Logfile for bbregister Tue May 25 22:50:07 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-03/scripts /opt/freesurfer/bin/bbregister --s sub-03 --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/orig/T2raw.mgz --lta /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/T2raw.auto.lta --init-coreg --T2 $Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $ Linux blg5611.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-03/mri/orig/T2raw.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/template.nii mri_convert.bin /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/orig/T2raw.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/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-03/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-03/mri/transforms/tmp.bbregister.129200/template.nii... mri_coreg --s sub-03 --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/template.nii --regdat /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/reg.init.dat --reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/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-03/scripts cmdline mri_coreg --s sub-03 --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/template.nii --regdat /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/reg.init.dat --reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/mri_coreg.lta --nthreads 4 --dof 6 --sep 4 --ftol .0001 --linmintol .01 --no-ref-mask sysname Linux hostname blg5611.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-03/mri/transforms/tmp.bbregister.129200/template.nii Reading in ref /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/brainmask.mgz Setting cras translation parameters to align centers Creating random numbers for coordinate dithering Performing intensity dithering Initial parameters -0.8024 0.0165 -0.7773 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 = 3432.0000 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 -1.0419778918 nhits = 309410 out of 32768000, Percent Overlap: 60.4 Initial RefRAS-to-MovRAS 1.00000 0.00000 0.00000 -0.80240; 0.00000 1.00000 0.00000 0.01649; 0.00000 0.00000 1.00000 -0.77727; 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 -9.99998; 0.00000 -1.00000 0.00000 318.99994; 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 -0.80240 0.01649 1.22273 2.00000 0.00000 0.00000 -1.0367672 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6 Starting OpenPowel2(), sep = 4 InitialCost -1.0428291559 #@# 4 188 -0.80240 0.01649 1.22273 2.00000 0.00000 0.00000 -1.0428292 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.042829 #@# 4 190 0.19760 0.01649 1.22273 2.00000 0.00000 0.00000 -1.0430363 #@# 4 195 0.04042 0.01649 1.22273 2.00000 0.00000 0.00000 -1.0430466 #@# 4 204 0.05042 -0.09851 1.22273 2.00000 0.00000 0.00000 -1.0430495 #@# 4 208 0.05042 -0.07327 1.22273 2.00000 0.00000 0.00000 -1.0430497 #@# 4 211 0.05042 -0.07327 2.22273 2.00000 0.00000 0.00000 -1.0431803 #@# 4 216 0.05042 -0.07327 2.03645 2.00000 0.00000 0.00000 -1.0431883 #@# 4 226 0.05042 -0.07327 2.01645 1.38197 0.00000 0.00000 -1.0432138 #@# 4 228 0.05042 -0.07327 2.01645 1.48188 0.00000 0.00000 -1.0432152 #@# 4 230 0.05042 -0.07327 2.01645 1.46475 0.00000 0.00000 -1.0432153 #@# 4 240 