Logfile for bbregister Thu Nov 21 15:12:49 EST 2019 setenv SUBJECTS_DIR /data/freesurfer/new_MPRAGE cd /data/freesurfer/new_MPRAGE/fMRI /data/freesurfer/bin/bbregister --mov pa0292_S004_bis_matrix_new_1_preprocessed_output_crop.nii.gz --s subj01 --reg register.dat --t1 $Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $ Linux an 4.15.0-66-generic #75~16.04.1-Ubuntu SMP Tue Oct 1 14:01:08 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /data/freesurfer mri_convert pa0292_S004_bis_matrix_new_1_preprocessed_output_crop.nii.gz ./tmp.bbregister.5872/template.nii mri_convert.bin pa0292_S004_bis_matrix_new_1_preprocessed_output_crop.nii.gz ./tmp.bbregister.5872/template.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from pa0292_S004_bis_matrix_new_1_preprocessed_output_crop.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, -0.983571, -0.180519) k_ras = (0, -0.180519, 0.983571) writing to ./tmp.bbregister.5872/template.nii... mri_coreg --s subj01 --mov ./tmp.bbregister.5872/template.nii --regdat ./tmp.bbregister.5872/reg.init.dat --reg ./tmp.bbregister.5872/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 $Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $ cwd /data/freesurfer/new_MPRAGE/fMRI cmdline mri_coreg --s subj01 --mov ./tmp.bbregister.5872/template.nii --regdat ./tmp.bbregister.5872/reg.init.dat --reg ./tmp.bbregister.5872/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 sysname Linux hostname an machine x86_64 user an 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 ./tmp.bbregister.5872/template.nii Reading in ref /data/freesurfer/new_MPRAGE/subj01/mri/brainmask.mgz Reading in and applying refmask /data/freesurfer/new_MPRAGE/subj01/mri/aparc+aseg.mgz Setting cras translation parameters to align centers Creating random numbers for coordinate dithering Performing intensity dithering Initial parameters -5.5000 7.9323 -75.3923 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 1 movsat = 785.4111 mov gstd 1.6917 1.6917 1.6917 Smoothing mov refsat = 119.0000 ref gstd 1.8914 1.8914 1.8914 Smoothing ref COREGpreproc() done Testing if mov and target overlap Init cost -1.0016336950 nhits = 109816 out of 16777216, Percent Overlap: 41.9 Initial RefRAS-to-MovRAS 1.00000 0.00000 0.00000 -5.50000; 0.00000 1.00000 0.00000 7.93227; 0.00000 0.00000 1.00000 -75.39230; 0.00000 0.00000 0.00000 1.00000; Initial RefVox-to-MovVox 0.50000 0.00000 0.00000 -9.25000; 0.00000 0.09026 -0.49179 105.69458; 0.00000 -0.49179 -0.09026 111.21078; 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 -35.50000 37.93227 -87.39230 2.00000 -8.00000 -20.00000 -1.0176424 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6 Starting OpenPowel2(), sep = 4 InitialCost -1.0016460419 #@# 4 188 -35.50000 37.93227 -87.39230 2.00000 -8.00000 -20.00000 -1.0016460 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.001646 #@# 4 190 -34.50000 37.93227 -87.39230 2.00000 -8.00000 -20.00000 -1.0017091 #@# 4 191 -32.88197 37.93227 -87.39230 2.00000 -8.00000 -20.00000 -1.0017759 #@# 4 192 -31.21396 37.93227 -87.39230 2.00000 -8.00000 -20.00000 -1.0018216 #@# 4 193 -28.78393 37.93227 -87.39230 2.00000 -8.00000 -20.00000 -1.0018293 #@# 4 194 -29.73425 37.93227 -87.39230 2.00000 -8.00000 -20.00000 -1.0018336 #@# 4 205 -29.73425 36.31424 -87.39230 2.00000 -8.00000 -20.00000 -1.0018873 #@# 4 206 -29.73425 33.69621 -87.39230 2.00000 -8.00000 -20.00000 -1.0019592 #@# 4 207 -29.73425 24.92757 -87.39230 2.00000 -8.00000 -20.00000 -1.0019922 #@# 4 210 -29.73425 31.67587 -87.39230 2.00000 -8.00000 -20.00000 -1.0020072 #@# 4 212 -29.73425 31.95787 -87.39230 2.00000 -8.00000 -20.00000 -1.0020169 #@# 4 214 -29.73425 32.22190 -87.39230 2.00000 -8.00000 -20.00000 -1.0020263 #@# 4 226 -29.73425 32.22190 -87.41714 2.00000 -8.00000 -20.00000 -1.0020278 #@# 4 238 -29.73425 32.22190 -87.41714 1.78395 -8.00000 -20.00000 -1.0020294 #@# 4 240 -29.73425 32.22190 -87.41714 1.75864 -8.00000 -20.00000 -1.0020295 #@# 4 244 -29.73425 32.22190 -87.41714 1.76864 -8.00000 -20.00000 -1.0020316 #@# 4 246 -29.73425 32.22190 -87.41714 1.76864 -7.00000 -20.00000 -1.0020400 #@# 4 247 -29.73425 32.22190 -87.41714 1.76864 -5.38197 -20.00000 -1.0020432 #@# 4 250 -29.73425 32.22190 -87.41714 1.76864 -6.53736 -20.00000 -1.0020461 #@# 4 254 -29.73425 32.22190 -87.41714 1.76864 -6.57207 -20.00000 -1.0020508 #@# 4 269 -23.96851 26.51153 -87.44199 1.53729 -5.14414 -20.00000 -1.0021099 #@# 4 272 -14.63934 17.27196 -87.48219 1.16294 -2.83371 -20.00000 -1.0021986 #@# 4 276 -1.32613 4.08662 -87.53955 0.62874 0.46340 -20.00000 -1.0022950 #@# 4 281 -1.77220 4.52841 -87.53763 0.64664 0.35293 -20.00000 -1.0023177 #@# 4 282 -1.82986 4.58551 -87.53738 0.64895 0.33865 -20.00000 -1.0023190 #@# 4 284 -1.89689 4.65190 -87.53709 0.65164 0.32205 -20.00000 -1.0023195 powell nthiter 1: fret = -1.002319 #@# 4 286 -0.89689 4.65190 -87.53709 0.65164 0.32205 -20.00000 -1.0023205 #@# 4 291 -0.66561 4.65190 -87.53709 0.65164 0.32205 -20.00000 -1.0023222 #@# 4 292 -0.64054 4.65190 -87.53709 0.65164 0.32205 -20.00000 -1.0023242 #@# 4 294 -0.58755 4.65190 -87.53709 0.65164 0.32205 -20.00000 -1.0023249 #@# 4 295 -0.60622 4.65190 -87.53709 0.65164 0.32205 -20.00000 -1.0023253 #@# 4 296 -0.61622 4.65190 -87.53709 0.65164 0.32205 -20.00000 -1.0023263 #@# 4 303 -0.61622 4.65190 -87.53709 0.65164 0.32205 -19.61803 -1.0023273 #@# 4 310 -0.61622 4.65190 -87.53709 0.65164 0.32205 -19.60488 -1.0023274 #@# 4 314 -0.61622 4.65190 -89.15512 0.65164 0.32205 -19.60488 -1.0024000 #@# 4 315 -0.61622 4.65190 -91.77316 0.65164 0.32205 -19.60488 -1.0025277 #@# 4 316 -0.61622 4.65190 -96.00922 0.65164 0.32205 -19.60488 -1.0025502 #@# 4 317 -0.61622 4.65190 -94.31071 0.65164 0.32205 -19.60488 -1.0025666 #@# 4 319 -0.61622 4.65190 -93.34145 0.65164 0.32205 -19.60488 -1.0025984 #@# 4 323 -0.61622 4.65190 -93.42725 0.65164 0.32205 -19.60488 -1.0026040 #@# 4 330 -0.61622 4.65190 -93.42725 -0.96639 0.32205 -19.60488 -1.0026494 #@# 4 335 -0.61622 4.65190 -93.42725 -0.34836 0.32205 -19.60488 -1.0026574 #@# 4 337 -0.61622 4.65190 -93.42725 -0.59625 0.32205 -19.60488 -1.0026705 #@# 4 338 -0.61622 4.65190 -93.42725 -0.62104 0.32205 -19.60488 -1.0026729 #@# 4 340 -0.61622 4.65190 -93.42725 -0.66229 0.32205 -19.60488 -1.0026749 #@# 4 349 -0.61622 4.65190 -93.42725 -0.66229 0.13864 -19.60488 -1.0026829 #@# 4 351 -0.61622 4.65190 -93.42725 -0.66229 0.16934 -19.60488 -1.0026832 #@# 