
Computing statistics for each segmentation

Reporting on  35 segmentations
Using PrintSegStat
mri_segstats done
Cleaning up
#-----------------------------------------
#@# Relabel Hypointensities Sat Oct 13 05:36:54 UTC 2018
/oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/mri

 mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz 

reading input surface ../surf/lh.white...
relabeling lh hypointensities...
1268 voxels changed to hypointensity...
reading input surface ../surf/rh.white...
relabeling rh hypointensities...
1540 voxels changed to hypointensity...
2752 hypointense voxels neighboring cortex changed
#-----------------------------------------
#@# AParc-to-ASeg aparc Sat Oct 13 05:37:09 UTC 2018
/oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1

 mri_aparc2aseg --s sub-S0563CCB1 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt 

relabeling unlikely voxels interior to white matter surface:
    norm: mri/norm.mgz
     XFORM: mri/transforms/talairach.m3z
    GCA: /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca
    label intensities: mri/aseg.auto_noCCseg.label_intensities.txt
SUBJECTS_DIR /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer
subject sub-S0563CCB1
outvol /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/surf/lh.white

Reading lh pial surface 
 /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/surf/lh.pial

Loading lh annotations from /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/label/lh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)

Reading rh white surface 
 /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/surf/rh.white

Reading rh pial surface 
 /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/surf/rh.pial

Loading rh annotations from /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/label/rh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Have color table for lh white annotation
Have color table for rh white annotation
Loading ribbon segmentation from /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/mri/ribbon.mgz

Building hash of lh white

Building hash of lh pial

Building hash of rh white

Building hash of rh pial

Loading aseg from /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: -----------
-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;
-------------------------

Labeling Slice
relabeling unlikely voxels in interior of white matter
setting orig areas to linear transform determinant scaled 5.47
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 107
rescaling Left_Cerebral_Cortex from 61 --> 63
rescaling Left_Lateral_Ventricle from 13 --> 23
rescaling Left_Inf_Lat_Vent from 34 --> 31
rescaling Left_Cerebellum_White_Matter from 86 --> 91
rescaling Left_Cerebellum_Cortex from 60 --> 62
rescaling Left_Thalamus from 94 --> 104
rescaling Left_Thalamus_Proper from 84 --> 93
rescaling Left_Caudate from 75 --> 73
rescaling Left_Putamen from 80 --> 83
rescaling Left_Pallidum from 98 --> 103
rescaling Third_Ventricle from 25 --> 33
rescaling Fourth_Ventricle from 22 --> 20
rescaling Brain_Stem from 81 --> 86
rescaling Left_Hippocampus from 57 --> 65
rescaling Left_Amygdala from 56 --> 69
rescaling CSF from 32 --> 46
rescaling Left_Accumbens_area from 62 --> 66
rescaling Left_VentralDC from 87 --> 97
rescaling Right_Cerebral_White_Matter from 105 --> 104
rescaling Right_Cerebral_Cortex from 58 --> 65
rescaling Right_Lateral_Ventricle from 13 --> 17
rescaling Right_Inf_Lat_Vent from 25 --> 27
rescaling Right_Cerebellum_White_Matter from 87 --> 90
rescaling Right_Cerebellum_Cortex from 59 --> 63
rescaling Right_Thalamus_Proper from 85 --> 86
rescaling Right_Caudate from 62 --> 75
rescaling Right_Putamen from 80 --> 81
rescaling Right_Pallidum from 97 --> 100
rescaling Right_Hippocampus from 53 --> 65
rescaling Right_Amygdala from 55 --> 65
rescaling Right_Accumbens_area from 65 --> 73
rescaling Right_VentralDC from 86 --> 96
rescaling Fifth_Ventricle from 40 --> 40
rescaling WM_hypointensities from 78 --> 78
rescaling non_WM_hypointensities from 40 --> 56
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 387911
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 101 changed.
pass 2: 4 changed.
pass 3: 0 changed.
nchanged = 0
Writing output aseg to /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/mri/aparc+aseg.mgz
#-----------------------------------------
#@# AParc-to-ASeg a2009s Sat Oct 13 05:40:06 UTC 2018
/oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1

