Logfile for bbregister Tue May 25 23:29:21 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-05/scripts /opt/freesurfer/bin/bbregister --s sub-05 --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/orig/T2raw.mgz --lta /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/T2raw.auto.lta --init-coreg --T2 $Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $ Linux blg4313.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-05/mri/orig/T2raw.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/template.nii mri_convert.bin /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/orig/T2raw.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/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-05/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-05/mri/transforms/tmp.bbregister.208641/template.nii... mri_coreg --s sub-05 --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/template.nii --regdat /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/reg.init.dat --reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/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-05/scripts cmdline mri_coreg --s sub-05 --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/template.nii --regdat /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/reg.init.dat --reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/mri_coreg.lta --nthreads 4 --dof 6 --sep 4 --ftol .0001 --linmintol .01 --no-ref-mask sysname Linux hostname blg4313.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-05/mri/transforms/tmp.bbregister.208641/template.nii Reading in ref /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/brainmask.mgz Setting cras translation parameters to align centers Creating random numbers for coordinate dithering Performing intensity dithering Initial parameters -0.8178 0.0283 -0.7568 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 = 3906.0000 mov gstd 1.9140 1.9140 1.9140 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 -1.0327892828 nhits = 309410 out of 32768000, Percent Overlap: 60.4 Initial RefRAS-to-MovRAS 1.00000 0.00000 0.00000 -0.81781; 0.00000 1.00000 0.00000 0.02825; 0.00000 0.00000 1.00000 -0.75679; 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 1.18219 0.02825 1.24321 0.00000 0.00000 0.00000 -1.0304538 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6 Starting OpenPowel2(), sep = 4 InitialCost -1.0336357355 #@# 4 188 1.18219 0.02825 1.24321 0.00000 0.00000 0.00000 -1.0336357 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.033636 #@# 4 193 0.56416 0.02825 1.24321 0.00000 0.00000 0.00000 -1.0337844 #@# 4 195 0.38827 0.02825 1.24321 0.00000 0.00000 0.00000 -1.0337927 #@# 4 203 0.37827 0.41022 1.24321 0.00000 0.00000 0.00000 -1.0338249 #@# 4 212 0.37827 0.42184 1.32620 0.00000 0.00000 0.00000 -1.0338255 #@# 4 222 0.37827 0.42184 1.29598 0.38197 0.00000 0.00000 -1.0338274 #@# 4 223 0.37827 0.42184 1.29598 0.20435 0.00000 0.00000 -1.0338329 #@# 4 227 0.37827 0.42184 1.29598 0.21435 1.00000 0.00000 -1.0338402 #@# 4 231 0.37827 0.42184 1.29598 0.21435 0.61803 0.00000 -1.0338731 #@# 4 232 0.37827 0.42184 1.29598 0.21435 0.48420 0.00000 -1.0338740 #@# 4 233 0.37827 0.42184 1.29598 0.21435 0.52786 0.00000 -1.0338743 #@# 4 241 0.37827 0.42184 1.29598 0.21435 0.51786 0.38197 -1.0338981 #@# 4 243 0.37827 0.42184 1.29598 0.21435 0.51786 0.36047 -1.0338982 powell nthiter 1: fret = -1.033898 #@# 4 256 0.11696 0.42184 1.29598 0.21435 0.51786 