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fmriprep MSC01 crash
Raw
fmriprep-log-230219
Node: _autorecon30
Working directory: /scratch/fmriprep_wf/single_subject_MSC01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon3/mapflow/_autorecon30
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 = lh
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-MSC01
subjects_dir = /out/freesurfer
talairach = <undefined>
use_FLAIR = False
use_T2 = True
xopts = <undefined>
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node
result['result'] = node.run(updatehash=updatehash)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 473, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 557, in _run_interface
return self._run_command(execute)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 637, in _run_command
result = self._interface.run(cwd=outdir)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 369, in run
runtime = self._run_interface(runtime)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 752, in _run_interface
self.raise_exception(runtime)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 689, in raise_exception
).format(**runtime.dictcopy()))
RuntimeError: Command:
recon-all -autorecon3 -hemi lh -openmp 8 -subjid sub-MSC01 -sd /out/freesurfer -T2pial -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 /out/freesurfer
Actual FREESURFER_HOME /opt/freesurfer
-rw-rw-r-- 1 root root 144454 Feb 18 10:37 /out/freesurfer/sub-MSC01/scripts/recon-all.log
Linux b0c54804ca5f 3.13.0-147-generic #196-Ubuntu SMP Wed May 2 15:51:34 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
'/opt/freesurfer/bin/recon-all' -> '/out/freesurfer/sub-MSC01/scripts/recon-all.local-copy'
#--------------------------------------------
#@# Refine Pial Surfs w/ T2/FLAIR Mon Feb 18 10:37:50 UTC 2019
bbregister --s sub-MSC01 --mov /out/freesurfer/sub-MSC01/mri/orig/T2raw.mgz --lta /out/freesurfer/sub-MSC01/mri/transforms/T2raw.auto.lta --init-coreg --T2
tmp /out/freesurfer/sub-MSC01/mri/transforms/tmp.bbregister.56705
Log file is /out/freesurfer/sub-MSC01/mri/transforms/T2raw.auto.dat.log
Mon Feb 18 10:37:50 UTC 2019
setenv SUBJECTS_DIR /out/freesurfer
cd /out/freesurfer/sub-MSC01/scripts
/opt/freesurfer/bin/bbregister --s sub-MSC01 --mov /out/freesurfer/sub-MSC01/mri/orig/T2raw.mgz --lta /out/freesurfer/sub-MSC01/mri/transforms/T2raw.auto.lta --init-coreg --T2
$Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $
Linux b0c54804ca5f 3.13.0-147-generic #196-Ubuntu SMP Wed May 2 15:51:34 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
FREESURFER_HOME /opt/freesurfer
mri_convert /out/freesurfer/sub-MSC01/mri/orig/T2raw.mgz /out/freesurfer/sub-MSC01/mri/transforms/tmp.bbregister.56705/template.nii
mri_convert.bin /out/freesurfer/sub-MSC01/mri/orig/T2raw.mgz /out/freesurfer/sub-MSC01/mri/transforms/tmp.bbregister.56705/template.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /out/freesurfer/sub-MSC01/mri/orig/T2raw.mgz...
TR=3200.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.998443, -0.0497087, -0.0253296)
j_ras = (0.0429192, 0.974438, -0.220519)
k_ras = (0.0356438, 0.219088, 0.975054)
writing to /out/freesurfer/sub-MSC01/mri/transforms/tmp.bbregister.56705/template.nii...
mri_coreg --s sub-MSC01 --mov /out/freesurfer/sub-MSC01/mri/transforms/tmp.bbregister.56705/template.nii --regdat /out/freesurfer/sub-MSC01/mri/transforms/tmp.bbregister.56705/reg.init.dat --reg /out/freesurfer/sub-MSC01/mri/transforms/tmp.bbregister.56705/mri_coreg.lta --nthreads 8 --dof 6 --sep 4 --ftol .0001 --linmintol .01 --no-ref-mask
$Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $
cwd /out/freesurfer/sub-MSC01/scripts
cmdline mri_coreg --s sub-MSC01 --mov /out/freesurfer/sub-MSC01/mri/transforms/tmp.bbregister.56705/template.nii --regdat /out/freesurfer/sub-MSC01/mri/transforms/tmp.bbregister.56705/reg.init.dat --reg /out/freesurfer/sub-MSC01/mri/transforms/tmp.bbregister.56705/mri_coreg.lta --nthreads 8 --dof 6 --sep 4 --ftol .0001 --linmintol .01 --no-ref-mask
