Logfile for bbregister Tue May 25 23:07:48 UTC 2021 setenv SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer cd /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/scripts /opt/freesurfer/bin/bbregister --s sub-02 --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/orig/T2raw.mgz --lta /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/T2raw.auto.lta --init-coreg --T2 $Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $ Linux blg8112.int.ets1.calculquebec.ca 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /opt/freesurfer mri_convert /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/orig/T2raw.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/template.nii mri_convert.bin /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/orig/T2raw.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/template.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/orig/T2raw.mgz... TR=3200.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/template.nii... mri_coreg --s sub-02 --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/template.nii --regdat /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/reg.init.dat --reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/mri_coreg.lta --nthreads 4 --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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/scripts cmdline mri_coreg --s sub-02 --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/template.nii --regdat /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/reg.init.dat --reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/mri_coreg.lta --nthreads 4 --dof 6 --sep 4 --ftol .0001 --linmintol .01 --no-ref-mask sysname Linux hostname blg8112.int.ets1.calculquebec.ca machine x86_64 user bpinsard 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/template.nii Reading in ref /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/brainmask.mgz Setting cras translation parameters to align centers Creating random numbers for coordinate dithering Performing intensity dithering Initial parameters -0.7992 -0.0326 -0.7944 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 4 movsat = 4095.0000 mov gstd 1.9140 1.9140 1.9140 Smoothing mov refsat = 117.0000 ref gstd 1.9140 1.9140 1.9140 Smoothing ref COREGpreproc() done Testing if mov and target overlap Init cost -1.0341397340 nhits = 309410 out of 32768000, Percent Overlap: 60.4 Initial RefRAS-to-MovRAS 1.00000 0.00000 0.00000 -0.79917; 0.00000 1.00000 0.00000 -0.03257; 0.00000 0.00000 1.00000 -0.79439; 0.00000 0.00000 0.00000 1.00000; Initial RefVox-to-MovVox -1.00000 0.00000 0.00000 262.99997; 0.00000 0.00000 1.00000 -9.99997; 0.00000 -1.00000 0.00000 318.99997; 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 -0.79917 -0.03257 -0.79439 0.00000 0.00000 0.00000 -1.0322699 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6 Starting OpenPowel2(), sep = 4 InitialCost -1.0341397524 #@# 4 188 -0.79917 -0.03257 -0.79439 0.00000 0.00000 0.00000 -1.0341398 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.034140 #@# 4 190 0.20083 -0.03257 -0.79439 0.00000 0.00000 0.00000 -1.0342592 #@# 4 194 -0.18114 -0.03257 -0.79439 0.00000 0.00000 0.00000 -1.0342776 #@# 4 195 -0.07101 -0.03257 -0.79439 0.00000 0.00000 0.00000 -1.0342813 #@# 4 207 -0.09176 0.10432 -0.79439 0.00000 0.00000 0.00000 -1.0342847 #@# 4 213 -0.09176 0.08432 0.20561 0.00000 0.00000 0.00000 -1.0343511 #@# 4 217 -0.09176 0.08432 -0.17635 0.00000 0.00000 0.00000 -1.0343649 #@# 