0.05042 -0.07327 2.01645 1.45475 -0.22627 0.00000 -1.0432191 #@# 4 242 0.05042 -0.07327 2.01645 1.45475 -0.20187 0.00000 -1.0432194 #@# 4 244 0.05042 -0.07327 2.01645 1.45475 -0.16678 0.00000 -1.0432198 #@# 4 246 0.05042 -0.07327 2.01645 1.45475 -0.15073 0.00000 -1.0432199 #@# 4 254 0.05042 -0.07327 2.01645 1.45475 -0.15073 -0.16685 -1.0432259 powell nthiter 1: fret = -1.043226 #@# 4 264 0.12409 -0.07327 2.01645 1.45475 -0.15073 -0.16685 -1.0432301 #@# 4 265 0.14303 -0.07327 2.01645 1.45475 -0.15073 -0.16685 -1.0432304 #@# 4 266 0.15670 -0.07327 2.01645 1.45475 -0.15073 -0.16685 -1.0432305 #@# 4 267 0.16670 -0.07327 2.01645 1.45475 -0.15073 -0.16685 -1.0432307 #@# 4 285 0.16670 -0.08327 1.84817 1.45475 -0.15073 -0.16685 -1.0432358 #@# 4 287 0.16670 -0.08327 1.86831 1.45475 -0.15073 -0.16685 -1.0432359 #@# 4 299 0.16670 -0.08327 1.87831 1.44475 -0.15073 -0.16685 -1.0432360 #@# 4 307 0.16670 -0.08327 1.87831 1.44475 -0.23715 -0.16685 -1.0432370 Powell done niters total = 1 OptTimeSec 7.8 sec OptTimeMin 0.13 min nEvals 325 Final parameters 0.16670455 -0.08326772 1.87831187 1.44474971 -0.26079917 -0.16684802 Final cost -1.043236928798848 --------------------------------- mri_coreg utimesec 175.245643 mri_coreg stimesec 1.004721 mri_coreg ru_maxrss 890760 mri_coreg ru_ixrss 0 mri_coreg ru_idrss 0 mri_coreg ru_isrss 0 mri_coreg ru_minflt 881872 mri_coreg ru_majflt 2 mri_coreg ru_nswap 0 mri_coreg ru_inblock 10600 mri_coreg ru_oublock 16 mri_coreg ru_msgsnd 0 mri_coreg ru_msgrcv 0 mri_coreg ru_nsignals 0 mri_coreg ru_nvcsw 514 mri_coreg ru_nivcsw 123 Final RefRAS-to-MovRAS 0.99999 -0.00291 -0.00455 0.16670; 0.00303 0.99968 0.02521 -0.08327; 0.00448 -0.02523 0.99967 1.87831; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox -0.99999 0.00455 -0.00291 263.98157; -0.00303 -0.02521 0.99968 -6.18447; -0.00448 -0.99967 -0.02523 326.35886; 0.00000 0.00000 0.00000 1.00000; Final parameters 0.1667 -0.0833 1.8783 1.4447 -0.2608 -0.1668 nhits = 306594 out of 32768000, Percent Overlap: 59.9 mri_coreg RunTimeSec 66.8 sec To check run: tkregisterfv --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/template.nii --targ /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/brainmask.mgz --reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/mri_coreg.lta --s sub-03 --surfs mri_coreg done mri_segreg --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/template.nii --init-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/reg.init.dat --out-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/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-03/scripts mri_segreg --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/template.nii --init-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/reg.init.dat --out-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/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 blg5611.int.ets1.calculquebec.ca machine x86_64 user bpinsard movvol /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/template.nii regfile /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/reg.init.dat subject sub-03 dof 6 outregfile /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/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 1622708522 