sysname Linux
hostname b0c54804ca5f
machine x86_64
user root
dof 6
nsep 1
cras0 1
ftol 0.000100
linmintol 0.010000
bf 1
bflim 30.000000
bfnsamp 30
SmoothRef 0
SatPct 99.990000
MovOOB 0
optschema 1
Reading in mov /out/freesurfer/sub-MSC01/mri/transforms/tmp.bbregister.56705/template.nii
Reading in ref /out/freesurfer/sub-MSC01/mri/brainmask.mgz
Setting cras translation parameters to align centers
Creating random numbers for coordinate dithering
Performing intensity dithering
Initial parameters -1.0321 0.8671 -0.7592 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000
Separation list (1): 4 min = 4
DoSmoothing 1
DoCoordDither 1
DoIntensityDither 1
nitersmax 4
ftol 1.000e-04
linmintol 1.000e-02
SatPct 99.990000
Hist FWHM 7.000000 7.000000
nthreads 8
movsat = 416.0000
mov gstd 1.9140 1.9139 1.9139
Smoothing mov
refsat = 116.0000
ref gstd 1.9140 1.9140 1.9140
Smoothing ref
COREGpreproc() done
Testing if mov and target overlap
Init cost -1.0538332339
nhits = 207319 out of 16777216, Percent Overlap: 79.1
Initial RefRAS-to-MovRAS
1.00000 0.00000 0.00000 -1.03211;
0.00000 1.00000 0.00000 0.86711;
0.00000 0.00000 1.00000 -0.75922;
0.00000 0.00000 0.00000 1.00000;
Initial RefVox-to-MovVox
-0.99844 0.02533 -0.04971 241.90976;
-0.04288 0.22031 0.97349 -19.24250;
-0.03561 -0.97411 0.21888 228.33237;
0.00000 0.00000 0.00000 1.00000;
sep = 4 -----------------------------------
COREGoptBruteForce() 30 1 30
Turning on MovOOB for BruteForce Search
#BF# sep= 4 iter=0 lim=30.0 delta=2.00 -1.03211 0.86711 -0.75922 2.00000 0.00000 0.00000 -1.0525229
Turning MovOOB back off after brute force search
---------------------------------
Init Powel Params dof = 6
Starting OpenPowel2(), sep = 4
InitialCost -1.0541201830
#@# 4 188 -1.03211 0.86711 -0.75922 2.00000 0.00000 0.00000 -1.0541202
fs_powell::minimize
nparams 6
maxfev 4
ftol 0.000100
linmin_xtol_ 0.010000
powell nthiter 0: fret = -1.054120
#@# 4 190 -0.03211 0.86711 -0.75922 2.00000 0.00000 0.00000 -1.0549204
#@# 4 195 -0.10721 0.86711 -0.75922 2.00000 0.00000 0.00000 -1.0549273
#@# 4 200 -0.10721 -0.75092 -0.75922 2.00000 0.00000 0.00000 -1.0553522
#@# 4 201 -0.10721 -0.20335 -0.75922 2.00000 0.00000 0.00000 -1.0557119
#@# 4 205 -0.10721 -0.11743 -0.75922 2.00000 0.00000 0.00000 -1.0557185
#@# 4 207 -0.10721 -0.10562 -0.75922 2.00000 0.00000 0.00000 -1.0557187
#@# 4 215 -0.10721 -0.10562 -0.37726 2.00000 0.00000 0.00000 -1.0558404
#@# 4 216 -0.10721 -0.10562 -0.38840 2.00000 0.00000 0.00000 -1.0558408
#@# 4 222 -0.10721 -0.10562 -0.38840 1.38197 0.00000 0.00000 -1.0558422
#@# 4 224 -0.10721 -0.10562 -0.38840 1.68873 0.00000 0.00000 -1.0558860
#@# 4 226 -0.10721 -0.10562 -0.38840 1.66873 0.00000 0.00000 -1.0558861
#@# 4 234 -0.10721 -0.10562 -0.38840 1.66873 -0.61803 0.00000 -1.0559115
#@# 4 236 -0.10721 -0.10562 -0.38840 1.66873 -0.34793 0.00000 -1.0559508
#@# 4 237 -0.10721 -0.10562 -0.38840 1.66873 -0.33793 0.00000 -1.0559509
#@# 4 238 -0.10721 -0.10562 -0.38840 1.66873 -0.32793 0.00000 -1.0559510
#@# 4 246 -0.10721 -0.10562 -0.38840 1.66873 -0.32793 -0.61803 -1.0561848
#@# 4 248 -0.10721 -0.10562 -0.38840 1.66873 -0.32793 -0.66175 -1.0561867
powell nthiter 1: fret = -1.056187
#@# 4 258 0.00695 -0.10562 -0.38840 1.66873 -0.32793 -0.67650 -1.0562115
#@# 4 275 0.01695 -0.11562 -0.46391 1.66873 -0.32793 -0.67650 -1.0562192
#@# 4 276 0.01695 -0.11562 -0.49195 1.66873 -0.32793 -0.67650 -1.0562199
#@# 4 286 0.01695 -0.11562 -0.48195 1.69276 -0.32793 -0.67650 -1.0562201
#@# 4 296 0.01695 -0.11562 -0.48195 1.68276 -0.34646 -0.67650 -1.0562202
#@# 4 297 0.01695 -0.11562 -0.48195 1.68276 -0.35646 -0.67650 -1.0562203
#@# 4 301 0.01695 -0.11562 -0.48195 1.68276 -0.36901 -0.67650 -1.0562204
#@# 4 309 0.01695 -0.11562 -0.48195 1.68276 -0.37901 -0.68809 -1.0562205
Powell done niters total = 1