0.34047 -1.0339202 #@# 4 257 0.10696 0.42184 1.29598 0.21435 0.51786 0.34047 -1.0339203 #@# 4 269 0.07950 0.28033 1.29598 0.21435 0.51786 0.34047 -1.0339247 #@# 4 289 0.07950 0.27033 1.24753 0.24972 0.51786 0.34047 -1.0339248 #@# 4 298 0.07950 0.27033 1.24753 0.23972 0.67566 0.34047 -1.0339293 #@# 4 299 0.07950 0.27033 1.24753 0.23972 0.68566 0.34047 -1.0339295 #@# 4 309 0.07950 0.27033 1.24753 0.23972 0.68566 0.43813 -1.0339314 Powell done niters total = 1 OptTimeSec 9.9 sec OptTimeMin 0.16 min nEvals 311 Final parameters 0.07950100 0.27032870 1.24753082 0.23971693 0.68565995 0.44813165 Final cost -1.033931332303622 --------------------------------- mri_coreg utimesec 202.812725 mri_coreg stimesec 2.950362 mri_coreg ru_maxrss 890724 mri_coreg ru_ixrss 0 mri_coreg ru_idrss 0 mri_coreg ru_isrss 0 mri_coreg ru_minflt 1893387 mri_coreg ru_majflt 2 mri_coreg ru_nswap 0 mri_coreg ru_inblock 10464 mri_coreg ru_oublock 16 mri_coreg ru_msgsnd 0 mri_coreg ru_msgrcv 0 mri_coreg ru_nsignals 0 mri_coreg ru_nvcsw 3550 mri_coreg ru_nivcsw 247 Final RefRAS-to-MovRAS 0.99990 0.00782 0.01197 0.07950; -0.00787 0.99996 0.00418 0.27033; -0.01193 -0.00428 0.99992 1.24753; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox -0.99990 -0.01197 0.00782 265.00970; 0.00787 -0.00418 0.99996 -10.28118; 0.01193 -0.99992 -0.00428 320.13733; 0.00000 0.00000 0.00000 1.00000; Final parameters 0.0795 0.2703 1.2475 0.2397 0.6857 0.4481 nhits = 307114 out of 32768000, Percent Overlap: 60.0 mri_coreg RunTimeSec 79.0 sec To check run: tkregisterfv --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/template.nii --targ /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/brainmask.mgz --reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/mri_coreg.lta --s sub-05 --surfs mri_coreg done mri_segreg --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/template.nii --init-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/reg.init.dat --out-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/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-05/scripts mri_segreg --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/template.nii --init-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/reg.init.dat --out-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/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 blg4313.int.ets1.calculquebec.ca machine x86_64 user bpinsard movvol /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/template.nii regfile /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/reg.init.dat subject sub-05 dof 6 outregfile /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/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 1622905986 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg -0.99990 -0.00782 -0.01197 -0.29019; -0.01193 -0.00428 0.99992 1.10014; 0.00787 -0.99996 -0.00418 -0.24197; 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 0.979810 1 -25.0 -25.0 25.0 0.971489 2 -25.0 25.0 -25.0 0.974906 3 -25.0 25.0 25.0 0.989773 4 25.0 -25.0 -25.0 0.996222 5 25.0 -25.0 25.0 0.968273 6 25.0 25.0 -25.0 0.978305 7 25.0 25.0 25.0 0.952391 REL: 8 0.204462 7.811169 0.976396 rel = 0.209405 Initial costs ---------------- Number of surface hits 4154 WM Intensity 804.3198 +/- 261.9725 Ctx Intensity 1060.0917 +/- 287.0919 Pct Contrast 28.6009 +/- 20.7152 Cost 0.2045 RelCost 0.2094 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.8983 0.8983 0.0 6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.8744 0.8744 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.8623 0.8623 0.0 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.8035 0.8035 0.0 34 -4.0000 -4.0000 0.0000 -4.0000 4.0000 0.0000 0.7685 0.7685 0.0 102 -4.0000 0.0000 -4.0000 4.0000 0.0000 -4.0000 0.7649 0.7649 0.0 120 -4.