 mri_aparc2aseg --s sub-S0563CCB1 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --a2009s 

relabeling unlikely voxels interior to white matter surface:
    norm: mri/norm.mgz
     XFORM: mri/transforms/talairach.m3z
    GCA: /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca
    label intensities: mri/aseg.auto_noCCseg.label_intensities.txt
SUBJECTS_DIR /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer
subject sub-S0563CCB1
outvol /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/mri/aparc.a2009s+aseg.mgz
useribbon 0
baseoffset 10100
RipUnknown 0

Reading lh white surface 
 /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/surf/lh.white

Reading lh pial surface 
 /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/surf/lh.pial

Loading lh annotations from /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/label/lh.aparc.a2009s.annot
reading colortable from annotation file...
colortable with 76 entries read (originally Simple_surface_labels2008.txt)

Reading rh white surface 
 /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/surf/rh.white

Reading rh pial surface 
 /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/surf/rh.pial

Loading rh annotations from /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/label/rh.aparc.a2009s.annot
reading colortable from annotation file...
colortable with 76 entries read (originally Simple_surface_labels2008.txt)
Have color table for lh white annotation
Have color table for rh white annotation
Loading ribbon segmentation from /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/mri/ribbon.mgz

Building hash of lh white

Building hash of lh pial

Building hash of rh white

Building hash of rh pial

Loading aseg from /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: -----------
-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;
-------------------------

Labeling Slice
relabeling unlikely voxels in interior of white matter
setting orig areas to linear transform determinant scaled 5.47
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 107
rescaling Left_Cerebral_Cortex from 61 --> 63
rescaling Left_Lateral_Ventricle from 13 --> 23
rescaling Left_Inf_Lat_Vent from 34 --> 31
rescaling Left_Cerebellum_White_Matter from 86 --> 91
rescaling Left_Cerebellum_Cortex from 60 --> 62
rescaling Left_Thalamus from 94 --> 104
rescaling Left_Thalamus_Proper from 84 --> 93
rescaling Left_Caudate from 75 --> 73
rescaling Left_Putamen from 80 --> 83
rescaling Left_Pallidum from 98 --> 103
rescaling Third_Ventricle from 25 --> 33
rescaling Fourth_Ventricle from 22 --> 20
rescaling Brain_Stem from 81 --> 86
rescaling Left_Hippocampus from 57 --> 65
rescaling Left_Amygdala from 56 --> 69
rescaling CSF from 32 --> 46
rescaling Left_Accumbens_area from 62 --> 66
rescaling Left_VentralDC from 87 --> 97
rescaling Right_Cerebral_White_Matter from 105 --> 104
rescaling Right_Cerebral_Cortex from 58 --> 65
rescaling Right_Lateral_Ventricle from 13 --> 17
rescaling Right_Inf_Lat_Vent from 25 --> 27
rescaling Right_Cerebellum_White_Matter from 87 --> 90
rescaling Right_Cerebellum_Cortex from 59 --> 63
rescaling Right_Thalamus_Proper from 85 --> 86
rescaling Right_Caudate from 62 --> 75
rescaling Right_Putamen from 80 --> 81
rescaling Right_Pallidum from 97 --> 100
rescaling Right_Hippocampus from 53 --> 65
rescaling Right_Amygdala from 55 --> 65
rescaling Right_Accumbens_area from 65 --> 73
rescaling Right_VentralDC from 86 --> 96
rescaling Fifth_Ventricle from 40 --> 40
rescaling WM_hypointensities from 78 --> 78
rescaling non_WM_hypointensities from 40 --> 56
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 388024
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 101 changed.
pass 2: 4 changed.
pass 3: 0 changed.
nchanged = 0
Writing output aseg to /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/mri/aparc.a2009s+aseg.mgz
#-----------------------------------------
#@# AParc-to-ASeg DKTatlas Sat Oct 13 05:43:04 UTC 2018
/oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1