OptTimeSec 4.8 sec
OptTimeMin 0.08 min
nEvals 310
Final parameters 0.01694914 -0.11561747 -0.48194548 1.68276346 -0.37901205 -0.68809235
Final cost -1.056220479959418
---------------------------------
mri_coreg utimesec 117.102566
mri_coreg stimesec 4.910237
mri_coreg ru_maxrss 446208
mri_coreg ru_ixrss 0
mri_coreg ru_idrss 0
mri_coreg ru_isrss 0
mri_coreg ru_minflt 1220152
mri_coreg ru_majflt 0
mri_coreg ru_nswap 0
mri_coreg ru_inblock 0
mri_coreg ru_oublock 16
mri_coreg ru_msgsnd 0
mri_coreg ru_msgrcv 0
mri_coreg ru_nsignals 0
mri_coreg ru_nvcsw 5958
mri_coreg ru_nivcsw 11806
Final RefRAS-to-MovRAS
0.99991 -0.01201 -0.00661 0.01695;
0.01220 0.99949 0.02936 -0.11562;
0.00626 -0.02944 0.99955 -0.48195;
0.00000 0.00000 0.00000 1.00000;
Final RefVox-to-MovVox
-0.99758 0.03338 -0.06093 243.29321;
-0.05337 0.19190 0.97897 -15.39121;
-0.04437 -0.97986 0.18966 234.05028;
0.00000 0.00000 0.00000 1.00000;
Final parameters 0.0169 -0.1156 -0.4819 1.6828 -0.3790 -0.6881
nhits = 209424 out of 16777216, Percent Overlap: 79.9
mri_coreg RunTimeSec 40.6 sec
To check run:
tkregisterfv --mov /out/freesurfer/sub-MSC01/mri/transforms/tmp.bbregister.56705/template.nii --targ /out/freesurfer/sub-MSC01/mri/brainmask.mgz --reg /out/freesurfer/sub-MSC01/mri/transforms/tmp.bbregister.56705/mri_coreg.lta --s sub-MSC01 --surfs
mri_coreg done
mri_segreg --mov /out/freesurfer/sub-MSC01/mri/transforms/tmp.bbregister.56705/template.nii --init-reg /out/freesurfer/sub-MSC01/mri/transforms/tmp.bbregister.56705/reg.init.dat --out-reg /out/freesurfer/sub-MSC01/mri/transforms/tmp.bbregister.56705/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5
$Id: mri_segreg.c,v 1.113 2016/05/10 03:23:20 greve Exp $
setenv SUBJECTS_DIR /out/freesurfer
cd /out/freesurfer/sub-MSC01/scripts
mri_segreg --mov /out/freesurfer/sub-MSC01/mri/transforms/tmp.bbregister.56705/template.nii --init-reg /out/freesurfer/sub-MSC01/mri/transforms/tmp.bbregister.56705/reg.init.dat --out-reg /out/freesurfer/sub-MSC01/mri/transforms/tmp.bbregister.56705/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5
sysname Linux
hostname b0c54804ca5f
machine x86_64
user root
movvol /out/freesurfer/sub-MSC01/mri/transforms/tmp.bbregister.56705/template.nii
regfile /out/freesurfer/sub-MSC01/mri/transforms/tmp.bbregister.56705/reg.init.dat
subject sub-MSC01
dof 6
outregfile /out/freesurfer/sub-MSC01/mri/transforms/tmp.bbregister.56705/bbr.pass1.dat
UseMask 0
UseLH 1
UseRH 1
nsubsamp 100
PenaltySign -1
PenaltySlope 0.500000
PenaltyCenter 0.000000
surfname white
GMProjFrac 0.500000
WMProjAbs 2.000000
lhcostfile (null)
rhcostfile (null)
interp trilinear (1)
frame 0
TolPowell 0.000100
nMaxItersPowell 36
n1dmin 3
Profile 0
Gdiag_no -1
AddNoise 0 (0)
SynthSeed 1550916254
TransRandMax 0.000000
RotRandMax 0.000000
Translations 0.000000 0.000000 0.000000
Rotations 0.000000 0.000000 0.000000
Input reg
-0.99758 0.06093 0.03338 -0.06135;
0.04442 0.18984 0.98081 -0.62082;
-0.05342 -0.97992 0.19209 0.28065;
0.00000 0.00000 0.00000 1.00000;
Loading mov
Projecting LH Surfs
Loading lh.white surf
Loading lh.thickness for GM
GM Proj: 1 0.500000 2.000000
WM Proj: 0 0.500000 2.000000
Projecting RH Surfs
Loading rh.white surf
Loading rh.thickness for GM
Projecting RH Surfs
Using lh.cortex.label
Using rh.cortex.label
Computing relative cost
0 -25.0 -25.0 -25.0 1.006586
1 -25.0 -25.0 25.0 1.006585
2 -25.0 25.0 -25.0 1.004363
3 -25.0 25.0 25.0 1.034075
4 25.0 -25.0 -25.0 0.988085
5 25.0 -25.0 25.0 0.994731
6 25.0 25.0 -25.0 1.032565
7 25.0 25.0 25.0 1.016231
REL: 8 0.141285 8.083222 1.010403 rel = 0.13983
Initial costs ----------------
Number of surface hits 4464
WM Intensity 96.4366 +/- 24.6410
Ctx Intensity 136.7516 +/- 23.8823
Pct Contrast 35.2459 +/- 22.2787
Cost 0.1413
RelCost 0.1398
------------------------------------
Brute force preopt -4 4 4, n = 729
0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 1.0088 1.0088 0.0