4 218 -0.09176 0.08432 -0.15842 0.00000 0.00000 0.00000 -1.0343655 #@# 4 219 -0.09176 0.08432 -0.08027 0.00000 0.00000 0.00000 -1.0343664 #@# 4 228 -0.09176 0.08432 -0.10660 -0.61803 0.00000 0.00000 -1.0344540 #@# 4 230 -0.09176 0.08432 -0.10660 -0.76948 0.00000 0.00000 -1.0344571 #@# 4 239 -0.09176 0.08432 -0.10660 -0.75948 0.11692 0.00000 -1.0344592 #@# 4 248 -0.09176 0.08432 -0.10660 -0.75948 0.11692 0.15584 -1.0344644 powell nthiter 1: fret = -1.034464 #@# 4 266 -0.03912 0.08432 -0.10660 -0.75948 0.11692 0.18732 -1.0344650 #@# 4 268 -0.05912 0.08432 -0.10660 -0.75948 0.11692 0.18732 -1.0344652 #@# 4 277 -0.05912 0.06874 -0.10660 -0.75948 0.11692 0.18732 -1.0344653 #@# 4 293 -0.05912 0.06874 -0.12143 -0.76948 0.11692 0.18732 -1.0344654 #@# 4 315 -0.05912 0.06874 -0.12143 -0.76948 0.07866 0.17646 -1.0344656 Powell done niters total = 1 OptTimeSec 8.7 sec OptTimeMin 0.14 min nEvals 315 Final parameters -0.05911822 0.06873842 -0.12143438 -0.76948369 0.07866431 0.17646255 Final cost -1.034465547068095 --------------------------------- mri_coreg utimesec 185.353647 mri_coreg stimesec 1.802833 mri_coreg ru_maxrss 890756 mri_coreg ru_ixrss 0 mri_coreg ru_idrss 0 mri_coreg ru_isrss 0 mri_coreg ru_minflt 1290565 mri_coreg ru_majflt 2 mri_coreg ru_nswap 0 mri_coreg ru_inblock 11440 mri_coreg ru_oublock 16 mri_coreg ru_msgsnd 0 mri_coreg ru_msgrcv 0 mri_coreg ru_nsignals 0 mri_coreg ru_nvcsw 590 mri_coreg ru_nivcsw 236 Final RefRAS-to-MovRAS 0.99999 0.00308 0.00137 -0.05912; -0.00306 0.99991 -0.01343 0.06874; -0.00141 0.01343 0.99991 -0.12143; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox -0.99999 -0.00137 0.00308 263.72699; 0.00306 0.01343 0.99990 -12.26554; 0.00141 -0.99991 0.01343 317.88937; 0.00000 0.00000 0.00000 1.00000; Final parameters -0.0591 0.0687 -0.1214 -0.7695 0.0787 0.1765 nhits = 307862 out of 32768000, Percent Overlap: 60.1 mri_coreg RunTimeSec 72.7 sec To check run: tkregisterfv --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/template.nii --targ /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/brainmask.mgz --reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/mri_coreg.lta --s sub-02 --surfs mri_coreg done mri_segreg --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/template.nii --init-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/reg.init.dat --out-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer cd /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/scripts mri_segreg --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/template.nii --init-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/reg.init.dat --out-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/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 blg8112.int.ets1.calculquebec.ca machine x86_64 user bpinsard movvol /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/template.nii regfile /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/reg.init.dat subject sub-02 dof 6 outregfile /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/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 1622325550 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg -0.99999 -0.00308 -0.00137 -0.00080; -0.00141 0.01343 0.99991 0.22266; 0.00306 -0.99990 0.01343 -0.28619; 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 0.953097 1 -25.0 -25.0 25.0 0.968256 2 -25.0 25.0 -25.0 0.908299 3 -25.0 25.0 25.0 0.979697 4 25.0 -25.0 -25.0 0.966936 5 25.0 -25.0 25.0 0.936912 6 25.0 25.0 -25.0 0.952659 