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February 23, 2019 15:22
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fmriprep MSC01 crash
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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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