1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.9731 0.9731 0.0
6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.9302 0.9302 0.0
7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.8762 0.8762 0.0
19 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.0000 0.8750 0.8750 0.0
33 -4.0000 -4.0000 0.0000 -4.0000 4.0000 -4.0000 0.8685 0.8685 0.0
34 -4.0000 -4.0000 0.0000 -4.0000 4.0000 0.0000 0.8477 0.8477 0.0
118 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.0000 0.8043 0.8043 0.0
120 -4.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.7834 0.7834 0.0
274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.7352 0.7352 0.0
361 0.0000 0.0000 0.0000 0.0000 -4.0000 0.0000 0.7262 0.7262 0.0
363 0.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.7255 0.7255 0.0
364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1413 0.1413 0.0
Brute Force --------------------------
Min cost was 0.141285
Number of iterations 729
Search time 1.902000 sec
Parameters at best (transmm, rotdeg)
0.000 0.000 0.000 0.000 0.000 0.000
--------------------------------------------
Starting Powell Minimization
Init Powel Params dof = 6
0 0
1 0
2 0
3 0
4 0
5 0
fs_powell::minimize
nparams 6
maxfev 36
ftol 0.000100
linmin_xtol_ 0.001000
powell nthiter 0: fret = 0.141285
7 -0.001 0.000 0.000 0.000 0.000 0.000 0.1412757356
9 -0.027 0.000 0.000 0.000 0.000 0.000 0.1412713014
10 -0.014 0.000 0.000 0.000 0.000 0.000 0.1412039316
11 -0.013 0.000 0.000 0.000 0.000 0.000 0.1412028836
17 -0.013 -0.618 0.000 0.000 0.000 0.000 0.0867108684
21 -0.013 -0.632 0.000 0.000 0.000 0.000 0.0867042381
23 -0.013 -0.625 0.000 0.000 0.000 0.000 0.0866681220
24 -0.013 -0.626 0.000 0.000 0.000 0.000 0.0866677147
34 -0.013 -0.626 0.013 0.000 0.000 0.000 0.0866157595
35 -0.013 -0.626 0.014 0.000 0.000 0.000 0.0866107003
36 -0.013 -0.626 0.022 0.000 0.000 0.000 0.0866045352
37 -0.013 -0.626 0.019 0.000 0.000 0.000 0.0866013931
50 -0.013 -0.626 0.019 0.002 0.000 0.000 0.0865987052
58 -0.013 -0.626 0.019 0.002 -0.023 0.000 0.0863140754
61 -0.013 -0.626 0.019 0.002 -0.020 0.000 0.0863097369
70 -0.013 -0.626 0.019 0.002 -0.020 0.124 0.0837661589
71 -0.013 -0.626 0.019 0.002 -0.020 0.143 0.0834708013
73 -0.013 -0.626 0.019 0.002 -0.020 0.176 0.0831682351
76 -0.013 -0.626 0.019 0.002 -0.020 0.177 0.0831681870
powell nthiter 1: fret = 0.083168
86 0.045 -0.626 0.019 0.002 -0.020 0.177 0.0822377758
88 0.048 -0.626 0.019 0.002 -0.020 0.177 0.0822274761
89 0.052 -0.626 0.019 0.002 -0.020 0.177 0.0822161945
91 0.057 -0.626 0.019 0.002 -0.020 0.177 0.0822135794
92 0.056 -0.626 0.019 0.002 -0.020 0.177 0.0822113256
101 0.056 -0.644 0.019 0.002 -0.020 0.177 0.0820796853
103 0.056 -0.639 0.019 0.002 -0.020 0.177 0.0820589511
104 0.056 -0.640 0.019 0.002 -0.020 0.177 0.0820589053
115 0.056 -0.640 0.020 0.002 -0.020 0.177 0.0820588868
123 0.056 -0.640 0.020 -0.006 -0.020 0.177 0.0820454794
125 0.056 -0.640 0.020 -0.004 -0.020 0.177 0.0820408084
134 0.056 -0.640 0.020 -0.004 -0.071 0.177 0.0811025151
136 0.056 -0.640 0.020 -0.004 -0.069 0.177 0.0810553899
137 0.056 -0.640 0.020 -0.004 -0.056 0.177 0.0808733417
139 0.056 -0.640 0.020 -0.004 -0.054 0.177 0.0808548467
140 0.056 -0.640 0.020 -0.004 -0.052 0.177 0.0808492708
142 0.056 -0.640 0.020 -0.004 -0.051 0.177 0.0808480624
152 0.056 -0.640 0.020 -0.004 -0.051 0.206 0.0806597859
153 0.056 -0.640 0.020 -0.004 -0.051 0.197 0.0806142294
155 0.056 -0.640 0.020 -0.004 -0.051 0.198 0.0806140884
powell nthiter 2: fret = 0.080614
178 0.056 -0.646 0.020 -0.004 -0.051 0.198 0.0805728443
190 0.056 -0.646 0.021 -0.004 -0.051 0.198 0.0805725180
201 0.056 -0.646 0.021 0.001 -0.051 0.198 0.0805607489
212 0.056 -0.646 0.021 0.001 -0.058 0.198 0.0805294079
213 0.056 -0.646 0.021 0.001 -0.057 0.198 0.0805225184
214 0.056 -0.646 0.021 0.001 -0.056 0.198 0.0805199374
224 0.056 -0.646 0.021 0.001 -0.056 0.201 0.0805197179