4 352 -0.61622 4.65190 -93.42725 -0.66229 0.15934 -19.60488 -1.0026853 powell nthiter 2: fret = -1.002685 #@# 4 371 -1.23425 4.65190 -93.42725 -0.66229 0.15934 -19.60488 -1.0026871 #@# 4 373 -1.15391 4.65190 -93.42725 -0.66229 0.15934 -19.60488 -1.0026881 #@# 4 378 -1.16391 4.65190 -93.42725 -0.66229 0.15934 -19.60488 -1.0026901 #@# 4 395 -1.16391 4.65190 -94.04528 -0.66229 0.15934 -19.60488 -1.0026928 #@# 4 398 -1.16391 4.65190 -94.08119 -0.66229 0.15934 -19.60488 -1.0026950 #@# 4 401 -1.16391 4.65190 -94.09931 -0.66229 0.15934 -19.60488 -1.0026953 #@# 4 402 -1.16391 4.65190 -94.10931 -0.66229 0.15934 -19.60488 -1.0026963 #@# 4 413 -1.16391 4.65190 -94.10931 -0.60766 0.15934 -19.60488 -1.0026982 #@# 4 415 -1.16391 4.65190 -94.10931 -0.62429 0.15934 -19.60488 -1.0026988 Powell done niters total = 2 OptTimeSec 13.1 sec OptTimeMin 0.22 min nEvals 438 Final parameters -1.16390514 4.65190411 -94.10931396 -0.62429339 0.15933746 -19.60487747 Final cost -1.002698780091612 --------------------------------- mri_coreg utimesec 56.867486 mri_coreg stimesec 0.167951 mri_coreg ru_maxrss 463020 mri_coreg ru_ixrss 0 mri_coreg ru_idrss 0 mri_coreg ru_isrss 0 mri_coreg ru_minflt 135895 mri_coreg ru_majflt 0 mri_coreg ru_nswap 0 mri_coreg ru_inblock 0 mri_coreg ru_oublock 16 mri_coreg ru_msgsnd 0 mri_coreg ru_msgrcv 0 mri_coreg ru_nsignals 0 mri_coreg ru_nvcsw 36 mri_coreg ru_nivcsw 395 Final RefRAS-to-MovRAS 0.94203 -0.33553 0.00278 -1.16391; 0.33554 0.94196 -0.01090 4.65190; 0.00104 0.01120 0.99994 -94.10931; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox 0.47101 0.00139 0.16777 -26.55700; 0.16511 0.08490 -0.46425 84.18485; 0.02978 -0.49274 -0.07951 97.17450; 0.00000 0.00000 0.00000 1.00000; Final parameters -1.1639 4.6519 -94.1093 -0.6243 0.1593 -19.6049 nhits = 108006 out of 16777216, Percent Overlap: 41.2 mri_coreg RunTimeSec 57.1 sec To check run: tkregisterfv --mov ./tmp.bbregister.5872/template.nii --targ /data/freesurfer/new_MPRAGE/subj01/mri/brainmask.mgz --reg ./tmp.bbregister.5872/mri_coreg.lta --s subj01 --surfs mri_coreg done mri_segreg --mov ./tmp.bbregister.5872/template.nii --init-reg ./tmp.bbregister.5872/reg.init.dat --out-reg ./tmp.bbregister.5872/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 --wm-gt-gm 0.5 $Id: mri_segreg.c,v 1.113 2016/05/10 03:23:20 greve Exp $ setenv SUBJECTS_DIR /data/freesurfer/new_MPRAGE cd /data/freesurfer/new_MPRAGE/fMRI mri_segreg --mov ./tmp.bbregister.5872/template.nii --init-reg ./tmp.bbregister.5872/reg.init.dat --out-reg ./tmp.bbregister.5872/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 --wm-gt-gm 0.5 sysname Linux hostname an machine x86_64 user an movvol ./tmp.bbregister.5872/template.nii regfile ./tmp.bbregister.5872/reg.init.dat subject subj01 dof 6 outregfile ./tmp.bbregister.5872/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 1574883162 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.94203 -0.33553 0.00278 -0.76910; -0.05955 -0.15903 0.98548 -19.52498; 0.33021 0.92851 0.16979 -3.52132; 0.00000 0.00000 0.00000 1.00000; Loading mov Extracting frame 0 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 0.963127 1 -25.0 -25.0 25.0 1.008963 2 -25.0 25.0 -25.0 