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.6865 0.6865 0.0 301 0.0000 -4.0000 4.0000 -4.0000 0.0000 0.0000 0.6776 0.6776 0.0 346 0.0000 0.0000 -4.0000 4.0000 0.0000 0.0000 0.6374 0.6374 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.2045 0.2045 0.0 Brute Force -------------------------- Min cost was 0.204462 Number of iterations 729 Search time 1.733000 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 = 0.204462 7 0.070 0.000 0.000 0.000 0.000 0.000 0.2030432312 9 0.093 0.000 0.000 0.000 0.000 0.000 0.2029453398 14 0.093 -1.618 0.000 0.000 0.000 0.000 0.1237897981 15 0.093 -1.131 0.000 0.000 0.000 0.000 0.0785780639 19 0.093 -1.016 0.000 0.000 0.000 0.000 0.0778297511 20 0.093 -1.052 0.000 0.000 0.000 0.000 0.0774849666 22 0.093 -1.050 0.000 0.000 0.000 0.000 0.0774829968 30 0.093 -1.050 0.382 0.000 0.000 0.000 0.0692065931 32 0.093 -1.050 0.343 0.000 0.000 0.000 0.0685013939 33 0.093 -1.050 0.335 0.000 0.000 0.000 0.0684782603 35 0.093 -1.050 0.336 0.000 0.000 0.000 0.0684779139 44 0.093 -1.050 0.336 -0.087 0.000 0.000 0.0671949200 46 0.093 -1.050 0.336 -0.069 0.000 0.000 0.0671457955 48 0.093 -1.050 0.336 -0.075 0.000 0.000 0.0671231014 49 0.093 -1.050 0.336 -0.076 0.000 0.000 0.0671215799 59 0.093 -1.050 0.336 -0.076 -0.006 0.000 0.0670725015 60 0.093 -1.050 0.336 -0.076 -0.011 0.000 0.0670588724 61 0.093 -1.050 0.336 -0.076 -0.010 0.000 0.0670580788 68 0.093 -1.050 0.336 -0.076 -0.010 0.382 0.0666619473 69 0.093 -1.050 0.336 -0.076 -0.010 0.197 0.0638280827 70 0.093 -1.050 0.336 -0.076 -0.010 0.198 0.0638235674 71 0.093 -1.050 0.336 -0.076 -0.010 0.218 0.0637764123 powell nthiter 1: fret = 0.063776 83 0.077 -1.050 0.336 -0.076 -0.010 0.218 0.0637530128 85 0.076 -1.050 0.336 -0.076 -0.010 0.218 0.0637510580 86 0.069 -1.050 0.336 -0.076 -0.010 0.218 0.0637487471 87 0.072 -1.050 0.336 -0.076 -0.010 0.218 0.0637476606 96 0.072 -1.004 0.336 -0.076 -0.010 0.218 0.0628888753 97 0.072 -0.967 0.336 -0.076 -0.010 0.218 0.0625044274 99 0.072 -0.915 0.336 -0.076 -0.010 0.218 0.0619493948 100 0.072 -0.912 0.336 -0.076 -0.010 0.218 0.0619416089 101 0.072 -0.904 0.336 -0.076 -0.010 0.218 0.0619256881 102 0.072 -0.885 0.336 -0.076 -0.010 0.218 0.0618848541 106 0.072 -0.887 0.336 -0.076 -0.010 0.218 0.0618815691 107 0.072 -0.886 0.336 -0.076 -0.010 0.218 0.0618813146 116 0.072 -0.886 0.350 -0.076 -0.010 0.218 0.0618542970 117 0.072 -0.886 0.345 -0.076 -0.010 0.218 0.0618406756 129 0.072 -0.886 0.345 -0.098 -0.010 0.218 0.0617655684 130 0.072 -0.886 0.345 -0.089 -0.010 0.218 0.0616817337 131 0.072 -0.886 0.345 -0.088 -0.010 0.218 0.0616783351 139 0.072 -0.886 0.345 -0.088 -0.045 0.218 0.0613349510 143 0.072 -0.886 0.345 -0.088 -0.041 0.218 0.0613244028 144 0.072 -0.886 0.345 -0.088 -0.040 0.218 0.0613243449 153 0.072 -0.886 0.345 -0.088 -0.040 0.213 0.0612879915 154 0.072 -0.886 0.345 -0.088 -0.040 0.202 0.0612539251 156 0.072 -0.886 0.345 -0.088 -0.040 0.200 0.0612515921 157 0.072 -0.886 0.345 -0.088 -0.040 0.198 0.0612511252 powell nthiter 2: fret = 0.061251 167 0.055 -0.886 0.345 -0.088 -0.040 0.198 0.0612298832 168 0.058 -0.886 0.345 -0.088 -0.040 0.198 