226 0.056 -0.646 0.021 0.001 -0.056 0.200 0.0805186864
powell nthiter 3: fret = 0.080519
238 0.059 -0.646 0.021 0.001 -0.056 0.200 0.0805114810
239 0.058 -0.646 0.021 0.001 -0.056 0.200 0.0805107381
250 0.058 -0.644 0.021 0.001 -0.056 0.200 0.0805067815
262 0.058 -0.644 0.022 0.001 -0.056 0.200 0.0805064397
274 0.058 -0.644 0.022 0.002 -0.056 0.200 0.0805062331
286 0.058 -0.644 0.022 0.002 -0.057 0.200 0.0805048065
powell nthiter 4: fret = 0.080505
330 0.058 -0.644 0.021 0.002 -0.057 0.200 0.0805037782
342 0.058 -0.644 0.021 0.001 -0.057 0.200 0.0805034512
Powell done niters = 4
Computing relative cost
0 -25.0 -25.0 -25.0 1.008239
1 -25.0 -25.0 25.0 1.018185
2 -25.0 25.0 -25.0 0.992822
3 -25.0 25.0 25.0 1.027918
4 25.0 -25.0 -25.0 0.986657
5 25.0 -25.0 25.0 0.989595
6 25.0 25.0 -25.0 1.016015
7 25.0 25.0 25.0 1.006547
REL: 8 0.080503 8.045978 1.005747 rel = 0.0800434
Number of iterations 4
Min cost was 0.080503
Number of FunctionCalls 364
TolPowell 0.000100
nMaxItersPowell 36
OptimizationTime 0.854000 sec
Parameters at optimum (transmm) 0.05814 -0.64412 0.02113
Parameters at optimum (rotdeg) 0.00078 -0.05697 0.19956
Final costs ----------------
Number of surface hits 4464
WM Intensity 96.1070 +/- 23.6276
Ctx Intensity 137.1309 +/- 22.7294
Pct Contrast 35.9110 +/- 19.9348
Cost 0.0805
RelCost 0.1398
Reg at min cost was
-0.99768 0.06124 0.02978 -0.00132;
0.04094 0.19007 0.98092 -1.26515;
-0.05441 -0.97986 0.19214 0.30172;
0.00000 0.00000 0.00000 1.00000;
Writing optimal reg to /out/freesurfer/sub-MSC01/mri/transforms/tmp.bbregister.56705/bbr.pass1.dat, type = 14
Original Reg
-0.99758 0.06093 0.03338 -0.06135;
0.04442 0.18984 0.98081 -0.62082;
-0.05342 -0.97992 0.19209 0.28065;
0.00000 0.00000 0.00000 1.00000;
Original Reg - Optimal Reg
0.00010 -0.00031 0.00361 -0.06003;
0.00347 -0.00023 -0.00011 0.64434;
0.00099 -0.00006 -0.00005 -0.02106;
0.00000 0.00000 0.00000 0.00000;
Computing change in lh position
LH rmsDiffMean 0.551158
Computing change in rh position
Surface-RMS-Diff-mm 0.646138 0.109725 0.871046
mri_segreg done
mri_segreg --mov /out/freesurfer/sub-MSC01/mri/transforms/tmp.bbregister.56705/template.nii --init-reg /out/freesurfer/sub-MSC01/mri/transforms/tmp.bbregister.56705/bbr.pass1.dat --out-reg /out/freesurfer/sub-MSC01/mri/transforms/T2raw.auto.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /out/freesurfer/sub-MSC01/mri/transforms/T2raw.auto.dat.mincost --dof 6 --nmax 36 --param /out/freesurfer/sub-MSC01/mri/transforms/T2raw.auto.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /out/freesurfer/sub-MSC01/mri/transforms/tmp.bbregister.56705/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5
$Id: mri_segreg.c,v 1.113 2016/05/10 03:23:20 greve Exp $
setenv SUBJECTS_DIR /out/freesurfer
cd /out/freesurfer/sub-MSC01/scripts
mri_segreg --mov /out/freesurfer/sub-MSC01/mri/transforms/tmp.bbregister.56705/template.nii --init-reg /out/freesurfer/sub-MSC01/mri/transforms/tmp.bbregister.56705/bbr.pass1.dat --out-reg /out/freesurfer/sub-MSC01/mri/transforms/T2raw.auto.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /out/freesurfer/sub-MSC01/mri/transforms/T2raw.auto.dat.mincost --dof 6 --nmax 36 --param /out/freesurfer/sub-MSC01/mri/transforms/T2raw.auto.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /out/freesurfer/sub-MSC01/mri/transforms/tmp.bbregister.56705/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5
sysname Linux
hostname b0c54804ca5f
machine x86_64
user root
movvol /out/freesurfer/sub-MSC01/mri/transforms/tmp.bbregister.56705/template.nii
regfile /out/freesurfer/sub-MSC01/mri/transforms/tmp.bbregister.56705/bbr.pass1.dat
subject sub-MSC01
dof 6
outregfile /out/freesurfer/sub-MSC01/mri/transforms/T2raw.auto.dat
UseMask 0
UseLH 1
UseRH 1
nsubsamp 1
PenaltySign -1
PenaltySlope 0.500000
PenaltyCenter 0.000000
surfname white
GMProjFrac 0.500000
WMProjAbs 2.000000
lhcostfile (null)
rhcostfile (null)
interp trilinear (1)