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg -0.99999 0.00291 0.00455 -0.19703; 0.00448 -0.02523 0.99967 1.32716; -0.00303 -0.99968 -0.02521 0.60342; 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 0.979306 1 -25.0 -25.0 25.0 0.981441 2 -25.0 25.0 -25.0 0.992603 3 -25.0 25.0 25.0 0.992560 4 25.0 -25.0 -25.0 0.989204 5 25.0 -25.0 25.0 0.993794 6 25.0 25.0 -25.0 0.974398 7 25.0 25.0 25.0 0.979559 REL: 8 0.396413 7.882866 0.985358 rel = 0.402304 Initial costs ---------------- Number of surface hits 4755 WM Intensity 840.0646 +/- 288.3324 Ctx Intensity 1066.8640 +/- 387.3010 Pct Contrast 22.8496 +/- 28.4583 Cost 0.3964 RelCost 0.4023 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9001 0.9001 0.0 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.8426 0.8426 0.0 21 -4.0000 -4.0000 -4.0000 4.0000 0.0000 -4.0000 0.8082 0.8082 0.0 39 -4.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.7301 0.7301 0.0 102 -4.0000 0.0000 -4.0000 4.0000 0.0000 -4.0000 0.7262 0.7262 0.0 120 -4.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.6884 0.6884 0.0 283 0.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.5419 0.5419 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.3964 0.3964 0.0 Brute Force -------------------------- Min cost was 0.396413 Number of iterations 729 Search time 1.472000 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 = 0.396413 7 0.112 0.000 0.000 0.000 0.000 0.000 0.3930577383 8 0.163 0.000 0.000 0.000 0.000 0.000 0.3920264926 11 0.167 0.000 0.000 0.000 0.000 0.000 0.3920233930 13 0.169 0.000 0.000 0.000 0.000 0.000 0.3920233158 17 0.169 -1.618 0.000 0.000 0.000 0.000 0.1601101220 22 0.169 -1.811 0.000 0.000 0.000 0.000 0.1558531787 23 0.169 -1.822 0.000 0.000 0.000 0.000 0.1556547163 25 0.169 -1.844 0.000 0.000 0.000 0.000 0.1553324032 26 0.169 -1.874 0.000 0.000 0.000 0.000 0.1552697331 27 0.169 -1.863 0.000 0.000 0.000 0.000 0.1551825568 29 0.169 -1.864 0.000 0.000 0.000 0.000 0.1551803398 31 0.169 -1.865 0.000 0.000 0.000 0.000 0.1551794268 38 0.169 -1.866 0.382 0.000 0.000 0.000 0.1479714814 41 0.169 -1.866 0.367 0.000 0.000 0.000 0.1479484631 43 0.169 -1.866 0.370 0.000 0.000 0.000 0.1479484068 45 0.169 -1.866 0.369 0.000 0.000 0.000 0.1479480919 51 0.169 -1.866 0.369 0.382 0.000 0.000 0.1116183901 53 0.169 -1.866 0.369 0.476 0.000 0.000 0.1080326605 54 0.169 -1.866 0.369 0.485 0.000 0.000 0.1078138735 56 0.169 -1.866 0.369 0.492 0.000 0.000 0.1077435819 58 0.169 -1.866 0.369 0.493 0.000 0.000 0.1077422030 66 0.169 -1.866 0.369 0.493 0.076 0.000 0.1072058127 67 0.169 -1.866 0.369 0.493 0.070 0.000 0.1069867449 68 0.169 -1.866 0.369 0.493 0.044 0.000 0.1066752923 70 0.169 -1.866 0.369 0.493 0.046 0.000 0.1066676570 71 0.169 -1.866 0.369 0.493 0.049 0.000 0.1066643663 72 0.169 -1.866 0.369 0.493 0.050 0.000 0.1066640724 80 0.169 -1.866 0.369 0.493 0.050 0.048 0.1066061256 81 0.169 -1.866 0.369 0.493 0.050 0.030 0.1064096070 82 0.169 -1.866 0.369 0.493 0.050 0.026 0.1064028864 powell nthiter 1: fret = 0.106403 97 0.168 -1.866 0.369 0.493 0.050 0.026 0.1064025809 104 0.168 -1.484 0.369 0.493 0.050 0.026 0.1003347697 105 0.168 -1.621 0.369 0.493 0.050 0.026 0.0973056971 106 0.168 -1.624 0.369 0.493 0.050 0.026 0.0972303721 108 0.168 -1.657 0.369 0.493 