0.0612163924 169 0.061 -0.886 0.345 -0.088 -0.040 0.198 0.0612132866 170 0.060 -0.886 0.345 -0.088 -0.040 0.198 0.0612131807 181 0.060 -0.902 0.345 -0.088 -0.040 0.198 0.0610612784 183 0.060 -0.901 0.345 -0.088 -0.040 0.198 0.0610601144 194 0.060 -0.901 0.344 -0.088 -0.040 0.198 0.0610597969 205 0.060 -0.901 0.344 -0.093 -0.040 0.198 0.0610433686 206 0.060 -0.901 0.344 -0.092 -0.040 0.198 0.0610412179 217 0.060 -0.901 0.344 -0.092 -0.044 0.198 0.0610357137 228 0.060 -0.901 0.344 -0.092 -0.044 0.197 0.0610354613 229 0.060 -0.901 0.344 -0.092 -0.044 0.196 0.0610350274 240 0.056 -0.906 0.343 -0.093 -0.045 0.195 0.0610229520 241 0.057 -0.905 0.344 -0.093 -0.045 0.195 0.0610216617 242 0.057 -0.905 0.344 -0.093 -0.045 0.195 0.0610216579 246 0.057 -0.905 0.344 -0.093 -0.045 0.195 0.0610214450 powell nthiter 3: fret = 0.061021 259 0.064 -0.905 0.344 -0.093 -0.045 0.195 0.0610117669 284 0.064 -0.905 0.354 -0.093 -0.045 0.195 0.0610098214 285 0.064 -0.905 0.349 -0.093 -0.045 0.195 0.0609983799 298 0.064 -0.905 0.349 -0.094 -0.045 0.195 0.0609905437 299 0.064 -0.905 0.349 -0.096 -0.045 0.195 0.0609868289 302 0.064 -0.905 0.349 -0.095 -0.045 0.195 0.0609867667 318 0.060 -0.910 0.348 -0.097 -0.046 0.194 0.0609643720 319 0.060 -0.910 0.348 -0.097 -0.046 0.194 0.0609641621 323 0.060 -0.910 0.348 -0.097 -0.046 0.194 0.0609640012 327 0.059 -0.920 0.353 -0.102 -0.049 0.193 0.0609258366 334 0.059 -0.920 0.353 -0.102 -0.049 0.193 0.0609255390 powell nthiter 4: fret = 0.060926 350 0.072 -0.920 0.353 -0.102 -0.049 0.193 0.0609141647 351 0.067 -0.920 0.353 -0.102 -0.049 0.193 0.0608920924 362 0.067 -0.920 0.353 -0.102 -0.049 0.206 0.0608730552 363 0.067 -0.920 0.353 -0.102 -0.049 0.203 0.0608728138 385 0.067 -0.920 0.353 -0.109 -0.049 0.203 0.0608024754 388 0.067 -0.920 0.353 -0.110 -0.049 0.203 0.0608022920 400 0.066 -0.929 0.358 -0.115 -0.051 0.202 0.0607092185 405 0.066 -0.930 0.358 -0.115 -0.051 0.202 0.0607081078 407 0.066 -0.930 0.358 -0.115 -0.051 0.202 0.0607079567 411 0.066 -0.930 0.358 -0.115 -0.051 0.202 0.0607079416 powell nthiter 5: fret = 0.060708 425 0.073 -0.930 0.358 -0.115 -0.051 0.202 0.0606695212 436 0.073 -0.930 0.358 -0.115 -0.051 0.220 0.0606081040 458 0.073 -0.930 0.358 -0.117 -0.051 0.220 0.0605866617 459 0.073 -0.930 0.358 -0.121 -0.051 0.220 0.0605702535 468 0.073 -0.930 0.358 -0.121 -0.044 0.220 0.0605615077 470 0.073 -0.930 0.358 -0.121 -0.046 0.220 0.0605599116 472 0.073 -0.930 0.358 -0.121 -0.045 0.220 0.0605597192 478 0.073 -0.934 0.360 -0.123 -0.046 0.219 0.0605307234 480 0.073 -0.935 0.360 -0.123 -0.046 0.219 0.0605300248 485 0.080 -0.939 0.362 -0.131 -0.041 0.236 0.0605247559 powell nthiter 6: fret = 0.060530 495 0.077 -0.935 0.360 -0.123 -0.046 0.219 0.0605178744 506 0.077 -0.935 0.360 -0.123 -0.046 0.228 0.0605032485 507 0.077 -0.935 0.360 -0.123 -0.046 0.227 0.0605032399 517 0.077 -0.935 0.362 -0.123 -0.046 0.227 0.0605018950 529 0.077 -0.935 0.362 -0.125 -0.046 0.227 0.0605007754 539 0.077 -0.935 0.362 -0.125 -0.044 0.227 0.0605001244 547 0.077 -0.936 0.362 -0.125 -0.045 0.226 0.0604973576 548 0.077 -0.936 0.362 -0.125 -0.045 0.226 0.0604971982 powell nthiter 7: fret = 0.060497 565 0.080 -0.936 0.362 -0.125 -0.045 0.226 0.0604961614 567 0.079 -0.936 0.362 -0.125 -0.045 0.226 0.0604946788 577 0.079 -0.936 0.362 -0.125 -0.045 0.229 0.0604937707 617 0.079 -0.937 0.363 -0.126 -0.045 0.229 0.0604926921 Powell done niters = 7 Computing relative cost 0 -25.0 -25.0 -25.0 0.971056 