frame 0
TolPowell 0.000000
nMaxItersPowell 36
n1dmin 3
Profile 0
Gdiag_no -1
AddNoise 0 (0)
SynthSeed 1550914271
TransRandMax 0.000000
RotRandMax 0.000000
Translations 0.000000 0.000000 0.000000
Rotations 0.000000 0.000000 0.000000
Input reg
-0.99768 0.06124 0.02978 -0.00132;
0.04094 0.19007 0.98092 -1.26515;
-0.05441 -0.97986 0.19214 0.30172;
0.00000 0.00000 0.00000 1.00000;
Loading mov
Projecting LH Surfs
Loading lh.white surf
Loading lh.thickness for GM
GM Proj: 1 0.500000 2.000000
WM Proj: 0 0.500000 2.000000
Projecting RH Surfs
Loading rh.white surf
Loading rh.thickness for GM
Projecting RH Surfs
Using lh.cortex.label
Using rh.cortex.label
Computing relative cost
0 -25.0 -25.0 -25.0 1.003566
1 -25.0 -25.0 25.0 1.009834
2 -25.0 25.0 -25.0 1.007062
3 -25.0 25.0 25.0 1.006604
4 25.0 -25.0 -25.0 0.999924
5 25.0 -25.0 25.0 1.011158
6 25.0 25.0 -25.0 1.002114
7 25.0 25.0 25.0 1.001894
REL: 8 0.079975 8.042155 1.005269 rel = 0.0795558
Initial costs ----------------
Number of surface hits 446077
WM Intensity 96.1391 +/- 23.0053
Ctx Intensity 137.1902 +/- 22.8633
Pct Contrast 35.8342 +/- 19.7422
Cost 0.0800
RelCost 0.0796
------------------------------------
Brute force preopt -0.1 0.1 0.1, n = 729
0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0881 0.0881 0.0
1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0866 0.0866 0.0
2 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.0863 0.0863 0.0
9 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 -0.1000 0.0856 0.0856 0.0
12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.0849 0.0849 0.0
39 -0.1000 -0.1000 0.0000 0.0000 0.0000 -0.1000 0.0844 0.0844 0.0
91 -0.1000 0.0000 -0.1000 0.0000 -0.1000 0.0000 0.0844 0.0844 0.0
121 -0.1000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0844 0.0844 0.0
124 -0.1000 0.0000 0.0000 0.0000 0.1000 0.0000 0.0840 0.0840 0.0
282 0.0000 -0.1000 0.0000 0.0000 0.0000 -0.1000 0.0838 0.0838 0.0
283 0.0000 -0.1000 0.0000 0.0000 0.0000 0.0000 0.0832 0.0832 0.0
364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0805 0.0805 0.0
Brute Force --------------------------
Min cost was 0.080503
Number of iterations 729
Search time 1.677000 sec
Parameters at best (transmm, rotdeg)
0.000 0.000 0.000 0.000 0.000 0.000
--------------------------------------------
Starting Powell Minimization
Init Powel Params dof = 6
0 0
1 0
2 0
3 0
4 0
5 0
fs_powell::minimize
nparams 6
maxfev 36
ftol 0.000000
linmin_xtol_ 0.001000
powell nthiter 0: fret = 0.079975
7 -0.034 0.000 0.000 0.000 0.000 0.000 0.0798413377
8 -0.037 0.000 0.000 0.000 0.000 0.000 0.0798391410
9 -0.041 0.000 0.000 0.000 0.000 0.000 0.0798375086
18 -0.041 0.005 0.000 0.000 0.000 0.000 0.0798201005
19 -0.041 0.016 0.000 0.000 0.000 0.000 0.0798013668
28 -0.041 0.016 -0.078 0.000 0.000 0.000 0.0792444330
31 -0.041 0.016 -0.079 0.000 0.000 0.000 0.0792441735
38 -0.041 0.016 -0.079 0.013 0.000 0.000 0.0792338594
39 -0.041 0.016 -0.079 0.010 0.000 0.000 0.0792330418
40 -0.041 0.016 -0.079 0.011 0.000 0.000 0.0792330062
48 -0.041 0.016 -0.079 0.011 -0.039 0.000 0.0789174772
49 -0.041 0.016 -0.079 0.011 -0.061 0.000 0.0788850588
51 -0.041 0.016 -0.079 0.011 -0.063 0.000 0.0788840838
55 -0.041 0.016 -0.079 0.011 -0.074 0.000 0.0788763291
58 -0.041 0.016 -0.079 0.011 -0.075 0.000 0.0788763279
67 -0.041 0.016 -0.079 0.011 -0.075 -0.108 0.0782659740
68 -0.041 0.016 -0.079 0.011 -0.075 -0.087 0.0782253396
69 -0.041 0.016 -0.079 0.011 -0.075 -0.086 0.0782253058
powell nthiter 1: fret = 0.078225
80 -0.047 0.016 -0.079 0.011 -0.075 -0.086 0.0782166337
81 -0.048 0.016 -0.079 0.011 -0.075 -0.086 0.0782158311
82 -0.049 0.016 -0.079 0.011 -0.075 -0.086 0.0782157741
91 -0.049 0.015 -0.079 0.011 -0.075 -0.086 0.0782156101
99 -0.049 0.015 -0.087 0.011 -0.075 -0.086 0.0781917961
100 -0.049 0.015 -0.101 0.011 -0.075 -0.086 0.0781682977
102 -0.049 0.015 -0.106 0.011 -0.075 -0.086 0.0781678783
