Logfile for bbregister Thu Nov 21 15:56:33 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 --t2 $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.7712/template.nii mri_convert.bin pa0292_S004_bis_matrix_new_1_preprocessed_output_crop.nii.gz ./tmp.bbregister.7712/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.7712/template.nii... mri_coreg --s subj01 --mov ./tmp.bbregister.7712/template.nii --regdat ./tmp.bbregister.7712/reg.init.dat --reg ./tmp.bbregister.7712/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.7712/template.nii --regdat ./tmp.bbregister.7712/reg.init.dat --reg ./tmp.bbregister.7712/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.7712/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 12.7 sec OptTimeMin 0.21 min nEvals 438 Final parameters -1.16390514 4.65190411 -94.10931396 -0.62429339 0.15933746 -19.60487747 Final cost -1.002698780091612 --------------------------------- mri_coreg utimesec 53.670087 mri_coreg stimesec 0.147994 mri_coreg ru_maxrss 463020 mri_coreg ru_ixrss 0 mri_coreg ru_idrss 0 mri_coreg ru_isrss 0 mri_coreg ru_minflt 135898 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 35 mri_coreg ru_nivcsw 32 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 53.9 sec To check run: tkregisterfv --mov ./tmp.bbregister.7712/template.nii --targ /data/freesurfer/new_MPRAGE/subj01/mri/brainmask.mgz --reg ./tmp.bbregister.7712/mri_coreg.lta --s subj01 --surfs mri_coreg done mri_segreg --mov ./tmp.bbregister.7712/template.nii --init-reg ./tmp.bbregister.7712/reg.init.dat --out-reg ./tmp.bbregister.7712/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 /data/freesurfer/new_MPRAGE cd /data/freesurfer/new_MPRAGE/fMRI mri_segreg --mov ./tmp.bbregister.7712/template.nii --init-reg ./tmp.bbregister.7712/reg.init.dat --out-reg ./tmp.bbregister.7712/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 an machine x86_64 user an movvol ./tmp.bbregister.7712/template.nii regfile ./tmp.bbregister.7712/reg.init.dat subject subj01 dof 6 outregfile ./tmp.bbregister.7712/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 1574449534 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 1.036873 1 -25.0 -25.0 25.0 0.991037 2 -25.0 25.0 -25.0 1.038009 3 -25.0 25.0 25.0 1.046119 4 25.0 -25.0 -25.0 1.055328 5 25.0 -25.0 25.0 0.999647 6 25.0 25.0 -25.0 1.013084 7 25.0 25.0 25.0 1.005662 REL: 8 0.991477 8.185759 1.023220 rel = 0.968978 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 0.9915 RelCost 0.9690 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 1.0338 1.0338 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 1.0002 1.0002 0.0 6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.9940 0.9940 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.9916 0.9916 0.0 12 -4.0000 -4.0000 -4.0000 0.0000 0.0000 -4.0000 0.9869 0.9869 0.0 21 -4.0000 -4.0000 -4.0000 4.0000 0.0000 -4.0000 0.9753 0.9753 0.0 22 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.0000 0.9611 0.9611 0.0 33 -4.0000 -4.0000 0.0000 -4.0000 4.0000 -4.0000 0.9497 0.9497 0.0 279 0.0000 -4.0000 0.0000 0.0000 -4.0000 -4.0000 0.9454 0.9454 0.0 408 0.0000 4.0000 -4.0000 -4.0000 0.0000 -4.0000 0.9280 0.9280 0.0 Brute Force -------------------------- Min cost was 0.927951 Number of iterations 729 Search time 0.964000 sec Parameters at best (transmm, rotdeg) 0.000 4.000 -4.000 -4.000 0.000 -4.