Logfile for bbregister Tue May 25 22:48:12 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-06/scripts /opt/freesurfer/bin/bbregister --s sub-06 --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/orig/T2raw.mgz --lta /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/T2raw.auto.lta --init-coreg --T2 $Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $ Linux blg6114.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-06/mri/orig/T2raw.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/template.nii mri_convert.bin /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/orig/T2raw.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/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-06/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-06/mri/transforms/tmp.bbregister.263970/template.nii... mri_coreg --s sub-06 --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/template.nii --regdat /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/reg.init.dat --reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/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-06/scripts cmdline mri_coreg --s sub-06 --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/template.nii --regdat /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/reg.init.dat --reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/mri_coreg.lta --nthreads 4 --dof 6 --sep 4 --ftol .0001 --linmintol .01 --no-ref-mask sysname Linux hostname blg6114.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-06/mri/transforms/tmp.bbregister.263970/template.nii Reading in ref /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/brainmask.mgz Setting cras translation parameters to align centers Creating random numbers for coordinate dithering Performing intensity dithering Initial parameters -0.8000 0.0000 -0.8000 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 = 116.0000 ref gstd 1.9140 1.9140 1.9140 Smoothing ref COREGpreproc() done Testing if mov and target overlap Init cost -1.0352140471 nhits = 309410 out of 32768000, Percent Overlap: 60.4 Initial RefRAS-to-MovRAS 1.00000 0.00000 0.00000 -0.80001; 0.00000 1.00000 0.00000 0.00001; 0.00000 0.00000 1.00000 -0.80000; 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 318.99997; 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 -0.80001 0.00001 1.20000 0.00000 0.00000 0.00000 -1.0313114 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6 Starting OpenPowel2(), sep = 4 InitialCost -1.0357244015 #@# 4 188 -0.80001 0.00001 1.20000 0.00000 0.00000 0.00000 -1.0357244 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.035724 #@# 4 190 0.19999 0.00001 1.20000 0.00000 0.00000 0.00000 -1.0360961 #@# 4 195 0.16250 0.00001 1.20000 0.00000 0.00000 0.00000 -1.0360968 #@# 4 196 0.15250 0.00001 1.20000 0.00000 0.00000 0.00000 -1.0360969 #@# 4 206 0.13023 0.38197 1.20000 0.00000 0.00000 0.00000 -1.0361168 #@# 4 207 0.13023 0.30600 1.20000 0.00000 0.00000 0.00000 -1.0361189 #@# 4 214 0.13023 0.29219 0.58196 0.00000 0.00000 0.00000 -1.0361660 #@# 4 216 0.13023 0.29219 0.75323 0.00000 0.00000 0.00000 -1.0361716 #@# 4 217 0.13023 0.29219 0.73470 