7 25.0 25.0 25.0 0.948138 REL: 8 0.052933 7.613993 0.951749 rel = 0.0556165 Initial costs ---------------- Number of surface hits 4368 WM Intensity 777.3781 +/- 267.5105 Ctx Intensity 1080.1838 +/- 319.8988 Pct Contrast 33.6743 +/- 16.9473 Cost 0.0529 RelCost 0.0556 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9693 0.9693 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.9455 0.9455 0.0 4 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.0000 0.9194 0.9194 0.0 6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.8535 0.8535 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.8168 0.8168 0.0 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.7874 0.7874 0.0 33 -4.0000 -4.0000 0.0000 -4.0000 4.0000 -4.0000 0.7607 0.7607 0.0 97 -4.0000 0.0000 -4.0000 0.0000 4.0000 0.0000 0.7544 0.7544 0.0 120 -4.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.7071 0.7071 0.0 123 -4.0000 0.0000 0.0000 0.0000 4.0000 -4.0000 0.6410 0.6410 0.0 124 -4.0000 0.0000 0.0000 0.0000 4.0000 0.0000 0.6339 0.6339 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.5894 0.5894 0.0 363 0.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.5659 0.5659 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0529 0.0529 0.0 Brute Force -------------------------- Min cost was 0.052933 Number of iterations 729 Search time 1.771000 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 = 0.052933 7 -0.065 0.000 0.000 0.000 0.000 0.000 0.0525446552 8 -0.078 0.000 0.000 0.000 0.000 0.000 0.0523925015 11 -0.105 0.000 0.000 0.000 0.000 0.000 0.0521963731 13 -0.104 0.000 0.000 0.000 0.000 0.000 0.0521962243 21 -0.104 -0.285 0.000 0.000 0.000 0.000 0.0458121304 22 -0.104 -0.278 0.000 0.000 0.000 0.000 0.0457553509 24 -0.104 -0.266 0.000 0.000 0.000 0.000 0.0457181712 25 -0.104 -0.267 0.000 0.000 0.000 0.000 0.0457134393 26 -0.104 -0.270 0.000 0.000 0.000 0.000 0.0457132475 29 -0.104 -0.269 0.000 0.000 0.000 0.000 0.0457104934 30 -0.104 -0.268 0.000 0.000 0.000 0.000 0.0457087239 37 -0.104 -0.268 0.100 0.000 0.000 0.000 0.0444169918 38 -0.104 -0.268 0.121 0.000 0.000 0.000 0.0443391510 40 -0.104 -0.268 0.116 0.000 0.000 0.000 0.0443297114 49 -0.104 -0.268 0.116 -0.067 0.000 0.000 0.0432371990 50 -0.104 -0.268 0.116 -0.129 0.000 0.000 0.0425212141 55 -0.104 -0.268 0.116 -0.112 0.000 0.000 0.0425178610 57 -0.104 -0.268 0.116 -0.120 0.000 0.000 0.0425078528 68 -0.104 -0.268 0.116 -0.120 0.029 0.000 0.0424617503 73 -0.104 -0.268 0.116 -0.120 0.034 0.000 0.0424577097 74 -0.104 -0.268 0.116 -0.120 0.035 0.000 0.0424571851 82 -0.104 -0.268 0.116 -0.120 0.035 -0.271 0.0392052412 83 -0.104 -0.268 0.116 -0.120 0.035 -0.274 0.0392032131 84 -0.104 -0.268 0.116 -0.120 0.035 -0.283 0.0391991065 powell nthiter 1: fret = 0.039199 95 -0.112 -0.268 0.116 -0.120 0.035 -0.283 0.0391774819 96 -0.124 -0.268 0.116 -0.120 0.035 -0.283 0.0391403399 112 -0.124 -0.372 0.116 -0.120 0.035 -0.283 0.0385429913 113 -0.124 -0.344 0.116 -0.120 0.035 -0.283 0.0383825381 114 -0.124 -0.339 0.116 -0.120 0.035 -0.283 0.0383404573 116 -0.124 -0.328 0.116 -0.120 0.035 -0.283 0.0383114908 128 -0.124 -0.328 0.117 -0.120 0.035 -0.283 0.0383112462 139 -0.124 -0.328 0.117 -0.115 0.035 -0.283 0.0383072575 140 -0.124 -0.328 0.117 -0.116 0.035 -0.283 0.0383064351 148 -0.124 -0.328 0.117 -0.116 -0.048 -0.283 0.0382531252 149 -0.124 -0.328 0.117 -0.116 -0.009 -0.283 0.0382252645 151 -0.124 -0.328 0.117 -0.116 0.008 -0.283 0.0381571504 154 -0.124 -0.328 0.117 -0.116 0.010 -0.283 0.0381552496 