0.961991 3 -25.0 25.0 25.0 0.953881 4 25.0 -25.0 -25.0 0.944672 5 25.0 -25.0 25.0 1.000353 6 25.0 25.0 -25.0 0.986916 7 25.0 25.0 25.0 0.994338 REL: 8 1.008523 7.814241 0.976780 rel = 1.0325 Initial costs ---------------- Number of surface hits 2191 WM Intensity 1.7577 +/- 66.1025 Ctx Intensity 1.5275 +/- 69.5355 Pct Contrast 74.0066 +/- 3976.4440 Cost 1.0085 RelCost 1.0325 WARNING: initial G-W contrast is positive, but expecting negative. If the mov data has a T2 contrast, re-run with --T2 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9662 0.9662 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.9642 0.9642 0.0 24 -4.0000 -4.0000 -4.0000 4.0000 4.0000 -4.0000 0.9580 0.9580 0.0 26 -4.0000 -4.0000 -4.0000 4.0000 4.0000 4.0000 0.9406 0.9406 0.0 53 -4.0000 -4.0000 0.0000 4.0000 4.0000 4.0000 0.9182 0.9182 0.0 Brute Force -------------------------- Min cost was 0.918200 Number of iterations 729 Search time 0.797000 sec Parameters at best (transmm, rotdeg) -4.000 -4.000 0.000 4.000 4.000 4.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 -4 1 -4 2 0 3 4 4 4 5 4 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000100 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.918200 23 -4.000 -4.136 0.000 4.000 4.000 4.000 0.9086565550 25 -4.000 -4.174 0.000 4.000 4.000 4.000 0.9017809508 43 -4.000 -4.174 -0.016 4.000 4.000 4.000 0.8998735666 45 -4.000 -4.174 -0.017 4.000 4.000 4.000 0.8998562219 46 -4.000 -4.174 -0.018 4.000 4.000 4.000 0.8998483820 47 -4.000 -4.174 -0.019 4.000 4.000 4.000 0.8982062172 49 -4.000 -4.174 -0.020 4.000 4.000 4.000 0.8976082902 60 -4.000 -4.174 -0.020 4.015 4.000 4.000 0.8946780831 61 -4.000 -4.174 -0.020 4.019 4.000 4.000 0.8934758960 78 -4.000 -4.174 -0.020 4.019 4.002 4.000 0.8934489671 79 -4.000 -4.174 -0.020 4.019 4.003 4.000 0.8925697608 94 -4.000 -4.174 -0.020 4.019 4.003 4.001 0.8924824886 powell nthiter 1: fret = 0.892482 107 -3.998 -4.174 -0.020 4.019 4.003 4.001 0.8920948463 108 -3.997 -4.174 -0.020 4.019 4.003 4.001 0.8914839940 powell nthiter 2: fret = 0.891484 Powell done niters = 2 Computing relative cost 0 -25.0 -25.0 -25.0 0.983715 1 -25.0 -25.0 25.0 0.974800 2 -25.0 25.0 -25.0 0.979868 3 -25.0 25.0 25.0 0.981657 4 25.0 -25.0 -25.0 0.961551 5 25.0 -25.0 25.0 0.971912 6 25.0 25.0 -25.0 0.989047 7 25.0 25.0 25.0 1.015183 REL: 8 0.891484 7.857733 0.982217 rel = 0.907625 Number of iterations 2 Min cost was 0.891484 Number of FunctionCalls 269 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.312000 sec Parameters at optimum (transmm) -3.99651 -4.17383 -0.01956 Parameters at optimum (rotdeg) 4.01907 4.00253 4.00100 Final costs ---------------- Number of surface hits 2170 WM Intensity 0.5405 +/- 71.3605 Ctx Intensity -0.3895 +/- 68.1213 Pct Contrast -609.5490 +/- 11148.1948 Cost 0.8915 RelCost 1.0325 Reg at min cost was 0.96584 -0.25457 -0.04839 -3.75998; -0.01520 -0.24207 0.97014 -23.43443; 0.25868 0.93627 0.23767 -4.83511; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to ./tmp.bbregister.5872/bbr.pass1.dat, type = 14 Original Reg 0.94203 -0.33553 0.00278 -0.76910; -0.05955 -0.15903 0.98548 -19.52498; 0.33021 0.92851 0.16979 -3.52132; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.02382 -0.08096 0.05117 2.99088; -0.04436 0.08304 0.01534 3.90945; 0.07153 -0.00776 -0.06788 1.31379; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 9.634814 Computing change in rh position Surface-RMS-Diff-mm 8.668209 1.983774 12.927540 WARNING: initial G-W contrast was positive, but expected negative. If the mov data has a T2 contrast, re-run with --T2 mri_segreg done mri_segreg --mov ./tmp.bbregister.5872/template.nii --init-reg ./tmp.bbregister.5872/bbr.pass1.dat --out-reg register.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost register.dat.mincost --dof 6 --nmax 36 --param register.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg ./tmp.bbregister.5872/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --wm-gt-gm 0.5 $Id: mri_segreg.c,v 1.113 2016/05/10 03:23:20 greve Exp $ setenv SUBJECTS_DIR /data/freesurfer/new_MPRAGE cd /data/freesurfer/new_MPRAGE/fMRI mri_segreg --mov ./tmp.bbregister.5872/template.nii --init-reg ./tmp.bbregister.5872/bbr.pass1.dat --out-reg register.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost register.dat.mincost --dof 6 --nmax 36 --param register.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg ./tmp.bbregister.5872/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --wm-gt-gm 0.5 sysname Linux hostname an machine x86_64 user an movvol ./tmp.bbregister.5872/template.nii regfile ./tmp.bbregister.5872/bbr.pass1.dat subject subj01 dof 6 outregfile register.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 1575049146 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.96584 -0.25457 -0.04839 -3.75998; -0.01520 -0.24207 0.97014 -23.43443; 0.25868 0.93627 0.23767 -4.83511; 0.00000 0.00000 0.00000 1.00000; Loading mov Extracting frame 0 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 0.974206 1 -25.0 -25.0 25.0 0.991062 2 -25.0 25.0 -25.0 0.989707 3 -25.0 25.0 25.0 0.986763 4 25.0 -25.0 -25.0 0.981931 5 25.0 -25.0 25.0 0.975738 6 25.0 25.0 -25.0 0.991439 7 25.0 25.0 25.0 0.995398 REL: 8 0.988078 7.886244 0.985781 rel = 1.00233 Initial costs ---------------- Number of surface hits 220921 WM Intensity 0.9388 +/- 70.9162 Ctx Intensity 1.1746 +/- 70.5053 Pct Contrast 136.6612 +/- 102160.5385 Cost 0.9881 RelCost 1.0023 WARNING: initial G-W contrast is positive, but expecting negative. If the mov data has a T2 contrast, re-run with --T2 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.9382 0.9382 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.9330 0.9330 0.0 5 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1000 0.9292 0.9292 0.0 7 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.0000 0.9226 0.9226 0.0 19 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 0.0000 0.9220 0.9220 0.0 20 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 0.1000 0.9164 0.9164 0.0 23 -0.1000 -0.1000 -0.1000 0.1000 0.0000 0.1000 0.9162 0.9162 0.0 37 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.0000 0.9140 0.9140 0.0 113 -0.1000 0.0000 0.0000 -0.1000 0.0000 0.1000 0.9105 0.9105 0.0 266 0.0000 -0.1000 -0.1000 0.1000 0.0000 0.1000 0.9070 0.9070 0.0 346 0.0000 0.0000 -0.1000 0.1000 0.0000 0.0000 0.9029 0.9029 0.0 356 0.0000 0.0000 0.0000 -0.1000 