0.00000 0.00000 0.00000 -1.0361718 #@# 4 218 0.13023 0.29219 0.72241 0.00000 0.00000 0.00000 -1.0361719 #@# 4 226 0.13023 0.29219 0.72241 0.38197 0.00000 0.00000 -1.0361809 #@# 4 227 0.13023 0.29219 0.72241 0.24212 0.00000 0.00000 -1.0361845 #@# 4 247 0.13023 0.29219 0.72241 0.26212 -0.01430 0.09870 -1.0361869 #@# 4 252 0.13023 0.29219 0.72241 0.26212 -0.01430 0.13337 -1.0361871 powell nthiter 1: fret = -1.036187 #@# 4 261 0.12023 0.29219 0.72241 0.26212 -0.01430 0.13337 -1.0361872 #@# 4 269 0.12023 0.13939 0.72241 0.26212 -0.01430 0.13337 -1.0361925 #@# 4 270 0.12023 0.14939 0.72241 0.26212 -0.01430 0.13337 -1.0361927 #@# 4 281 0.12023 0.17249 0.80086 0.26212 -0.01430 0.13337 -1.0361941 #@# 4 282 0.12023 0.17249 0.79086 0.26212 -0.01430 0.13337 -1.0361942 #@# 4 292 0.12023 0.17249 0.78086 0.34279 -0.01430 0.13337 -1.0361953 #@# 4 297 0.12023 0.17249 0.78086 0.36383 -0.01430 0.13337 -1.0361954 #@# 4 305 0.12023 0.17249 0.78086 0.36383 -0.07726 0.13337 -1.0361961 Powell done niters total = 1 OptTimeSec 9.9 sec OptTimeMin 0.17 min nEvals 319 Final parameters 0.12023165 0.17248644 0.78086489 0.36382699 -0.08772265 0.12100271 Final cost -1.036196141705566 --------------------------------- mri_coreg utimesec 201.449723 mri_coreg stimesec 1.120573 mri_coreg ru_maxrss 890536 mri_coreg ru_ixrss 0 mri_coreg ru_idrss 0 mri_coreg ru_isrss 0 mri_coreg ru_minflt 880456 mri_coreg ru_majflt 2 mri_coreg ru_nswap 0 mri_coreg ru_inblock 10064 mri_coreg ru_oublock 16 mri_coreg ru_msgsnd 0 mri_coreg ru_msgrcv 0 mri_coreg ru_nsignals 0 mri_coreg ru_nvcsw 802 mri_coreg ru_nivcsw 135 Final RefRAS-to-MovRAS 1.00000 0.00211 -0.00153 0.12023; -0.00210 0.99998 0.00635 0.17249; 0.00154 -0.00635 0.99998 0.78086; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox -1.00000 0.00153 0.00211 263.66193; 0.00210 -0.00635 0.99998 -9.21173; -0.00154 -0.99998 -0.00635 322.02945; 0.00000 0.00000 0.00000 1.00000; Final parameters 0.1202 0.1725 0.7809 0.3638 -0.0877 0.1210 nhits = 307655 out of 32768000, Percent Overlap: 60.1 mri_coreg RunTimeSec 78.6 sec To check run: tkregisterfv --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/template.nii --targ /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/brainmask.mgz --reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/mri_coreg.lta --s sub-06 --surfs mri_coreg done mri_segreg --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/template.nii --init-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/reg.init.dat --out-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/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-06/scripts mri_segreg --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/template.nii --init-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/reg.init.dat --out-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/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 blg6114.int.ets1.calculquebec.ca machine x86_64 user bpinsard movvol /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/template.nii regfile /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/reg.init.dat subject sub-06 dof 6 outregfile /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/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 1622974622 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg -1.00000 -0.00211 0.00153 -0.19631; 0.00154 -0.00635 0.99998 0.61626; 0.00210 -0.99998 -0.00635 -0.08401; 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 0.938148 1 -25.0 -25.0 25.0 0.945252 2 -25.0 25.0 -25.0 0.975470 3 -25.0 25.0 25.0 0.941900 4 25.0 -25.0 -25.0 0.972514 5 25.0 -25.0 25.0 0.990208 6 25.0 25.0 -25.0 0.973561 7 25.0 25.0 25.0 0.993441 REL: 8 0.108777 7.730496 0.966312 rel = 0.112569 Initial costs ---------------- Number of surface hits 4125 WM Intensity 729.7891 +/- 223.7845 Ctx Intensity 1002.3210 +/- 233.5627 Pct Contrast 32.8407 +/- 19.2404 Cost 0.1088 RelCost 0.1126 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9322 0.9322 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.9116 0.9116 0.0 6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.8737 0.8737 0.0 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.8094 0.8094 0.0 39 -4.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.7559 0.7559 0.0 102 -4.0000 0.0000 -4.0000 4.0000 0.0000 -4.0000 0.7259 0.7259 0.0 120 -4.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.6361 0.6361 0.0 346 0.0000 0.0000 -4.0000 4.0000 0.0000 0.0000 0.5915 0.5915 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1088 0.1088 0.0 Brute Force -------------------------- Min cost was 0.108777 Number of iterations 729 Search time 1.968000 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 = 0.108777 7 -0.075 0.000 0.000 0.000 0.000 0.000 0.1078655362 8 -0.099 0.000 0.000 0.000 0.000 0.000 0.1075977237 11 -0.133 0.000 0.000 0.000 0.000 0.000 0.1075635888 12 -0.127 0.000 0.000 0.000 0.000 0.000 0.1075605991 13 -0.126 0.000 0.000 0.000 0.000 0.000 0.1075570166 14 -0.115 0.000 0.000 0.000 0.000 0.000 0.1075444865 16 -0.117 0.000 0.000 0.000 0.000 0.000 0.1075438823 22 -0.117 -0.618 0.000 0.000 0.000 0.000 0.0764554062 24 -0.117 -0.507 0.000 0.000 0.000 0.000 0.0754279906 25 -0.117 -0.529 0.000 0.000 0.000 0.000 0.0753597247 27 -0.117 -0.522 0.000 0.000 0.000 0.000 0.0753387735 36 -0.117 -0.522 0.382 0.000 0.000 0.000 0.0588365137 37 -0.117 -0.522 0.403 0.000 0.000 0.000 0.0586650939 39 -0.117 -0.522 0.411 0.000 0.000 0.000 0.0586559325 40 -0.117 -0.522 0.409 0.000 0.000 0.000 0.0586555977 48 -0.117 -0.522 0.409 0.056 0.000 0.000 0.0578889440 52 -0.117 -0.522 0.409 0.048 0.000 0.000 0.0578871941 53 -0.117 -0.522 0.409 0.050 0.000 0.000 0.0578837951 54 -0.117 -0.522 0.409 0.052 0.000 0.000 0.0578829048 62 -0.117 -0.522 0.409 0.052 0.148 0.000 0.0567980266 63 -0.117 -0.522 0.409 0.052 0.126 0.000 0.0567397169 65 -0.117 -0.522 0.409 0.052 0.134 0.000 0.0567198316 66 -0.117 -0.522 0.409 0.052 0.133 0.000 0.0567193190 74 -0.117 -0.522 0.409 0.052 0.133 -0.037 0.0559333640 76 -0.117 -0.522 0.409 0.052 0.133 -0.084 0.0558933730 77 -0.117 -0.522 0.409 0.052 0.133 -0.062 0.0558092599 80 -0.117 -0.522 0.409 0.052 0.133 -0.059 0.0558062664 powell nthiter 1: fret = 0.055806 90 -0.021 -0.522 0.409 0.052 0.133 -0.059 0.0557302883 92 0.088 -0.522 0.409 0.052 0.133 -0.059 0.0549374314 