156 -0.124 -0.328 0.117 -0.116 0.011 -0.283 0.0381549855 157 -0.124 -0.328 0.117 -0.116 0.012 -0.283 0.0381549291 164 -0.124 -0.328 0.117 -0.116 0.012 -0.279 0.0381233859 165 -0.124 -0.328 0.117 -0.116 0.012 -0.226 0.0378770850 168 -0.124 -0.328 0.117 -0.116 0.012 -0.237 0.0378727158 170 -0.124 -0.328 0.117 -0.116 0.012 -0.232 0.0378651193 powell nthiter 2: fret = 0.037865 180 -0.114 -0.328 0.117 -0.116 0.012 -0.232 0.0377580310 182 -0.097 -0.328 0.117 -0.116 0.012 -0.232 0.0377317931 183 -0.103 -0.328 0.117 -0.116 0.012 -0.232 0.0377157824 193 -0.103 -0.342 0.117 -0.116 0.012 -0.232 0.0376064268 194 -0.103 -0.348 0.117 -0.116 0.012 -0.232 0.0376035954 195 -0.103 -0.346 0.117 -0.116 0.012 -0.232 0.0376022107 205 -0.103 -0.346 0.103 -0.116 0.012 -0.232 0.0375969613 206 -0.103 -0.346 0.104 -0.116 0.012 -0.232 0.0375939236 207 -0.103 -0.346 0.109 -0.116 0.012 -0.232 0.0375858994 209 -0.103 -0.346 0.110 -0.116 0.012 -0.232 0.0375858763 216 -0.103 -0.346 0.110 -0.130 0.012 -0.232 0.0375467164 218 -0.103 -0.346 0.110 -0.126 0.012 -0.232 0.0375388016 219 -0.103 -0.346 0.110 -0.125 0.012 -0.232 0.0375384540 227 -0.103 -0.346 0.110 -0.125 -0.059 -0.232 0.0373402329 228 -0.103 -0.346 0.110 -0.125 -0.036 -0.232 0.0373200986 229 -0.103 -0.346 0.110 -0.125 -0.042 -0.232 0.0373124528 232 -0.103 -0.346 0.110 -0.125 -0.043 -0.232 0.0373123932 243 -0.103 -0.346 0.110 -0.125 -0.043 -0.230 0.0373108215 powell nthiter 3: fret = 0.037311 253 -0.079 -0.346 0.110 -0.125 -0.043 -0.230 0.0370367568 255 -0.062 -0.346 0.110 -0.125 -0.043 -0.230 0.0370277824 256 -0.069 -0.346 0.110 -0.125 -0.043 -0.230 0.0370197858 258 -0.067 -0.346 0.110 -0.125 -0.043 -0.230 0.0370179783 268 -0.067 -0.351 0.110 -0.125 -0.043 -0.230 0.0370099115 277 -0.067 -0.351 0.078 -0.125 -0.043 -0.230 0.0369066611 279 -0.067 -0.351 0.083 -0.125 -0.043 -0.230 0.0369048066 281 -0.067 -0.351 0.081 -0.125 -0.043 -0.230 0.0369042755 301 -0.067 -0.351 0.081 -0.125 -0.052 -0.230 0.0368984212 303 -0.067 -0.351 0.081 -0.125 -0.048 -0.230 0.0368904049 314 -0.067 -0.351 0.081 -0.125 -0.048 -0.228 0.0368894383 315 -0.067 -0.351 0.081 -0.125 -0.048 -0.227 0.0368890987 powell nthiter 4: fret = 0.036889 326 -0.073 -0.351 0.081 -0.125 -0.048 -0.227 0.0368643196 337 -0.073 -0.354 0.081 -0.125 -0.048 -0.227 0.0368615726 339 -0.073 -0.353 0.081 -0.125 -0.048 -0.227 0.0368615186 348 -0.073 -0.353 0.087 -0.125 -0.048 -0.227 0.0368587364 349 -0.073 -0.353 0.086 -0.125 -0.048 -0.227 0.0368581383 350 -0.073 -0.353 0.085 -0.125 -0.048 -0.227 0.0368579792 371 -0.073 -0.353 0.085 -0.125 -0.046 -0.227 0.0368556940 383 -0.073 -0.353 0.085 -0.125 -0.046 -0.226 0.0368535307 384 -0.073 -0.353 0.085 -0.125 -0.046 -0.223 0.0368521671 387 -0.080 -0.355 0.089 -0.125 -0.044 -0.219 0.0368422289 394 -0.080 -0.355 0.089 -0.125 -0.044 -0.219 0.0368422129 395 -0.080 -0.355 0.089 -0.125 -0.044 -0.219 0.0368421549 powell nthiter 5: fret = 0.036842 429 -0.080 -0.355 0.090 -0.125 -0.044 -0.219 0.0368419548 440 -0.080 -0.355 0.090 -0.124 -0.044 -0.219 0.0368406774 451 -0.080 -0.355 0.090 -0.124 -0.041 -0.219 0.0368395169 453 -0.080 -0.355 0.090 -0.124 -0.042 -0.219 0.0368388407 463 -0.080 -0.355 0.090 -0.124 -0.042 -0.219 0.0368388264 Powell done niters = 5 Computing relative cost 0 -25.0 -25.0 -25.0 0.944049 1 -25.0 -25.0 25.0 0.967834 2 -25.0 25.0 -25.0 0.924407 3 -25.0 25.0 25.0 0.982311 4 25.0 -25.0 -25.0 0.965107 5 25.0 -25.0 25.0 0.938819 6 25.0 25.0 -25.0 0.946237 7 25.0 25.0 25.0 0.939212 REL: 8 0.036839 7.607973 0.950997 