 mri_aparc2aseg --s sub-S0563CCB1 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --annot aparc.DKTatlas --o mri/aparc.DKTatlas+aseg.mgz 

relabeling unlikely voxels interior to white matter surface:
    norm: mri/norm.mgz
     XFORM: mri/transforms/talairach.m3z
    GCA: /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca
    label intensities: mri/aseg.auto_noCCseg.label_intensities.txt
SUBJECTS_DIR /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer
subject sub-S0563CCB1
outvol mri/aparc.DKTatlas+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/surf/lh.white

Reading lh pial surface 
 /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/surf/lh.pial

Loading lh annotations from /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/label/lh.aparc.DKTatlas.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)

Reading rh white surface 
 /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/surf/rh.white

Reading rh pial surface 
 /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/surf/rh.pial

Loading rh annotations from /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/label/rh.aparc.DKTatlas.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Have color table for lh white annotation
Have color table for rh white annotation
Loading ribbon segmentation from /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/mri/ribbon.mgz

Building hash of lh white

Building hash of lh pial

Building hash of rh white

Building hash of rh pial

Loading aseg from /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: -----------
-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;
-------------------------

Labeling Slice
relabeling unlikely voxels in interior of white matter
setting orig areas to linear transform determinant scaled 5.47
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 107
rescaling Left_Cerebral_Cortex from 61 --> 63
rescaling Left_Lateral_Ventricle from 13 --> 23
rescaling Left_Inf_Lat_Vent from 34 --> 31
rescaling Left_Cerebellum_White_Matter from 86 --> 91
rescaling Left_Cerebellum_Cortex from 60 --> 62
rescaling Left_Thalamus from 94 --> 104
rescaling Left_Thalamus_Proper from 84 --> 93
rescaling Left_Caudate from 75 --> 73
rescaling Left_Putamen from 80 --> 83
rescaling Left_Pallidum from 98 --> 103
rescaling Third_Ventricle from 25 --> 33
rescaling Fourth_Ventricle from 22 --> 20
rescaling Brain_Stem from 81 --> 86
rescaling Left_Hippocampus from 57 --> 65
rescaling Left_Amygdala from 56 --> 69
rescaling CSF from 32 --> 46
rescaling Left_Accumbens_area from 62 --> 66
rescaling Left_VentralDC from 87 --> 97
rescaling Right_Cerebral_White_Matter from 105 --> 104
rescaling Right_Cerebral_Cortex from 58 --> 65
rescaling Right_Lateral_Ventricle from 13 --> 17
rescaling Right_Inf_Lat_Vent from 25 --> 27
rescaling Right_Cerebellum_White_Matter from 87 --> 90
rescaling Right_Cerebellum_Cortex from 59 --> 63
rescaling Right_Thalamus_Proper from 85 --> 86
rescaling Right_Caudate from 62 --> 75
rescaling Right_Putamen from 80 --> 81
rescaling Right_Pallidum from 97 --> 100
rescaling Right_Hippocampus from 53 --> 65
rescaling Right_Amygdala from 55 --> 65
rescaling Right_Accumbens_area from 65 --> 73
rescaling Right_VentralDC from 86 --> 96
rescaling Fifth_Ventricle from 40 --> 40
rescaling WM_hypointensities from 78 --> 78
rescaling non_WM_hypointensities from 40 --> 56
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 388024
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 101 changed.
pass 2: 4 changed.
pass 3: 0 changed.
nchanged = 0
Writing output aseg to mri/aparc.DKTatlas+aseg.mgz
#-----------------------------------------
#@# APas-to-ASeg Sat Oct 13 05:46:00 UTC 2018
/oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/mri

 apas2aseg --i aparc+aseg.mgz --o aseg.mgz 

Sat Oct 13 05:46:00 UTC 2018

setenv SUBJECTS_DIR /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer
cd /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/mri
/opt/freesurfer/bin/apas2aseg --i aparc+aseg.mgz --o aseg.mgz

freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
$Id: apas2aseg,v 1.2 2016/02/12 21:43:14 zkaufman Exp $
Linux sh-102-16.int 3.10.0-862.14.4.el7.x86_64 #1 SMP Wed Sep 26 15:12:11 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
mri_binarize --i aparc+aseg.mgz --o aseg.mgz --replace 1000 3 --replace 2000 42 --replace 1001 3 --replace 2001 42 --replace 1002 3 --replace 2002 42 --replace 1003 3 --replace 2003 42 --replace 1004 3 --replace 2004 42 --replace 1005 3 --replace 2005 42 --replace 1006 3 --replace 2006 42 --replace 1007 3 --replace 2007 42 --replace 1008 3 --replace 2008 42 --replace 1009 3 --replace 2009 42 --replace 1010 3 --replace 2010 42 --replace 1011 3 --replace 2011 42 --replace 1012 3 --replace 2012 42 --replace 1013 3 --replace 2013 42 --replace 1014 3 --replace 2014 42 --replace 1015 3 --replace 2015 42 --replace 1016 3 --replace 2016 42 --replace 1017 3 --replace 2017 42 --replace 1018 3 --replace 2018 42 --replace 1019 3 --replace 2019 42 --replace 1020 3 --replace 2020 42 --replace 1021 3 --replace 2021 42 --replace 1022 3 --replace 2022 42 --replace 1023 3 --replace 2023 42 --replace 1024 3 --replace 2024 42 --replace 1025 3 --replace 2025 42 --replace 1026 3 --replace 2026 42 --replace 1027 3 --replace 2027 42 --replace 1028 3 --replace 2028 42 --replace 1029 3 --replace 2029 42 --replace 1030 3 --replace 2030 42 --replace 1031 3 --replace 2031 42 --replace 1032 3 --replace 2032 42 --replace 1033 3 --replace 2033 42 --replace 1034 3 --replace 2034 42 --replace 1035 3 --replace 2035 42

$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/mri
cmdline mri_binarize.bin --i aparc+aseg.mgz --o aseg.mgz --replace 1000 3 --replace 2000 42 --replace 1001 3 --replace 2001 42 --replace 1002 3 --replace 2002 42 --replace 1003 3 --replace 2003 42 --replace 1004 3 --replace 2004 42 --replace 1005 3 --replace 2005 42 --replace 1006 3 --replace 2006 42 --replace 1007 3 --replace 2007 42 --replace 1008 3 --replace 2008 42 --replace 1009 3 --replace 2009 42 --replace 1010 3 --replace 2010 42 --replace 1011 3 --replace 2011 42 --replace 1012 3 --replace 2012 42 --replace 1013 3 --replace 2013 42 --replace 1014 3 --replace 2014 42 --replace 1015 3 --replace 2015 42 --replace 1016 3 --replace 2016 42 --replace 1017 3 --replace 2017 42 --replace 1018 3 --replace 2018 42 --replace 1019 3 --replace 2019 42 --replace 1020 3 --replace 2020 42 --replace 1021 3 --replace 2021 42 --replace 1022 3 --replace 2022 42 --replace 1023 3 --replace 2023 42 --replace 1024 3 --replace 2024 42 --replace 1025 3 --replace 2025 42 --replace 1026 3 --replace 2026 42 --replace 1027 3 --replace 2027 42 --replace 1028 3 --replace 2028 42 --replace 1029 3 --replace 2029 42 --replace 1030 3 --replace 2030 42 --replace 1031 3 --replace 2031 42 --replace 1032 3 --replace 2032 42 --replace 1033 3 --replace 2033 42 --replace 1034 3 --replace 2034 42 --replace 1035 3 --replace 2035 42 
sysname  Linux
hostname sh-102-16.int
machine  x86_64
user     oesteban