96 0.071 -0.522 0.409 0.052 0.133 -0.059 0.0548324139 105 0.071 -0.489 0.409 0.052 0.133 -0.059 0.0548275235 106 0.071 -0.505 0.409 0.052 0.133 -0.059 0.0548117464 107 0.071 -0.504 0.409 0.052 0.133 -0.059 0.0548099356 108 0.071 -0.499 0.409 0.052 0.133 -0.059 0.0548077826 111 0.071 -0.501 0.409 0.052 0.133 -0.059 0.0548075311 119 0.071 -0.501 0.328 0.052 0.133 -0.059 0.0531633859 121 0.071 -0.501 0.310 0.052 0.133 -0.059 0.0529819631 123 0.071 -0.501 0.309 0.052 0.133 -0.059 0.0529815270 131 0.071 -0.501 0.309 0.121 0.133 -0.059 0.0517641867 132 0.071 -0.501 0.309 0.127 0.133 -0.059 0.0517551752 134 0.071 -0.501 0.309 0.125 0.133 -0.059 0.0517538355 144 0.071 -0.501 0.309 0.125 0.126 -0.059 0.0517263903 158 0.071 -0.501 0.309 0.125 0.126 -0.054 0.0517137343 powell nthiter 2: fret = 0.051714 172 0.084 -0.501 0.309 0.125 0.126 -0.054 0.0517016723 173 0.078 -0.501 0.309 0.125 0.126 -0.054 0.0516886587 184 0.078 -0.495 0.309 0.125 0.126 -0.054 0.0516793157 185 0.078 -0.496 0.309 0.125 0.126 -0.054 0.0516781690 193 0.078 -0.496 0.265 0.125 0.126 -0.054 0.0512447295 194 0.078 -0.496 0.245 0.125 0.126 -0.054 0.0511358878 197 0.078 -0.496 0.239 0.125 0.126 -0.054 0.0511200552 198 0.078 -0.496 0.236 0.125 0.126 -0.054 0.0511156996 208 0.078 -0.496 0.236 0.162 0.126 -0.054 0.0511069517 209 0.078 -0.496 0.236 0.144 0.126 -0.054 0.0510461324 210 0.078 -0.496 0.236 0.143 0.126 -0.054 0.0510450670 211 0.078 -0.496 0.236 0.140 0.126 -0.054 0.0510450030 214 0.078 -0.496 0.236 0.141 0.126 -0.054 0.0510442426 215 0.078 -0.496 0.236 0.142 0.126 -0.054 0.0510441648 224 0.078 -0.496 0.236 0.142 0.120 -0.054 0.0510062011 227 0.078 -0.496 0.236 0.142 0.117 -0.054 0.0510015919 228 0.078 -0.496 0.236 0.142 0.116 -0.054 0.0510013665 238 0.078 -0.496 0.236 0.142 0.116 -0.021 0.0509045465 239 0.078 -0.496 0.236 0.142 0.116 -0.033 0.0508254250 240 0.078 -0.496 0.236 0.142 0.116 -0.034 0.0508247208 248 0.081 -0.494 0.208 0.148 0.112 -0.027 0.0507533703 249 0.081 -0.494 0.211 0.147 0.112 -0.028 0.0507479241 250 0.080 -0.495 0.215 0.146 0.113 -0.029 0.0507423866 253 0.080 -0.495 0.216 0.146 0.113 -0.029 0.0507422261 powell nthiter 3: fret = 0.050742 267 0.098 -0.495 0.216 0.146 0.113 -0.029 0.0506926649 268 0.092 -0.495 0.216 0.146 0.113 -0.029 0.0506780812 277 0.092 -0.469 0.216 0.146 0.113 -0.029 0.0503306083 279 0.092 -0.466 0.216 0.146 0.113 -0.029 0.0503269879 292 0.092 -0.466 0.216 0.146 0.113 -0.026 0.0503195315 293 0.092 -0.466 0.216 0.146 0.113 -0.025 0.0503191804 302 0.092 -0.466 0.216 0.159 0.113 -0.025 0.0502043282 303 0.092 -0.466 0.216 0.161 0.113 -0.025 0.0502030357 313 0.092 -0.466 0.216 0.161 0.122 -0.025 0.0502008420 314 0.092 -0.466 0.216 0.161 0.118 -0.025 0.0501920799 318 0.099 -0.461 0.143 0.177 0.107 -0.005 0.0501401161 322 0.096 -0.463 0.171 0.171 0.111 -0.012 0.0499932596 324 0.096 -0.463 0.172 0.170 0.111 -0.013 0.0499923532 328 0.096 -0.463 0.172 0.170 0.111 -0.013 0.0499922617 powell nthiter 4: fret = 0.049992 339 0.098 -0.463 0.172 0.170 0.111 -0.013 0.0499819159 342 0.100 -0.463 0.172 0.170 0.111 -0.013 0.0499777623 351 0.100 -0.460 0.172 0.170 0.111 -0.013 0.0499489072 353 0.100 -0.450 0.172 0.170 0.111 -0.013 0.0499177998 354 0.100 -0.453 0.172 0.170 0.111 -0.013 0.0499152048 367 0.100 -0.453 0.172 0.170 0.111 -0.019 0.0499053006 368 0.100 -0.453 0.172 0.170 0.111 -0.018 0.0499051823 377 0.100 -0.453 0.172 0.180 0.111 -0.018 0.0498214789 378 0.100 -0.453 0.172 0.183 0.111 -0.018 0.0498197247 389 0.100 -0.453 0.172 0.183 0.117 -0.018 0.0497901165 390 0.100 -0.453 0.172 0.183 0.119 -0.018 0.0497898343 398 0.102 -0.452 0.159 0.185 0.117 -0.014 0.0497552229 399 0.102 -0.452 0.159 0.186 0.117 -0.014 0.0497552129 powell nthiter 5: fret = 0.049755 419 0.102 -0.451 0.159 0.186 0.117 -0.014 0.0497486287 421 0.102 -0.444 0.159 0.186 0.117 -0.014 0.0497321380 422 0.102 -0.445 0.159 0.186 0.117 -0.014 0.0497314184 435 0.102 -0.445 0.159 0.186 0.117 -0.018 0.0497247339 446 0.102 -0.445 0.159 0.190 0.117 -0.018 0.0497176017 447 0.102 -0.445 0.159 0.189 0.117 -0.018 0.0497172015 471 0.102 -0.438 0.159 0.192 0.117 -0.022 0.0497100503 478 0.102 -0.439 0.159 0.191 0.117 -0.021 0.0497099721 481 0.102 -0.439 0.159 0.191 0.117 -0.021 0.0497099228 484 0.102 -0.440 0.159 0.191 0.117 -0.021 0.0497098372 powell nthiter 6: fret = 0.049710 495 0.097 -0.440 0.159 0.191 0.117 -0.021 0.0497064349 496 0.098 -0.440 0.159 0.191 0.117 -0.021 0.0497049338 497 0.099 -0.440 0.159 0.191 0.117 -0.021 0.0497045737 505 0.099 -0.439 0.156 0.192 0.117 -0.021 0.0497034388 506 0.099 -0.439 0.157 0.192 0.117 -0.021 0.0497034227 507 0.099 -0.439 0.157 0.191 0.117 -0.021 0.0497033674 509 0.099 -0.439 0.157 0.191 0.117 -0.021 0.0497031999 524 0.099 -0.439 0.157 0.191 0.117 -0.022 0.0497022130 534 0.099 -0.439 0.157 0.193 0.117 -0.022 0.0497010227 544 0.099 -0.439 0.157 0.193 0.115 -0.022 0.0496994252 552 0.099 -0.437 0.157 0.194 0.115 -0.024 0.0496947543 555 0.099 -0.437 0.157 0.194 0.115 -0.024 0.0496945590 557 0.099 -0.437 0.157 0.194 0.115 -0.024 0.0496944603 powell nthiter 7: fret = 0.049694 573 0.098 -0.437 0.157 0.194 0.115 -0.024 0.0496941633 630 0.098 -0.436 0.157 0.195 0.115 -0.025 0.0496939136 631 0.098 -0.436 0.157 0.195 0.115 -0.024 0.0496938930 634 0.098 -0.436 0.157 0.195 0.115 -0.024 0.0496938178 Powell done niters = 7 Computing relative cost 0 -25.0 -25.0 -25.0 0.937009 1 -25.0 -25.0 25.0 0.949760 2 -25.0 25.0 -25.0 0.942077 3 -25.0 25.0 25.0 0.950495 4 25.0 -25.0 -25.0 0.960005 5 25.0 -25.0 25.0 0.992166 6 25.0 25.0 -25.0 0.971376 7 25.0 25.0 25.0 0.980256 REL: 8 0.049694 7.683145 0.960393 rel = 0.0517432 Number of iterations 7 Min cost was 0.049694 Number of FunctionCalls 639 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 1.457000 sec Parameters at optimum (transmm) 0.09777 -0.43578 0.15703 Parameters at optimum (rotdeg) 0.19480 0.11478 -0.02443 Final costs ---------------- Number of surface hits 4125 WM Intensity 721.7407 +/- 217.0764 Ctx Intensity 996.4421 +/- 220.2374 Pct Contrast 33.4733 +/- 17.2933 Cost 0.0497 RelCost 0.1126 Reg at min cost was -0.99999 -0.00412 0.00195 -0.09845; 0.00196 -0.00295 0.99999 0.18084; 0.00411 -0.99999 -0.00295 0.07552; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/bbr.pass1.dat, type = 14 Original Reg -1.00000 -0.00211 0.00153 -0.19631; 0.00154 -0.00635 0.99998 0.61626; 0.00210 -0.99998 -0.00635 -0.08401; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00001 0.00200 -0.00042 -0.09786; -0.00042 -0.00340 -0.00002 0.43542; -0.00201 0.00001 -0.00340 -0.15952; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.578499 Computing change in rh position Surface-RMS-Diff-mm 0.598816 0.130064 0.839589 mri_segreg done mri_segreg --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/template.nii --init-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/bbr.pass1.dat --out-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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-06/mri/transforms/T2raw.auto.dat.mincost --dof 6 --nmax 36 --param /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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-06/mri/transforms/tmp.bbregister.263970/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-06/scripts mri_segreg --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/template.nii --init-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/bbr.pass1.dat --out-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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-06/mri/transforms/T2raw.auto.dat.mincost --dof 6 --nmax 36 --param /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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-06/mri/transforms/tmp.bbregister.263970/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname blg6114.int.ets1.calculquebec.ca machine x86_64 user bpinsard movvol /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/template.nii regfile /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/tmp.bbregister.263970/bbr.pass1.dat subject sub-06 dof 6 outregfile /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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 1622417094 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg -0.99999 -0.00412 0.00195 -0.09845; 0.00196 -0.00295 0.99999 0.18084; 0.00411 -0.99999 -0.00295 0.07552; 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 0.961865 1 -25.0 -25.0 25.0 0.969815 2 -25.0 25.0 -25.0 0.962056 3 -25.0 25.0 25.0 0.949137 4 25.0 -25.0 -25.0 0.962483 5 25.0 -25.0 25.0 0.982092 6 25.0 25.0 -25.0 0.965111 7 25.0 25.0 25.0 0.961618 REL: 8 0.060522 7.714178 0.964272 rel = 0.0627639 Initial costs ---------------- Number of surface hits 410587 WM Intensity 729.0519 +/- 217.4000 Ctx Intensity 1003.3675 +/- 221.1589 Pct Contrast 33.1290 +/- 17.5346 Cost 0.0605 RelCost 0.0628 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0634 0.0634 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0594 0.0594 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.0579 0.0579 0.0 9 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 -0.1000 0.0568 0.0568 0.0 10 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.0000 0.0556 0.0556 0.0 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.0553 0.0553 0.0 13 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.0545 0.0545 0.0 16 -0.1000 -0.1000 -0.1000 0.0000 0.1000 0.0000 0.0541 0.0541 0.0 31 -0.1000 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.0539 