0.0000 0.1000 0.9013 0.9013 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.8915 0.8915 0.0 Brute Force -------------------------- Min cost was 0.891484 Number of iterations 729 Search time 0.924000 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 = 0.988078 10 0.002 0.000 0.000 0.000 0.000 0.000 0.9880736799 16 0.002 -1.618 0.000 0.000 0.000 0.000 0.9852442208 17 0.002 -1.278 0.000 0.000 0.000 0.000 0.9827634469 24 0.002 -1.275 0.000 0.000 0.000 0.000 0.9827303156 25 0.002 -1.268 0.000 0.000 0.000 0.000 0.9825352395 29 0.002 -1.270 0.000 0.000 0.000 0.000 0.9825342218 30 0.002 -1.271 0.000 0.000 0.000 0.000 0.9825064784 34 0.002 -1.271 -1.618 0.000 0.000 0.000 0.9770265001 38 0.002 -1.271 -2.618 0.000 0.000 0.000 0.9736306302 39 0.002 -1.271 -3.236 0.000 0.000 0.000 0.9730059008 41 0.002 -1.271 -2.958 0.000 0.000 0.000 0.9718082691 42 0.002 -1.271 -2.972 0.000 0.000 0.000 0.9713556978 43 0.002 -1.271 -3.081 0.000 0.000 0.000 0.9712694558 45 0.002 -1.271 -3.028 0.000 0.000 0.000 0.9705964932 49 0.002 -1.271 -3.024 0.000 0.000 0.000 0.9704503197 50 0.002 -1.271 -3.025 0.000 0.000 0.000 0.9704272547 51 0.002 -1.271 -3.026 0.000 0.000 0.000 0.9704098364 68 0.002 -1.271 -3.026 0.002 0.000 0.000 0.9703511308 80 0.002 -1.271 -3.026 0.002 -0.013 0.000 0.9701141590 82 0.002 -1.271 -3.026 0.002 -0.009 0.000 0.9699027647 powell nthiter 1: fret = 0.969903 Powell done niters = 1 Computing relative cost 0 -25.0 -25.0 -25.0 0.979165 1 -25.0 -25.0 25.0 1.002296 2 -25.0 25.0 -25.0 0.988417 3 -25.0 25.0 25.0 0.986801 4 25.0 -25.0 -25.0 0.986063 5 25.0 -25.0 25.0 0.992788 6 25.0 25.0 -25.0 0.988774 7 25.0 25.0 25.0 0.995498 REL: 8 0.969903 7.919803 0.989975 rel = 0.979724 Number of iterations 1 Min cost was 0.969903 Number of FunctionCalls 193 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 12.420000 sec Parameters at optimum (transmm) 0.00177 -1.27118 -3.02595 Parameters at optimum (rotdeg) 0.00152 -0.00884 0.00000 Final costs ---------------- Number of surface hits 219282 WM Intensity 1.1713 +/- 72.3166 Ctx Intensity 1.2420 +/- 71.4819 Pct Contrast -662.4825 +/- 249711.1626 Cost 0.9699 RelCost 1.0023 Reg at min cost was 0.96580 -0.25471 -0.04843 -3.75747; -0.01520 -0.24209 0.97013 -24.70548; 0.25883 0.93622 0.23769 -7.86226; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to register.dat, type = 14 Original Reg 0.96584 -0.25457 -0.04839 -3.75998; -0.01520 -0.24207 0.97014 -23.43443; 0.25868 0.93627 0.23767 -4.83511; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00004 0.00014 0.00004 -0.00251; 0.00001 0.00002 0.00001 1.27106; -0.00015 0.00005 -0.00002 3.02715; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 3.285258 Computing change in rh position Surface-RMS-Diff-mm 3.281485 0.004695 3.291151 WARNING: initial G-W contrast was positive, but expected negative. If the mov data has a T2 contrast, re-run with --T2 mri_segreg done MinCost: 0.969903 1.171304 1.242019 -662.482460 Cleaning up Started at Thu Nov 21 15:12:49 EST 2019 Ended at Thu Nov 21 15:14:14 EST 2019 BBR-Run-Time-Sec 85 bbregister Done To check results, run: tkregisterfv --mov pa0292_S004_bis_matrix_new_1_preprocessed_output_crop.nii.gz --reg register.dat --surfs