0.050 0.026 0.0967635732 110 0.168 -1.654 0.369 0.493 0.050 0.026 0.0967603705 111 0.168 -1.655 0.369 0.493 0.050 0.026 0.0967595658 117 0.168 -1.655 -0.249 0.493 0.050 0.026 0.0734131214 119 0.168 -1.655 -0.093 0.493 0.050 0.026 0.0721645220 120 0.168 -1.655 -0.131 0.493 0.050 0.026 0.0718052953 121 0.168 -1.655 -0.144 0.493 0.050 0.026 0.0717905267 122 0.168 -1.655 -0.141 0.493 0.050 0.026 0.0717875881 123 0.168 -1.655 -0.140 0.493 0.050 0.026 0.0717874212 130 0.168 -1.655 -0.140 0.875 0.050 0.026 0.0596714167 131 0.168 -1.655 -0.140 0.782 0.050 0.026 0.0566453415 133 0.168 -1.655 -0.140 0.783 0.050 0.026 0.0566401971 134 0.168 -1.655 -0.140 0.793 0.050 0.026 0.0566304972 136 0.168 -1.655 -0.140 0.790 0.050 0.026 0.0566291636 145 0.168 -1.655 -0.140 0.790 0.079 0.026 0.0565296132 147 0.168 -1.655 -0.140 0.790 0.071 0.026 0.0565175458 149 0.168 -1.655 -0.140 0.790 0.072 0.026 0.0565174303 150 0.168 -1.655 -0.140 0.790 0.073 0.026 0.0565171462 161 0.168 -1.655 -0.140 0.790 0.073 -0.008 0.0563738367 162 0.168 -1.655 -0.140 0.790 0.073 -0.002 0.0563686869 165 0.167 -1.443 -0.648 1.087 0.097 -0.029 0.0478954639 171 0.167 -1.524 -0.454 0.973 0.088 -0.018 0.0472596858 172 0.167 -1.490 -0.535 1.020 0.092 -0.023 0.0463633257 173 0.167 -1.489 -0.538 1.022 0.092 -0.023 0.0463623996 174 0.167 -1.489 -0.538 1.022 0.092 -0.023 0.0463621310 powell nthiter 2: fret = 0.046362 184 0.164 -1.489 -0.538 1.022 0.092 -0.023 0.0463600522 193 0.164 -1.472 -0.538 1.022 0.092 -0.023 0.0462104221 195 0.164 -1.465 -0.538 1.022 0.092 -0.023 0.0461946064 196 0.164 -1.463 -0.538 1.022 0.092 -0.023 0.0461928143 198 0.164 -1.462 -0.538 1.022 0.092 -0.023 0.0461924605 206 0.164 -1.462 -0.538 1.022 0.092 -0.006 0.0460765121 207 0.164 -1.462 -0.538 1.022 0.092 0.003 0.0460566329 216 0.164 -1.462 -0.538 1.006 0.092 0.003 0.0458808249 228 0.164 -1.462 -0.538 1.006 0.084 0.003 0.0458393624 231 0.164 -1.462 -0.538 1.006 0.083 0.003 0.0458382152 239 0.164 -1.471 -0.515 0.993 0.082 0.004 0.0457659097 powell nthiter 3: fret = 0.045766 250 0.194 -1.471 -0.515 0.993 0.082 0.004 0.0456728705 252 0.202 -1.471 -0.515 0.993 0.082 0.004 0.0456662120 255 0.205 -1.471 -0.515 0.993 0.082 0.004 0.0456642592 256 0.206 -1.471 -0.515 0.993 0.082 0.004 0.0456641116 264 0.206 -1.479 -0.515 0.993 0.082 0.004 0.0456542489 265 0.206 -1.480 -0.515 0.993 0.082 0.004 0.0456527153 268 0.206 -1.481 -0.515 0.993 0.082 0.004 0.0456519694 269 0.206 -1.482 -0.515 0.993 0.082 0.004 0.0456517448 278 0.206 -1.482 -0.515 0.993 0.082 0.065 0.0456064477 279 0.206 -1.482 -0.515 0.993 0.082 0.039 0.0455048146 281 0.206 -1.482 -0.515 0.993 0.082 0.040 0.0455045873 289 0.206 -1.482 -0.515 0.988 0.082 0.040 0.0454737298 291 0.206 -1.482 -0.515 0.986 0.082 0.040 0.0454703284 301 0.206 -1.482 -0.515 0.986 0.079 0.040 0.0454546592 302 0.206 -1.482 -0.515 0.986 0.071 0.040 0.0454306154 312 0.206 -1.483 -0.512 0.984 0.071 0.041 0.0454232534 313 0.206 -1.485 -0.508 0.982 0.071 0.041 0.0454204394 314 0.206 -1.485 -0.508 0.982 0.071 0.041 0.0454203982 316 0.248 -1.498 -0.501 0.970 0.060 0.077 0.0451029446 321 0.274 -1.507 -0.497 0.963 0.054 0.100 0.0451020181 323 0.261 -1.502 -0.499 0.967 0.057 0.089 0.0450562335 324 0.261 -1.502 -0.499 0.967 0.057 0.089 0.0450561682 325 