0.0539 0.0 34 -0.1000 -0.1000 0.0000 -0.1000 0.1000 0.0000 0.0528 0.0528 0.0 117 -0.1000 0.0000 0.0000 0.0000 -0.1000 -0.1000 0.0524 0.0524 0.0 118 -0.1000 0.0000 0.0000 0.0000 -0.1000 0.0000 0.0516 0.0516 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0497 0.0497 0.0 Brute Force -------------------------- Min cost was 0.049694 Number of iterations 729 Search time 1.677000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000000 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.060522 7 -0.126 0.000 0.000 0.000 0.000 0.000 0.0592212289 8 -0.114 0.000 0.000 0.000 0.000 0.000 0.0592141076 9 -0.117 0.000 0.000 0.000 0.000 0.000 0.0592131121 18 -0.117 -0.021 0.000 0.000 0.000 0.000 0.0591193945 19 -0.117 -0.028 0.000 0.000 0.000 0.000 0.0591121746 20 -0.117 -0.029 0.000 0.000 0.000 0.000 0.0591120606 28 -0.117 -0.029 -0.002 0.000 0.000 0.000 0.0591010127 29 -0.117 -0.029 -0.022 0.000 0.000 0.000 0.0590529973 31 -0.117 -0.029 -0.026 0.000 0.000 0.000 0.0590527345 32 -0.117 -0.029 -0.024 0.000 0.000 0.000 0.0590523965 40 -0.117 -0.029 -0.024 0.016 0.000 0.000 0.0590320904 41 -0.117 -0.029 -0.024 0.011 0.000 0.000 0.0590303150 42 -0.117 -0.029 -0.024 0.012 0.000 0.000 0.0590300561 50 -0.117 -0.029 -0.024 0.012 -0.052 0.000 0.0586889825 51 -0.117 -0.029 -0.024 0.012 -0.054 0.000 0.0586868768 52 -0.117 -0.029 -0.024 0.012 -0.057 0.000 0.0586845702 55 -0.117 -0.029 -0.024 0.012 -0.059 0.000 0.0586843821 56 -0.117 -0.029 -0.024 0.012 -0.060 0.000 0.0586843627 63 -0.117 -0.029 -0.024 0.012 -0.060 0.079 0.0582940669 64 -0.117 -0.029 -0.024 0.012 -0.060 0.065 0.0582750526 powell nthiter 1: fret = 0.058275 74 -0.061 -0.029 -0.024 0.012 -0.060 0.065 0.0579056364 75 -0.059 -0.029 -0.024 0.012 -0.060 0.065 0.0579045465 76 -0.058 -0.029 -0.024 0.012 -0.060 0.065 0.0579043257 85 -0.058 -0.026 -0.024 0.012 -0.060 0.065 0.0579017969 86 -0.058 -0.025 -0.024 0.012 -0.060 0.065 0.0579017802 95 -0.058 -0.025 -0.037 0.012 -0.060 0.065 0.0578904478 96 -0.058 -0.025 -0.034 0.012 -0.060 0.065 0.0578892025 106 -0.058 -0.025 -0.034 0.016 -0.060 0.065 0.0578856798 116 -0.058 -0.025 -0.034 0.016 -0.062 0.065 0.0578854056 124 -0.058 -0.025 -0.034 0.016 -0.062 0.115 0.0577840918 125 -0.058 -0.025 -0.034 0.016 -0.062 0.101 0.0577555435 126 -0.058 -0.025 -0.034 0.016 -0.062 0.099 0.0577553285 128 0.002 -0.020 -0.044 0.020 -0.063 0.133 0.0577283636 134 -0.021 -0.022 -0.040 0.019 -0.063 0.120 0.0576586043 136 -0.024 -0.022 -0.040 0.019 -0.062 0.119 0.0576575352 137 -0.024 -0.022 -0.040 0.019 -0.062 0.119 0.0576575255 139 -0.024 -0.022 -0.040 0.019 -0.063 0.119 0.0576575177 powell nthiter 2: fret = 0.057658 157 -0.024 -0.016 -0.040 0.019 -0.063 0.119 0.0576548775 158 -0.024 -0.017 -0.040 0.019 -0.063 0.119 0.0576543002 178 -0.024 -0.017 -0.040 0.020 -0.063 0.119 0.0576541750 188 -0.024 -0.017 -0.040 0.020 -0.064 0.119 0.0576539420 197 -0.023 -0.017 -0.040 0.020 -0.064 0.119 0.0576538346 198 -0.023 -0.017 -0.040 0.020 -0.064 0.119 0.0576538201 201 -0.022 -0.017 -0.040 0.020 -0.064 0.119 0.0576538195 202 -0.023 -0.017 -0.040 0.020 -0.064 0.119 0.0576538060 powell nthiter 3: fret = 0.057654 249 -0.023 -0.017 -0.040 