input      aparc+aseg.mgz
frame      0
nErode3d   0
nErode2d   0
output     aseg.mgz
Binarizing based on threshold
min        -infinity
max        +infinity
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Replacing 72
 1:  1000    3
 2:  2000   42
 3:  1001    3
 4:  2001   42
 5:  1002    3
 6:  2002   42
 7:  1003    3
 8:  2003   42
 9:  1004    3
10:  2004   42
11:  1005    3
12:  2005   42
13:  1006    3
14:  2006   42
15:  1007    3
16:  2007   42
17:  1008    3
18:  2008   42
19:  1009    3
20:  2009   42
21:  1010    3
22:  2010   42
23:  1011    3
24:  2011   42
25:  1012    3
26:  2012   42
27:  1013    3
28:  2013   42
29:  1014    3
30:  2014   42
31:  1015    3
32:  2015   42
33:  1016    3
34:  2016   42
35:  1017    3
36:  2017   42
37:  1018    3
38:  2018   42
39:  1019    3
40:  2019   42
41:  1020    3
42:  2020   42
43:  1021    3
44:  2021   42
45:  1022    3
46:  2022   42
47:  1023    3
48:  2023   42
49:  1024    3
50:  2024   42
51:  1025    3
52:  2025   42
53:  1026    3
54:  2026   42
55:  1027    3
56:  2027   42
57:  1028    3
58:  2028   42
59:  1029    3
60:  2029   42
61:  1030    3
62:  2030   42
63:  1031    3
64:  2031   42
65:  1032    3
66:  2032   42
67:  1033    3
68:  2033   42
69:  1034    3
70:  2034   42
71:  1035    3
72:  2035   42
Found 0 values in range
Counting number of voxels in first frame
Found 0 voxels in final mask
Count: 0 0.000000 16777216 0.000000
mri_binarize done

Started at Sat Oct 13 05:46:00 UTC 2018 
Ended   at Sat Oct 13 05:46:04 UTC 2018
Apas2aseg-Run-Time-Sec 4

apas2aseg Done
#--------------------------------------------
#@# ASeg Stats Sat Oct 13 05:46:04 UTC 2018
/oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1

 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /opt/freesurfer/ASegStatsLUT.txt --subject sub-S0563CCB1 

$Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
cwd 
cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /opt/freesurfer/ASegStatsLUT.txt --subject sub-S0563CCB1 
sysname  Linux
hostname sh-102-16.int
machine  x86_64
user     oesteban
UseRobust  0
atlas_icv (eTIV) = 1251282 mm^3    (det: 1.556888 )
mghRead(mri/aseg.mgz, -1): read error
Computing euler number
orig.nofix lheno =  -28, rheno = -30
orig.nofix lhholes =   15, rhholes = 16
Loading mri/aseg.mgz
No such file or directory
ERROR: loading mri/aseg.mgz
Linux sh-102-16.int 3.10.0-862.14.4.el7.x86_64 #1 SMP Wed Sep 26 15:12:11 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-S0563CCB1 exited with ERRORS at Sat Oct 13 05:46:07 UTC 2018

For more details, see the log file /oak/stanford/groups/russpold/data/BSNIP2-BIDS/derivatives/fmriprep_1.2.0/freesurfer/sub-S0563CCB1/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Standard error:

Return code: 1
oesteban commented 5 years ago

@effigies maybe the SUBJECTS_DIR is not properly set?

effigies commented 5 years ago

Looks fine. Not hitting quotas or anything?

oesteban commented 5 years ago

Not apparently. Just re-ran the subject without issues. I'll close for now, although I had 61 more like this one.

Shotgunosine commented 5 years ago

Not to revive a zombie, but I had 12 subjects out of 167 do this and then work fine when rerun with more memory. Running a singularity container with 1.4.1. The first run was 24 cores and 32G ram, the second was 24 cores with 64G ram. Just FYI.

effigies commented 5 years ago

Thanks @Shotgunosine. I've marked it memory, so hopefully if this comes up for people, it'll be easy to find the fix.