rel = 0.0387371 Number of iterations 5 Min cost was 0.036839 Number of FunctionCalls 469 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.958000 sec Parameters at optimum (transmm) -0.07989 -0.35528 0.08970 Parameters at optimum (rotdeg) -0.12379 -0.04217 -0.21922 Final costs ---------------- Number of surface hits 4368 WM Intensity 773.2077 +/- 264.4077 Ctx Intensity 1077.6959 +/- 319.8867 Pct Contrast 33.9525 +/- 16.3422 Cost 0.0368 RelCost 0.0556 Reg at min cost was -0.99999 -0.00230 0.00244 -0.07963; 0.00242 0.01127 0.99993 -0.13323; 0.00233 -0.99993 0.01127 -0.19697; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/bbr.pass1.dat, type = 14 Original Reg -0.99999 -0.00308 -0.00137 -0.00080; -0.00141 0.01343 0.99991 0.22266; 0.00306 -0.99990 0.01343 -0.28619; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00000 -0.00078 -0.00382 0.07883; -0.00383 0.00215 -0.00002 0.35589; 0.00073 0.00003 0.00216 -0.08922; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.436140 Computing change in rh position Surface-RMS-Diff-mm 0.340431 0.134726 0.617613 mri_segreg done mri_segreg --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/template.nii --init-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/bbr.pass1.dat --out-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/T2raw.auto.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/T2raw.auto.dat.mincost --dof 6 --nmax 36 --param /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/T2raw.auto.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer cd /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/scripts mri_segreg --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/template.nii --init-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/bbr.pass1.dat --out-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/T2raw.auto.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/T2raw.auto.dat.mincost --dof 6 --nmax 36 --param /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/T2raw.auto.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname blg8112.int.ets1.calculquebec.ca machine x86_64 user bpinsard movvol /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/template.nii regfile /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/tmp.bbregister.64021/bbr.pass1.dat subject sub-02 dof 6 outregfile /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/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 1622196159 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg -0.99999 -0.00230 0.00244 -0.07963; 0.00242 0.01127 0.99993 -0.13323; 0.00233 -0.99993 0.01127 -0.19697; 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 0.959044 1 -25.0 -25.0 25.0 0.970090 2 -25.0 25.0 -25.0 0.957144 3 -25.0 25.0 25.0 0.969944 4 25.0 -25.0 -25.0 0.947720 5 25.0 -25.0 25.0 0.953069 6 25.0 25.0 -25.0 0.955544 7 25.0 25.0 25.0 0.951301 REL: 8 0.040606 7.663855 0.957982 rel = 0.0423869 Initial costs ---------------- Number of surface hits 438318 WM Intensity 771.6843 +/- 261.4513 Ctx Intensity 1078.8109 +/- 320.8907 Pct Contrast 34.1664 +/- 16.0298 Cost 0.0406 RelCost 0.0424 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0437 0.0437 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.0431 0.0431 0.0 6 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 0.0419 0.0419 0.0 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.0419 0.0419 0.0 27 -0.1000 -0.1000 0.0000 -0.1000 -0.1000 -0.1000 0.0412 0.0412 0.0 30 -0.1000 -0.1000 0.0000 -0.1000 