1 -25.0 -25.0 25.0 0.982991 2 -25.0 25.0 -25.0 0.961614 3 -25.0 25.0 25.0 0.977821 4 25.0 -25.0 -25.0 0.962561 5 25.0 -25.0 25.0 0.970800 6 25.0 25.0 -25.0 0.973439 7 25.0 25.0 25.0 0.971351 REL: 8 0.060493 7.771635 0.971454 rel = 0.0622702 Number of iterations 7 Min cost was 0.060493 Number of FunctionCalls 624 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 1.362000 sec Parameters at optimum (transmm) 0.07921 -0.93683 0.36267 Parameters at optimum (rotdeg) -0.12576 -0.04490 0.22919 Final costs ---------------- Number of surface hits 4154 WM Intensity 788.7582 +/- 253.1406 Ctx Intensity 1052.4076 +/- 260.2808 Pct Contrast 30.3521 +/- 16.6186 Cost 0.0605 RelCost 0.2094 Reg at min cost was -0.99985 -0.00701 -0.01596 -0.21518; -0.01592 -0.00650 0.99985 0.16161; 0.00711 -0.99995 -0.00639 0.11805; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/bbr.pass1.dat, type = 14 Original Reg -0.99990 -0.00782 -0.01197 -0.29019; -0.01193 -0.00428 0.99992 1.10014; 0.00787 -0.99996 -0.00418 -0.24197; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00005 -0.00081 0.00399 -0.07501; 0.00398 0.00222 0.00007 0.93853; 0.00076 -0.00001 0.00220 -0.36003; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.848310 Computing change in rh position Surface-RMS-Diff-mm 0.943407 0.133758 1.234396 mri_segreg done mri_segreg --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/template.nii --init-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/bbr.pass1.dat --out-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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-05/mri/transforms/T2raw.auto.dat.mincost --dof 6 --nmax 36 --param /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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-05/mri/transforms/tmp.bbregister.208641/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-05/scripts mri_segreg --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/template.nii --init-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/bbr.pass1.dat --out-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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-05/mri/transforms/T2raw.auto.dat.mincost --dof 6 --nmax 36 --param /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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-05/mri/transforms/tmp.bbregister.208641/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname blg4313.int.ets1.calculquebec.ca machine x86_64 user bpinsard movvol /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/template.nii regfile /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/tmp.bbregister.208641/bbr.pass1.dat subject sub-05 dof 6 outregfile /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 1622269029 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg -0.99985 -0.00701 -0.01596 -0.21518; -0.01592 -0.00650 0.99985 0.16161; 0.00711 -0.99995 -0.00639 0.11805; 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 0.980598 1 -25.0 -25.0 25.0 0.970003 2 -25.0 25.0 -25.0 0.969964 3 -25.0 25.0 25.0 0.983508 4 25.0 -25.0 -25.0 0.975738 5 25.0 -25.0 25.0 0.964835 6 25.0 25.0 -25.0 0.956883 7 25.0 25.0 25.0 0.968609 REL: 8 0.063363 7.770139 0.971267 rel = 0.0652377 Initial costs ---------------- Number of surface hits 413992 WM Intensity 790.9959 +/- 248.9912 Ctx Intensity 1058.1995 +/- 259.2725 Pct Contrast 30.4992 +/- 16.5520 Cost 0.0634 RelCost 0.0652 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0677 