0.020 -0.065 0.119 0.0576538025 258 -0.022 -0.017 -0.040 0.020 -0.065 0.119 0.0576537731 267 -0.022 -0.017 -0.040 0.020 -0.065 0.120 0.0576537694 powell nthiter 4: fret = 0.057654 329 -0.022 -0.017 -0.040 0.020 -0.065 0.120 0.0576537647 powell nthiter 5: fret = 0.057654 Powell done niters = 5 Computing relative cost 0 -25.0 -25.0 -25.0 0.962578 1 -25.0 -25.0 25.0 0.969735 2 -25.0 25.0 -25.0 0.963039 3 -25.0 25.0 25.0 0.949601 4 25.0 -25.0 -25.0 0.961506 5 25.0 -25.0 25.0 0.980436 6 25.0 25.0 -25.0 0.964538 7 25.0 25.0 25.0 0.961307 REL: 8 0.057654 7.712740 0.964093 rel = 0.0598011 Number of iterations 5 Min cost was 0.057654 Number of FunctionCalls 388 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 44.335000 sec Parameters at optimum (transmm) -0.02194 -0.01726 -0.04028 Parameters at optimum (rotdeg) 0.01976 -0.06506 0.11975 Final costs ---------------- Number of surface hits 410587 WM Intensity 728.7081 +/- 216.9927 Ctx Intensity 1002.8839 +/- 220.3977 Pct Contrast 33.1325 +/- 17.4295 Cost 0.0577 RelCost 0.0628 Reg at min cost was -1.00000 -0.00298 -0.00014 -0.12085; -0.00013 -0.00261 1.00000 0.16334; 0.00298 -0.99999 -0.00261 0.03519; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/T2raw.auto.dat, type = 14 Original Reg -0.99999 -0.00412 0.00195 -0.09845; 0.00196 -0.00295 0.99999 0.18084; 0.00411 -0.99999 -0.00295 0.07552; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00001 -0.00114 0.00209 0.02241; 0.00209 -0.00034 -0.00000 0.01750; 0.00113 0.00000 -0.00035 0.04033; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.129204 Computing change in rh position Surface-RMS-Diff-mm 0.146713 0.053455 0.252195 mri_segreg done MinCost: 0.057654 728.708102 1002.883896 33.132550 tkregister2_cmdl --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/orig/T2raw.mgz --reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/T2raw.auto.dat --noedit --ltaout /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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-06/mri/orig/T2raw.mgz reg file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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 -0.00298 -0.00014 -0.12085; -0.00013 -0.00261 1.00000 0.16334; 0.00298 -0.99999 -0.00261 0.03519; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: loading target /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/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-06/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 -0.00298 -0.00014 -0.12085; -0.00013 -0.00261 1.00000 0.16334; 0.00298 -0.99999 -0.00261 0.03519; 0.00000 0.00000 0.00000 1.00000; Determinant -1 subject = sub-06 RegMat --------------------------- -1.00000 -0.00298 -0.00014 -0.12085; -0.00013 -0.00261 1.00000 0.16334; 0.00298 -0.99999 -0.00261 0.03519; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Tue May 25 22:48:12 UTC 2021 Ended at Tue May 25 22:50:44 UTC 2021 BBR-Run-Time-Sec 152 bbregister Done To check results, run: tkregisterfv --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/orig/T2raw.mgz --reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-06/mri/transforms/T2raw.auto.lta --surfs