0.0000 -0.1000 0.0401 0.0401 0.0 33 -0.1000 -0.1000 0.0000 -0.1000 0.1000 -0.1000 0.0398 0.0398 0.0 39 -0.1000 -0.1000 0.0000 0.0000 0.0000 -0.1000 0.0397 0.0397 0.0 61 -0.1000 -0.1000 0.1000 -0.1000 0.1000 0.0000 0.0389 0.0389 0.0 273 0.0000 -0.1000 0.0000 -0.1000 0.0000 -0.1000 0.0386 0.0386 0.0 274 0.0000 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.0380 0.0380 0.0 363 0.0000 0.0000 0.0000 0.0000 0.0000 -0.1000 0.0376 0.0376 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0368 0.0368 0.0 688 0.1000 0.1000 0.0000 0.0000 0.0000 0.0000 0.0368 0.0368 0.0 Brute Force -------------------------- Min cost was 0.036753 Number of iterations 729 Search time 1.409000 sec Parameters at best (transmm, rotdeg) 0.100 0.100 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0.1 1 0.1 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 = 0.041079 7 0.024 0.100 0.000 0.000 0.000 0.000 0.0408025151 8 0.040 0.100 0.000 0.000 0.000 0.000 0.0407884339 9 0.038 0.100 0.000 0.000 0.000 0.000 0.0407879402 17 0.038 0.025 0.000 0.000 0.000 0.000 0.0404870908 18 0.038 0.039 0.000 0.000 0.000 0.000 0.0404825500 19 0.038 0.035 0.000 0.000 0.000 0.000 0.0404802387 28 0.038 0.035 0.073 0.000 0.000 0.000 0.0401575746 30 0.038 0.035 0.071 0.000 0.000 0.000 0.0401572399 39 0.038 0.035 0.071 0.012 0.000 0.000 0.0401533131 40 0.038 0.035 0.071 0.008 0.000 0.000 0.0401508921 49 0.038 0.035 0.071 0.008 -0.042 0.000 0.0401048792 50 0.038 0.035 0.071 0.008 -0.027 0.000 0.0400721727 52 0.038 0.035 0.071 0.008 -0.028 0.000 0.0400720370 60 0.038 0.035 0.071 0.008 -0.028 0.117 0.0396891137 61 0.038 0.035 0.071 0.008 -0.028 0.101 0.0396783160 powell nthiter 1: fret = 0.039678 71 0.046 0.035 0.071 0.008 -0.028 0.101 0.0396496596 72 0.063 0.035 0.071 0.008 -0.028 0.101 0.0396234920 74 0.062 0.035 0.071 0.008 -0.028 0.101 0.0396233592 83 0.062 0.027 0.071 0.008 -0.028 0.101 0.0396111638 85 0.062 0.024 0.071 0.008 -0.028 0.101 0.0396102267 94 0.062 0.024 0.070 0.008 -0.028 0.101 0.0396084919 95 0.062 0.024 0.060 0.008 -0.028 0.101 0.0396035483 97 0.062 0.024 0.062 0.008 -0.028 0.101 0.0396028219 107 0.062 0.024 0.062 -0.003 -0.028 0.101 0.0396008474 109 0.062 0.024 0.062 0.002 -0.028 0.101 0.0395975537 119 0.062 0.024 0.062 0.002 -0.040 0.101 0.0395938808 120 0.062 0.024 0.062 0.002 -0.038 0.101 0.0395932821 130 0.062 0.024 0.062 0.002 -0.038 0.108 0.0395887292 131 0.062 0.024 0.062 0.002 -0.038 0.110 0.0395884261 powell nthiter 2: fret = 0.039588 142 0.064 0.024 0.062 0.002 -0.038 0.110 0.0395883531 150 0.064 0.023 0.062 0.002 -0.038 0.110 0.0395880203 169 0.064 0.023 0.062 0.000 -0.038 0.110 0.0395877015 179 0.064 0.023 0.062 0.000 -0.039 0.110 0.0395874328 189 0.064 0.023 0.062 0.000 -0.039 0.111 0.0395874282 191 0.066 0.022 0.062 -0.001 -0.040 0.112 0.0395874258 powell nthiter 3: fret = 0.039587 209 0.064 0.019 0.062 0.000 -0.039 0.111 0.0395873308 212 0.064 0.021 0.062 0.000 -0.039 0.111 0.0395870569 231 0.064 0.021 0.062 -0.001 -0.039 0.111 0.0395867113 253 0.064 0.019 0.062 -0.002 -0.039 0.111 0.0395863723 258 0.064 0.017 0.062 -0.003 -0.039 0.111 0.0395863009 259 0.064 0.017 0.062 -0.003 -0.039 0.111 0.0395862264 powell nthiter 4: fret = 0.039586 289 0.064 0.017 0.062 -0.003 -0.039 0.112 0.0395861462 298 0.064 0.017 0.064 -0.003 -0.039 0.112 0.0395857627 309 0.064 0.017 0.064 -0.004 -0.039 0.112 0.0395857473 322 0.064 0.015 0.064 -0.005 -0.039 0.112 0.0395856746 326 0.064 0.015 0.064 -0.005 -0.039 0.112 0.0395856523 327 0.064 0.015 0.064 -0.005 -0.039 0.112 0.0395856357 329 0.064 0.015 0.064 -0.005 -0.039 0.112 0.0395856311 330 0.064 0.015 0.064 -0.005 -0.039 0.112 0.0395856291 powell nthiter 5: fret = 0.039586 362 0.064 0.015 0.065 -0.005 -0.039 0.112 0.0395856016 388 0.064 0.014 0.065 -0.005 -0.039 0.112 0.0395855548 389 0.064 0.014 0.065 -0.006 -0.039 0.112 0.0395855150 395 0.064 0.014 0.065 -0.006 -0.039 0.112 0.0395855148 powell nthiter 6: fret = 0.039586 410 0.065 0.014 0.065 -0.006 -0.039 0.112 0.0395854902 420 0.065 0.014 0.065 -0.006 -0.039 0.113 0.0395853489 powell nthiter 7: fret = 0.039585 Powell done niters = 7 Computing relative cost 0 -25.0 -25.0 -25.0 0.959254 1 -25.0 -25.0 25.0 0.969806 2 -25.0 25.0 -25.0 0.957942 3 -25.0 25.0 25.0 0.971125 4 25.0 -25.0 -25.0 0.947928 5 25.0 -25.0 25.0 0.953762 6 25.0 25.0 -25.0 0.956370 7 25.0 25.0 25.0 0.951489 REL: 8 0.039585 7.667676 0.958460 rel = 0.041301 Number of iterations 7 Min cost was 0.039585 Number of FunctionCalls 534 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 62.869000 sec Parameters at optimum (transmm) 0.06545 0.01405 0.06516 Parameters at optimum (rotdeg) -0.00561 -0.03856 0.11317 Final costs ---------------- Number of surface hits 438318 WM Intensity 771.9051 +/- 262.0067 Ctx Intensity 1079.0478 +/- 320.9891 Pct Contrast 34.1771 +/- 16.0155 Cost 0.0396 RelCost 0.0424 Reg at min cost was -1.00000 -0.00165 0.00046 -0.01378; 0.00044 0.01117 0.99994 -0.11936; 0.00165 -0.99994 0.01117 -0.13185; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/T2raw.auto.dat, type = 14 Original Reg -0.99999 -0.00230 0.00244 -0.07963; 0.00242 0.01127 0.99993 -0.13323; 0.00233 -0.99993 0.01127 -0.19697; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00000 -0.00065 0.00198 -0.06585; 0.00197 0.00010 -0.00000 -0.01387; 0.00067 0.00000 0.00010 -0.06512; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.125091 Computing change in rh position Surface-RMS-Diff-mm 0.107070 0.033584 0.206688 mri_segreg done MinCost: 0.039585 771.905145 1079.047757 34.177113 tkregister2_cmdl --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/orig/T2raw.mgz --reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/T2raw.auto.dat --noedit --ltaout /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/orig/T2raw.mgz reg file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/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 -------- -1.00000 -0.00165 0.00046 -0.01378; 0.00044 0.01117 0.99994 -0.11936; 0.00165 -0.99994 0.01117 -0.13185; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: loading target /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/orig/T2raw.mgz Tmov: -------------------- -0.80000 0.00000 0.00000 83.20000; 0.00000 0.00000 0.80000 -128.00000; 0.00000 -0.80000 0.00000 120.00000; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- -1.00000 -0.00165 0.00046 -0.01378; 0.00044 0.01117 0.99994 -0.11936; 0.00165 -0.99994 0.01117 -0.13185; 0.00000 0.00000 0.00000 1.00000; Determinant -1 subject = sub-02 RegMat --------------------------- -1.00000 -0.00165 0.00046 -0.01378; 0.00044 0.01117 0.99994 -0.11936; 0.00165 -0.99994 0.01117 -0.13185; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Tue May 25 23:07:48 UTC 2021 Ended at Tue May 25 23:10:33 UTC 2021 BBR-Run-Time-Sec 165 bbregister Done To check results, run: tkregisterfv --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/orig/T2raw.mgz --reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-02/mri/transforms/T2raw.auto.lta --surfs