0.263 -1.503 -0.498 0.966 0.057 0.090 0.0450550930 328 0.263 -1.503 -0.498 0.966 0.057 0.090 0.0450550765 powell nthiter 4: fret = 0.045055 339 0.268 -1.503 -0.498 0.966 0.057 0.090 0.0450263589 340 0.271 -1.503 -0.498 0.966 0.057 0.090 0.0450218788 341 0.272 -1.503 -0.498 0.966 0.057 0.090 0.0450218371 350 0.272 -1.501 -0.498 0.966 0.057 0.090 0.0450170305 351 0.272 -1.499 -0.498 0.966 0.057 0.090 0.0450163073 359 0.272 -1.498 -0.502 0.968 0.057 0.090 0.0449977224 361 0.272 -1.495 -0.510 0.973 0.057 0.090 0.0449766504 362 0.272 -1.494 -0.512 0.974 0.057 0.089 0.0449750568 363 0.272 -1.493 -0.512 0.974 0.057 0.089 0.0449750034 371 0.272 -1.493 -0.512 0.981 0.057 0.089 0.0449230137 373 0.272 -1.493 -0.512 0.987 0.057 0.089 0.0449158766 374 0.272 -1.493 -0.512 0.985 0.057 0.089 0.0449134807 383 0.272 -1.493 -0.512 0.985 0.048 0.089 0.0448510925 384 0.272 -1.493 -0.512 0.985 0.045 0.089 0.0448481324 385 0.272 -1.493 -0.512 0.985 0.046 0.089 0.0448481215 393 0.275 -1.494 -0.512 0.984 0.045 0.092 0.0448417447 394 0.276 -1.495 -0.512 0.984 0.045 0.093 0.0448412038 powell nthiter 5: fret = 0.044841 408 0.281 -1.495 -0.512 0.984 0.045 0.093 0.0448186314 409 0.283 -1.495 -0.512 0.984 0.045 0.093 0.0448170728 417 0.283 -1.490 -0.512 0.984 0.045 0.093 0.0448155718 418 0.283 -1.491 -0.512 0.984 0.045 0.093 0.0448145505 419 0.283 -1.492 -0.512 0.984 0.045 0.093 0.0448144399 439 0.283 -1.492 -0.512 0.987 0.045 0.093 0.0448106172 440 0.283 -1.492 -0.512 0.986 0.045 0.093 0.0448100533 450 0.283 -1.492 -0.512 0.986 0.041 0.093 0.0448058138 451 0.283 -1.492 -0.512 0.986 0.042 0.093 0.0448052961 459 0.280 -1.491 -0.512 0.987 0.042 0.091 0.0448026591 460 0.281 -1.491 -0.512 0.987 0.042 0.091 0.0448025552 462 0.281 -1.492 -0.512 0.987 0.042 0.091 0.0448024219 463 0.281 -1.492 -0.512 0.987 0.042 0.091 0.0448023373 466 0.285 -1.488 -0.513 0.990 0.040 0.089 0.0447883681 473 0.287 -1.487 -0.513 0.991 0.039 0.088 0.0447877032 475 0.287 -1.487 -0.513 0.991 0.039 0.088 0.0447876488 478 0.287 -1.487 -0.513 0.991 0.039 0.088 0.0447875525 powell nthiter 6: fret = 0.044788 492 0.287 -1.487 -0.513 0.991 0.039 0.088 0.0447875291 501 0.287 -1.488 -0.513 0.991 0.039 0.088 0.0447870773 510 0.287 -1.489 -0.510 0.990 0.039 0.088 0.0447854610 521 0.287 -1.490 -0.510 0.988 0.039 0.088 0.0447839666 531 0.287 -1.490 -0.510 0.988 0.036 0.088 0.0447832694 533 0.287 -1.490 -0.510 0.988 0.037 0.088 0.0447823878 534 0.287 -1.490 -0.510 0.988 0.038 0.088 0.0447823080 541 0.288 -1.489 -0.510 0.988 0.037 0.088 0.0447818328 543 0.288 -1.489 -0.510 0.988 0.037 0.088 0.0447818133 547 0.288 -1.489 -0.510 0.988 0.037 0.088 0.0447816339 powell nthiter 7: fret = 0.044782 559 0.285 -1.488 -0.510 0.989 0.038 0.086 0.0447787611 560 0.285 -1.488 -0.510 0.989 0.038 0.085 0.0447786930 564 0.285 -1.488 -0.510 0.989 0.038 0.085 0.0447785458 573 0.285 -1.489 -0.510 0.989 0.038 0.085 0.0447785132 592 0.285 -1.489 -0.510 0.988 0.038 0.085 0.0447780016 604 0.285 -1.489 -0.510 0.988 0.037 0.085 0.0447778706 610 0.287 -1.488 -0.510 0.989 0.036 0.085 0.0447777238 611 0.286 -1.488 -0.510 0.989 0.036 0.085 0.0447774031 612 0.286 -1.488 -0.510 0.989 0.036 0.085 0.0447773339 Powell done niters = 7 Computing relative cost 0 -25.0 -25.0 -25.0 0.983942 1 -25.0 -25.0 25.0 0.972793 2 -25.0 25.0 -25.0 0.973125 3 -25.0 25.0 25.0 0.988273 4 25.0 -25.0 -25.0 0.962400 5 25.0 -25.0 25.0 0.990656 6 25.0 25.0 -25.0 0.973856 7 25.0 25.0 25.0 0.967412 REL: 8 0.044777 7.812458 0.976557 rel = 0.0458522 Number of iterations 7 Min cost was 0.044777 Number of FunctionCalls 619 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 1.212000 sec Parameters at optimum (transmm) 0.28570 -1.48848 -0.51028 Parameters at optimum (rotdeg) 0.98867 0.03642 0.08492 Final costs ---------------- Number of surface hits 4755 WM Intensity 778.9781 +/- 235.5277 Ctx Intensity 1047.3860 +/- 260.1751 Pct Contrast 30.5612 +/- 15.3889 Cost 0.0448 RelCost 0.4023 Reg at min cost was -0.99999 0.00229 0.00306 0.08712; 0.00305 -0.00797 0.99996 -0.17222; -0.00231 -0.99997 -0.00796 0.11608; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/bbr.pass1.dat, type = 14 Original Reg -0.99999 0.00291 0.00455 -0.19703; 0.00448 -0.02523 0.99967 1.32716; -0.00303 -0.99968 -0.02521 0.60342; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00001 0.00062 0.00149 -0.28415; 0.00143 -0.01726 -0.00029 1.49938; -0.00071 0.00029 -0.01725 0.48735; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 1.764248 Computing change in rh position Surface-RMS-Diff-mm 1.830926 0.684858 3.153883 mri_segreg done mri_segreg --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/template.nii --init-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/bbr.pass1.dat --out-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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-03/mri/transforms/T2raw.auto.dat.mincost --dof 6 --nmax 36 --param /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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-03/mri/transforms/tmp.bbregister.129200/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-03/scripts mri_segreg --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/template.nii --init-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/bbr.pass1.dat --out-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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-03/mri/transforms/T2raw.auto.dat.mincost --dof 6 --nmax 36 --param /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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-03/mri/transforms/tmp.bbregister.129200/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname blg5611.int.ets1.calculquebec.ca machine x86_64 user bpinsard movvol /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/template.nii regfile /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/tmp.bbregister.129200/bbr.pass1.dat subject sub-03 dof 6 outregfile /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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 1622258830 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg -0.99999 0.00229 0.00306 0.08712; 0.00305 -0.00797 0.99996 -0.17222; -0.00231 -0.99997 -0.00796 0.11608; 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 0.998525 1 -25.0 -25.0 25.0 0.972817 2 -25.0 25.0 -25.0 0.977586 3 -25.0 25.0 25.0 0.990926 4 25.0 -25.0 -25.0 0.966947 5 25.0 -25.0 25.0 0.981464 6 25.0 25.0 -25.0 0.972770 7 25.0 25.0 25.0 0.974843 REL: 8 0.049489 7.835879 0.979485 rel = 0.0505257 