103 -0.049 0.015 -0.104 0.011 -0.075 -0.086 0.0781676048
112 -0.049 0.015 -0.104 0.010 -0.075 -0.086 0.0781675420
121 -0.049 0.015 -0.104 0.010 -0.061 -0.086 0.0781368023
131 -0.049 0.015 -0.104 0.010 -0.061 -0.094 0.0781305494
133 -0.049 0.015 -0.104 0.010 -0.061 -0.093 0.0781305378
powell nthiter 2: fret = 0.078131
145 -0.055 0.015 -0.104 0.010 -0.061 -0.093 0.0781243757
146 -0.056 0.015 -0.104 0.010 -0.061 -0.093 0.0781243467
155 -0.056 0.016 -0.104 0.010 -0.061 -0.093 0.0781243335
164 -0.056 0.016 -0.103 0.010 -0.061 -0.093 0.0781240085
165 -0.056 0.016 -0.102 0.010 -0.061 -0.093 0.0781238987
175 -0.056 0.016 -0.102 0.011 -0.061 -0.093 0.0781238168
185 -0.056 0.016 -0.102 0.011 -0.058 -0.093 0.0781231663
195 -0.056 0.016 -0.102 0.011 -0.058 -0.097 0.0781202042
196 -0.056 0.016 -0.102 0.011 -0.058 -0.099 0.0781200149
powell nthiter 3: fret = 0.078120
207 -0.057 0.016 -0.102 0.011 -0.058 -0.099 0.0781200015
235 -0.057 0.016 -0.102 0.012 -0.058 -0.099 0.0781198990
245 -0.057 0.016 -0.102 0.012 -0.057 -0.099 0.0781198536
255 -0.057 0.016 -0.102 0.012 -0.057 -0.100 0.0781196913
258 -0.058 0.016 -0.102 0.013 -0.056 -0.101 0.0781196887
powell nthiter 4: fret = 0.078120
286 -0.057 0.016 -0.103 0.012 -0.057 -0.100 0.0781196650
295 -0.057 0.016 -0.103 0.013 -0.057 -0.100 0.0781195924
powell nthiter 5: fret = 0.078120
335 -0.057 0.015 -0.103 0.013 -0.057 -0.100 0.0781195811
powell nthiter 6: fret = 0.078120
Powell done niters = 6
Computing relative cost
0 -25.0 -25.0 -25.0 1.003298
1 -25.0 -25.0 25.0 1.008885
2 -25.0 25.0 -25.0 1.007222
3 -25.0 25.0 25.0 1.006010
4 25.0 -25.0 -25.0 1.000579
5 25.0 -25.0 25.0 1.011947
6 25.0 25.0 -25.0 1.002719
7 25.0 25.0 25.0 1.001574
REL: 8 0.078120 8.042234 1.005279 rel = 0.0777093
Number of iterations 6
Min cost was 0.078120
Number of FunctionCalls 433
TolPowell 0.000000
nMaxItersPowell 36
OptimizationTime 53.228000 sec
Parameters at optimum (transmm) -0.05737 0.01509 -0.10299
Parameters at optimum (rotdeg) 0.01268 -0.05724 -0.09952
Final costs ----------------
Number of surface hits 446077
WM Intensity 96.1459 +/- 22.9917
Ctx Intensity 137.2135 +/- 22.8178
Pct Contrast 35.8482 +/- 19.6447
Cost 0.0781
RelCost 0.0796
Reg at min cost was
-0.99755 0.06255 0.03129 -0.06119;
0.04269 0.19018 0.98082 -1.25013;
-0.05540 -0.97976 0.19238 0.19845;
0.00000 0.00000 0.00000 1.00000;
Writing optimal reg to /out/freesurfer/sub-MSC01/mri/transforms/T2raw.auto.dat, type = 14
Original Reg
-0.99768 0.06124 0.02978 -0.00132;
0.04094 0.19007 0.98092 -1.26515;
-0.05441 -0.97986 0.19214 0.30172;
0.00000 0.00000 0.00000 1.00000;
Original Reg - Optimal Reg
-0.00013 -0.00131 -0.00151 0.05987;
-0.00174 -0.00011 0.00010 -0.01503;
0.00099 -0.00010 -0.00025 0.10327;
0.00000 0.00000 0.00000 0.00000;
Computing change in lh position
LH rmsDiffMean 0.116817
Computing change in rh position
Surface-RMS-Diff-mm 0.139381 0.041523 0.241233
mri_segreg done
MinCost: 0.078120 96.145946 137.213469 35.848172
tkregister2_cmdl --mov /out/freesurfer/sub-MSC01/mri/orig/T2raw.mgz --reg /out/freesurfer/sub-MSC01/mri/transforms/T2raw.auto.dat --noedit --ltaout /out/freesurfer/sub-MSC01/mri/transforms/T2raw.auto.lta
tkregister_tcl /opt/freesurfer/tktools/tkregister2.tcl
INFO: no target volume specified, assuming FreeSurfer orig volume.
target volume orig
movable volume /out/freesurfer/sub-MSC01/mri/orig/T2raw.mgz
reg file /out/freesurfer/sub-MSC01/mri/transforms/T2raw.auto.dat
LoadVol 0
ZeroCRAS 0
$Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $
Diagnostic Level -1
---- Input registration matrix --------
-0.99755 0.06255 0.03129 -0.06119;
0.04269 0.19018 0.98082 -1.25013;
-0.05540 -0.97976 0.19238 0.19845;
0.00000 0.00000 0.00000 1.00000;
float2int = 0
---------------------------------------
INFO: loading target /out/freesurfer/sub-MSC01/mri/orig.mgz
INFO: target does not conform to COR format, so I'm going to
reslice to COR. This will not affect the final registration.