0.0677 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0668 0.0668 0.0 10 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.0000 0.0661 0.0661 0.0 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.0655 0.0655 0.0 13 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.0649 0.0649 0.0 28 -0.1000 -0.1000 0.0000 -0.1000 -0.1000 0.0000 0.0645 0.0645 0.0 30 -0.1000 -0.1000 0.0000 -0.1000 0.0000 -0.1000 0.0635 0.0635 0.0 39 -0.1000 -0.1000 0.0000 0.0000 0.0000 -0.1000 0.0630 0.0630 0.0 42 -0.1000 -0.1000 0.0000 0.0000 0.1000 -0.1000 0.0629 0.0629 0.0 43 -0.1000 -0.1000 0.0000 0.0000 0.1000 0.0000 0.0625 0.0625 0.0 57 -0.1000 -0.1000 0.1000 -0.1000 0.0000 -0.1000 0.0620 0.0620 0.0 58 -0.1000 -0.1000 0.1000 -0.1000 0.0000 0.0000 0.0617 0.0617 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0605 0.0605 0.0 Brute Force -------------------------- Min cost was 0.060493 Number of iterations 729 Search time 1.559000 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 = 0.063363 7 0.071 0.000 0.000 0.000 0.000 0.000 0.0627813036 8 0.072 0.000 0.000 0.000 0.000 0.000 0.0627801144 9 0.076 0.000 0.000 0.000 0.000 0.000 0.0627792329 11 0.075 0.000 0.000 0.000 0.000 0.000 0.0627788591 19 0.075 -0.082 0.000 0.000 0.000 0.000 0.0618798065 21 0.075 -0.083 0.000 0.000 0.000 0.000 0.0618795719 29 0.075 -0.083 -0.051 0.000 0.000 0.000 0.0613067904 30 0.075 -0.083 -0.081 0.000 0.000 0.000 0.0612588987 31 0.075 -0.083 -0.073 0.000 0.000 0.000 0.0612517577 40 0.075 -0.083 -0.073 0.046 0.000 0.000 0.0610758919 41 0.075 -0.083 -0.073 0.036 0.000 0.000 0.0610604251 42 0.075 -0.083 -0.073 0.035 0.000 0.000 0.0610601190 43 0.075 -0.083 -0.073 0.034 0.000 0.000 0.0610599000 45 0.075 -0.083 -0.073 0.032 0.000 0.000 0.0610598094 47 0.075 -0.083 -0.073 0.033 0.000 0.000 0.0610597286 54 0.075 -0.083 -0.073 0.033 0.007 0.000 0.0610216826 55 0.075 -0.083 -0.073 0.033 0.024 0.000 0.0609860914 57 0.075 -0.083 -0.073 0.033 0.025 0.000 0.0609860310 67 0.075 -0.083 -0.073 0.033 0.025 -0.008 0.0609797022 powell nthiter 1: fret = 0.060980 77 0.052 -0.083 -0.073 0.033 0.025 -0.008 0.0609568392 78 0.059 -0.083 -0.073 0.033 0.025 -0.008 0.0609496678 87 0.059 -0.077 -0.073 0.033 0.025 -0.008 0.0609414509 88 0.059 -0.075 -0.073 0.033 0.025 -0.008 0.0609412470 90 0.059 -0.076 -0.073 0.033 0.025 -0.008 0.0609410561 98 0.059 -0.076 -0.087 0.033 0.025 -0.008 0.0609240535 100 0.059 -0.076 -0.084 0.033 0.025 -0.008 0.0609236715 109 0.059 -0.076 -0.084 0.053 0.025 -0.008 0.0609182126 110 0.059 -0.076 -0.084 0.044 0.025 -0.008 0.0609113082 111 0.059 -0.076 -0.084 0.045 0.025 -0.008 0.0609112167 120 0.059 -0.076 -0.084 0.045 0.027 -0.008 0.0609112036 122 0.059 -0.076 -0.084 0.045 0.026 -0.008 0.0609109404 130 0.059 -0.076 -0.084 0.045 0.026 -0.015 0.0609068690 powell nthiter 2: fret = 0.060907 141 0.058 -0.076 -0.084 0.045 0.026 -0.015 0.0609063509 142 0.057 -0.076 -0.084 0.045 0.026 -0.015 0.0609063197 150 0.057 -0.073 -0.084 0.045 0.026 -0.015 0.0609030532 151 0.057 -0.069 -0.084 0.045 0.026 -0.015 0.0609015478 152 0.057 -0.070 -0.084 0.045 0.026 -0.015 0.0609014579 161 0.057 -0.070 -0.090 0.045 0.026 -0.015 0.0608991052 162 0.057 -0.070 -0.089 0.045 0.026 -0.015 0.0608990997 171 0.057 -0.070 -0.089 0.049 0.026 -0.015 0.0608976685 172 0.057 -0.070 -0.089 0.048 0.026 -0.015 0.0608975890 182 0.057 -0.070 -0.089 0.048 0.025 -0.015 0.0608974968 191 0.057 -0.070 -0.089 0.048 0.025 -0.016 0.0608974937 powell nthiter 