Initial costs ---------------- Number of surface hits 476337 WM Intensity 784.7650 +/- 240.5626 Ctx Intensity 1051.3769 +/- 265.5817 Pct Contrast 30.2423 +/- 15.5869 Cost 0.0495 RelCost 0.0505 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0537 0.0537 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0531 0.0531 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.0519 0.0519 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.0516 0.0516 0.0 9 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 -0.1000 0.0511 0.0511 0.0 10 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.0000 0.0502 0.0502 0.0 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.0498 0.0498 0.0 13 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.0493 0.0493 0.0 16 -0.1000 -0.1000 -0.1000 0.0000 0.1000 0.0000 0.0489 0.0489 0.0 35 -0.1000 -0.1000 0.0000 -0.1000 0.1000 0.1000 0.0486 0.0486 0.0 43 -0.1000 -0.1000 0.0000 0.0000 0.1000 0.0000 0.0479 0.0479 0.0 120 -0.1000 0.0000 0.0000 0.0000 0.0000 -0.1000 0.0463 0.0463 0.0 363 0.0000 0.0000 0.0000 0.0000 0.0000 -0.1000 0.0463 0.0463 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0448 0.0448 0.0 Brute Force -------------------------- Min cost was 0.044777 Number of iterations 729 Search time 1.438000 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 = 0.049489 7 -0.047 0.000 0.000 0.000 0.000 0.000 0.0491758049 8 -0.055 0.000 0.000 0.000 0.000 0.000 0.0491650411 9 -0.057 0.000 0.000 0.000 0.000 0.000 0.0491639107 10 -0.059 0.000 0.000 0.000 0.000 0.000 0.0491637759 12 -0.058 0.000 0.000 0.000 0.000 0.000 0.0491637182 19 -0.058 -0.029 0.000 0.000 0.000 0.000 0.0488499981 20 -0.058 -0.058 0.000 0.000 0.000 0.000 0.0487730192 21 -0.058 -0.053 0.000 0.000 0.000 0.000 0.0487676084 22 -0.058 -0.052 0.000 0.000 0.000 0.000 0.0487674785 30 -0.058 -0.052 0.048 0.000 0.000 0.000 0.0485622085 31 -0.058 -0.052 0.044 0.000 0.000 0.000 0.0485581165 32 -0.058 -0.052 0.041 0.000 0.000 0.000 0.0485570579 42 -0.058 -0.052 0.041 0.001 0.000 0.000 0.0485567418 51 -0.058 -0.052 0.041 0.001 0.012 0.000 0.0485429525 52 -0.058 -0.052 0.041 0.001 0.011 0.000 0.0485424795 61 -0.058 -0.052 0.041 0.001 0.011 -0.010 0.0485303588 powell nthiter 1: fret = 0.048530 71 -0.059 -0.052 0.041 0.001 0.011 -0.010 0.0485281644 72 -0.069 -0.052 0.041 0.001 0.011 -0.010 0.0485178220 84 -0.069 -0.051 0.041 0.001 0.011 -0.010 0.0485175067 102 -0.069 -0.051 0.041 0.003 0.011 -0.010 0.0485169935 110 -0.069 -0.051 0.041 0.003 0.014 -0.010 0.0485150776 111 -0.069 -0.051 0.041 0.003 0.015 -0.010 0.0485147533 120 -0.069 -0.051 0.041 0.003 0.015 -0.016 0.0485111203 121 -0.069 -0.051 0.041 0.003 0.015 -0.015 0.0485110919 123 -0.080 -0.049 0.041 0.005 0.019 -0.020 0.0485022990 130 -0.083 -0.049 0.041 0.006 0.021 -0.021 0.0485016419 powell nthiter 2: fret = 0.048502 165 -0.083 -0.049 0.039 0.006 0.021 -0.021 0.0485012546 184 -0.083 -0.049 0.039 0.006 0.022 -0.021 0.0485011084 185 -0.083 -0.049 0.039 0.006 0.023 -0.021 0.0485010274 194 -0.085 -0.049 0.039 0.006 0.023 -0.022 0.0485009881 195 -0.085 -0.049 0.039 0.006 0.023 -0.022 0.0485008647 198 -0.085 -0.049 0.039 0.006 0.023 -0.022 0.0485008603 powell nthiter 3: fret = 0.048501 222 -0.085 -0.050 0.039 0.006 0.023 -0.022 0.0485008454 261 -0.085 -0.050 0.039 0.006 0.023 -0.022 0.0485008401 263 -0.085 -0.050 0.039 0.006 0.023 -0.022 0.0485008388 powell nthiter 4: fret = 0.048501 322 -0.085 -0.050 0.039 0.006 0.023 -0.022 0.0485008330 326 -0.085 -0.050 0.039 0.006 0.023 -0.022 0.0485008267 327 -0.085 -0.050 0.039 0.006 0.023 -0.022 0.0485008239 powell nthiter 5: fret = 0.048501 Powell done niters = 5 Computing relative cost 0 -25.0 -25.0 -25.0 0.998287 1 -25.0 -25.0 25.0 0.972938 2 -25.0 25.0 -25.0 0.978167 3 -25.0 25.0 25.0 0.990750 4 25.0 -25.0 -25.0 0.967053 5 25.0 -25.0 25.0 0.981527 6 25.0 25.0 -25.0 0.972196 7 25.0 25.0 25.0 0.975655 REL: 8 0.048501 7.836574 0.979572 rel = 0.0495123 Number of iterations 5 Min cost was 0.048501 Number of FunctionCalls 407 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 45.330000 sec Parameters at optimum (transmm) -0.08480 -0.04975 0.03909 Parameters at optimum (rotdeg) 0.00592 0.02326 -0.02199 Final costs ---------------- Number of surface hits 476337 WM Intensity 784.5522 +/- 240.8351 Ctx Intensity 1051.0080 +/- 266.0569 Pct Contrast 30.2354 +/- 15.5644 Cost 0.0485 RelCost 0.0505 Reg at min cost was -0.99999 0.00188 0.00345 0.00231; 0.00343 -0.00787 0.99996 -0.22201; -0.00191 -0.99997 -0.00786 0.15511; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/T2raw.auto.dat, type = 14 Original Reg -0.99999 0.00229 0.00306 0.08712; 0.00305 -0.00797 0.99996 -0.17222; -0.00231 -0.99997 -0.00796 0.11608; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00000 0.00041 -0.00038 0.08482; -0.00038 -0.00010 0.00000 0.04979; -0.00041 0.00000 -0.00010 -0.03904; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.098146 Computing change in rh position Surface-RMS-Diff-mm 0.096985 0.010817 0.124480 mri_segreg done MinCost: 0.048501 784.552237 1051.008000 30.235351 tkregister2_cmdl --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/orig/T2raw.mgz --reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/T2raw.auto.dat --noedit --ltaout /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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-03/mri/orig/T2raw.mgz reg file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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 -------- -0.99999 0.00188 0.00345 0.00231; 0.00343 -0.00787 0.99996 -0.22201; -0.00191 -0.99997 -0.00786 0.15511; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: loading target /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/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-03/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 -------- -0.99999 0.00188 0.00345 0.00231; 0.00343 -0.00787 0.99996 -0.22201; -0.00191 -0.99997 -0.00786 0.15511; 0.00000 0.00000 0.00000 1.00000; Determinant -1 subject = sub-03 RegMat --------------------------- -0.99999 0.00188 0.00345 0.00231; 0.00343 -0.00787 0.99996 -0.22201; -0.00191 -0.99997 -0.00786 0.15511; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Tue May 25 22:50:07 UTC 2021 Ended at Tue May 25 22:52:27 UTC 2021 BBR-Run-Time-Sec 140 bbregister Done To check results, run: tkregisterfv --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/orig/T2raw.mgz --reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-03/mri/transforms/T2raw.auto.lta --surfs