Ttarg: --------------------
-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;
INFO: loading movable /out/freesurfer/sub-MSC01/mri/orig/T2raw.mgz
Tmov: --------------------
-0.80001 0.00000 0.00000 89.60059;
0.00000 0.00000 0.80078 -102.50000;
0.00000 -0.80078 0.00000 102.50000;
0.00000 0.00000 0.00000 1.00000;
mkheaderreg = 0, float2int = 0
---- Input registration matrix --------
-0.99755 0.06255 0.03129 -0.06118;
0.04269 0.19018 0.98082 -1.25012;
-0.05540 -0.97976 0.19238 0.19845;
0.00000 0.00000 0.00000 1.00000;
Determinant -1
subject = sub-MSC01
RegMat ---------------------------
-0.99755 0.06255 0.03129 -0.06119;
0.04269 0.19018 0.98082 -1.25013;
-0.05540 -0.97976 0.19238 0.19845;
0.00000 0.00000 0.00000 1.00000;
Cleaning up
Started at Mon Feb 18 10:37:50 UTC 2019
Ended at Mon Feb 18 10:40:01 UTC 2019
BBR-Run-Time-Sec 131
bbregister Done
To check results, run:
tkregisterfv --mov /out/freesurfer/sub-MSC01/mri/orig/T2raw.mgz --reg /out/freesurfer/sub-MSC01/mri/transforms/T2raw.auto.lta --surfs
cp /out/freesurfer/sub-MSC01/mri/transforms/T2raw.auto.lta /out/freesurfer/sub-MSC01/mri/transforms/T2raw.lta
mri_convert -odt float -at /out/freesurfer/sub-MSC01/mri/transforms/T2raw.lta -rl /out/freesurfer/sub-MSC01/mri/orig.mgz /out/freesurfer/sub-MSC01/mri/orig/T2raw.mgz /out/freesurfer/sub-MSC01/mri/T2.prenorm.mgz
mri_convert.bin -odt float -at /out/freesurfer/sub-MSC01/mri/transforms/T2raw.lta -rl /out/freesurfer/sub-MSC01/mri/orig.mgz /out/freesurfer/sub-MSC01/mri/orig/T2raw.mgz /out/freesurfer/sub-MSC01/mri/T2.prenorm.mgz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /out/freesurfer/sub-MSC01/mri/orig/T2raw.mgz...
TR=3200.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.998443, -0.0497087, -0.0253296)
j_ras = (0.0429192, 0.974438, -0.220519)
k_ras = (0.0356438, 0.219088, 0.975054)
INFO: Reading transformation from file /out/freesurfer/sub-MSC01/mri/transforms/T2raw.lta...
Reading transform with LTAreadEx()
reading template info from volume /out/freesurfer/sub-MSC01/mri/orig.mgz...
INFO: Applying transformation from file /out/freesurfer/sub-MSC01/mri/transforms/T2raw.lta...
---------------------------------
INFO: Transform Matrix (linear_ras_to_ras)
0.99990 0.01375 0.00414 0.04115;
-0.01362 0.99949 -0.02904 0.14071;
-0.00453 0.02898 0.99957 1.11024;
0.00000 0.00000 0.00000 1.00000;
---------------------------------
Applying LTAtransformInterp (resample_type 1)
writing to /out/freesurfer/sub-MSC01/mri/T2.prenorm.mgz...
mri_normalize -sigma 0.5 -nonmax_suppress 0 -min_dist 1 -aseg /out/freesurfer/sub-MSC01/mri/aseg.presurf.mgz -surface /out/freesurfer/sub-MSC01/surf/rh.white identity.nofile -surface /out/freesurfer/sub-MSC01/surf/lh.white identity.nofile /out/freesurfer/sub-MSC01/mri/T2.prenorm.mgz /out/freesurfer/sub-MSC01/mri/T2.norm.mgz
mghRead(/out/freesurfer/sub-MSC01/mri/T2.prenorm.mgz): could not read 262144 bytes at slice 172
using Gaussian smoothing of bias field, sigma=0.500
disabling nonmaximum suppression
retaining points that are at least 1.000mm from the boundary
using segmentation for initial intensity normalization
reading from /out/freesurfer/sub-MSC01/mri/T2.prenorm.mgz...
No such file or directory
mri_normalize: could not open source file /out/freesurfer/sub-MSC01/mri/T2.prenorm.mgz
No such file or directory
Linux b0c54804ca5f 3.13.0-147-generic #196-Ubuntu SMP Wed May 2 15:51:34 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s sub-MSC01 exited with ERRORS at Mon Feb 18 10:40:06 UTC 2019
For more details, see the log file /out/freesurfer/sub-MSC01/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Standard error:
Return code: 1
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