3: fret = 0.060897 201 0.059 -0.070 -0.089 0.048 0.025 -0.016 0.0608974840 210 0.059 -0.068 -0.089 0.048 0.025 -0.016 0.0608971472 219 0.059 -0.068 -0.091 0.048 0.025 -0.016 0.0608969831 221 0.059 -0.068 -0.090 0.048 0.025 -0.016 0.0608969290 229 0.059 -0.068 -0.090 0.050 0.025 -0.016 0.0608966372 248 0.059 -0.068 -0.090 0.050 0.025 -0.015 0.0608966328 powell nthiter 4: fret = 0.060897 259 0.058 -0.068 -0.090 0.050 0.025 -0.015 0.0608965953 305 0.058 -0.068 -0.090 0.050 0.025 -0.016 0.0608965645 powell nthiter 5: fret = 0.060897 Powell done niters = 5 Computing relative cost 0 -25.0 -25.0 -25.0 0.979760 1 -25.0 -25.0 25.0 0.969871 2 -25.0 25.0 -25.0 0.969018 3 -25.0 25.0 25.0 0.983653 4 25.0 -25.0 -25.0 0.975831 5 25.0 -25.0 25.0 0.964628 6 25.0 25.0 -25.0 0.957090 7 25.0 25.0 25.0 0.968355 REL: 8 0.060897 7.768205 0.971026 rel = 0.0627136 Number of iterations 5 Min cost was 0.060897 Number of FunctionCalls 362 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 52.484000 sec Parameters at optimum (transmm) 0.05759 -0.06841 -0.09004 Parameters at optimum (rotdeg) 0.05048 0.02524 -0.01640 Final costs ---------------- Number of surface hits 413992 WM Intensity 790.0398 +/- 248.4195 Ctx Intensity 1056.9888 +/- 258.5034 Pct Contrast 30.5068 +/- 16.4886 Cost 0.0609 RelCost 0.0652 Reg at min cost was -0.99985 -0.00745 -0.01568 -0.15749; -0.01564 -0.00562 0.99986 0.09316; 0.00754 -0.99996 -0.00550 0.02825; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/T2raw.auto.dat, type = 14 Original Reg -0.99985 -0.00701 -0.01596 -0.21518; -0.01592 -0.00650 0.99985 0.16161; 0.00711 -0.99995 -0.00639 0.11805; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00000 0.00044 -0.00028 -0.05769; -0.00028 -0.00088 -0.00001 0.06845; -0.00043 0.00000 -0.00089 0.08980; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.152952 Computing change in rh position Surface-RMS-Diff-mm 0.139752 0.035932 0.216314 mri_segreg done MinCost: 0.060897 790.039762 1056.988755 30.506751 tkregister2_cmdl --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/orig/T2raw.mgz --reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/T2raw.auto.dat --noedit --ltaout /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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-05/mri/orig/T2raw.mgz reg file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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 -------- -0.99985 -0.00745 -0.01568 -0.15749; -0.01564 -0.00562 0.99986 0.09316; 0.00754 -0.99996 -0.00550 0.02825; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: loading target /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/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-05/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 -------- -0.99985 -0.00745 -0.01568 -0.15749; -0.01564 -0.00562 0.99986 0.09316; 0.00754 -0.99996 -0.00550 0.02825; 0.00000 0.00000 0.00000 1.00000; Determinant -1 subject = sub-05 RegMat --------------------------- -0.99985 -0.00745 -0.01568 -0.15749; -0.01564 -0.00562 0.99986 0.09316; 0.00754 -0.99996 -0.00550 0.02825; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Tue May 25 23:29:21 UTC 2021 Ended at Tue May 25 23:32:08 UTC 2021 BBR-Run-Time-Sec 167 bbregister Done To check results, run: tkregisterfv --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/orig/T2raw.mgz --reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-05/mri/transforms/T2raw.auto.lta --surfs