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 4 2 -4 3 -4 4 0 5 -4 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000100 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.927951 5 -0.618 4.000 -4.000 -4.000 0.000 -4.000 0.9235377785 15 -0.617 4.000 -4.000 -4.000 0.000 -4.000 0.9226486425 30 -0.617 4.008 -4.000 -4.000 0.000 -4.000 0.9213403467 40 -0.617 4.008 -3.618 -4.000 0.000 -4.000 0.9128928201 43 -0.617 4.008 -3.528 -4.000 0.000 -4.000 0.9094371080 48 -0.617 4.008 -3.526 -4.000 0.000 -4.000 0.9094285478 50 -0.617 4.008 -3.527 -4.000 0.000 -4.000 0.9094211513 62 -0.617 4.008 -3.527 -4.018 0.000 -4.000 0.9086652087 64 -0.617 4.008 -3.527 -4.017 0.000 -4.000 0.9078280643 85 -0.617 4.008 -3.527 -4.017 0.000 -4.073 0.9070534736 89 -0.617 4.008 -3.527 -4.017 0.000 -4.085 0.9057547583 93 -0.617 4.008 -3.527 -4.017 0.000 -4.083 0.9053115796 94 -0.617 4.008 -3.527 -4.017 0.000 -4.082 0.9050448647 powell nthiter 1: fret = 0.905045 107 -0.606 4.008 -3.527 -4.017 0.000 -4.082 0.9047747390 110 -0.604 4.008 -3.527 -4.017 0.000 -4.082 0.9042729129 112 -0.605 4.008 -3.527 -4.017 0.000 -4.082 0.9041969727 125 -0.605 4.011 -3.527 -4.017 0.000 -4.082 0.9038770319 138 -0.605 4.011 -3.552 -4.017 0.000 -4.082 0.9036731387 139 -0.605 4.011 -3.541 -4.017 0.000 -4.082 0.9010725164 141 -0.605 4.011 -3.545 -4.017 0.000 -4.082 0.9006974039 156 -0.605 4.011 -3.545 -4.012 0.000 -4.082 0.8995727093 powell nthiter 2: fret = 0.899573 Powell done niters = 2 Computing relative cost 0 -25.0 -25.0 -25.0 0.974841 1 -25.0 -25.0 25.0 1.045500 2 -25.0 25.0 -25.0 1.016949 3 -25.0 25.0 25.0 1.042235 4 25.0 -25.0 -25.0 0.972695 5 25.0 -25.0 25.0 1.037888 6 25.0 25.0 -25.0 1.007543 7 25.0 25.0 25.0 1.001550 REL: 8 0.899573 8.099202 1.012400 rel = 0.888554 Number of iterations 2 Min cost was 0.899573 Number of FunctionCalls 281 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.318000 sec Parameters at optimum (transmm) -0.60492 4.01095 -3.54470 Parameters at optimum (rotdeg) -4.01173 0.00000 -4.08195 Final costs ---------------- Number of surface hits 2168 WM Intensity 2.1703 +/- 62.5576 Ctx Intensity 3.0412 +/- 70.2225 Pct Contrast 448.4069 +/- 13581.8472 Cost 0.8996 RelCost 0.9690 Reg at min cost was 0.93705 -0.34135 0.07360 -2.77606; -0.10327 -0.06956 0.99222 -15.60777; 0.33357 0.93736 0.10043 -5.69140; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to ./tmp.bbregister.7712/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 0.00497 0.00582 -0.07082 2.00695; 0.04372 -0.08947 -0.00674 -3.91721; -0.00336 -0.00885 0.06936 2.17009; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 6.784609 Computing change in rh position Surface-RMS-Diff-mm 6.383775 2.184994 12.159040 mri_segreg done mri_segreg --mov ./tmp.bbregister.7712/template.nii --init-reg ./tmp.bbregister.7712/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.7712/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 /data/freesurfer/new_MPRAGE cd /data/freesurfer/new_MPRAGE/fMRI mri_segreg --mov ./tmp.bbregister.7712/template.nii --init-reg ./tmp.bbregister.7712/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.7712/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname an machine x86_64 user an movvol ./tmp.bbregister.7712/template.nii regfile ./tmp.bbregister.7712/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 1574723332 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.93705 -0.34135 0.07360 -2.77606; -0.10327 -0.06956 0.99222 -15.60777; 0.33357 0.93736 0.10043 -5.69140; 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 1.009587 1 -25.0 -25.0 25.0 1.019154 2 -25.0 25.0 -25.0 1.000437 3 -25.0 25.0 25.0 1.029404 4 25.0 -25.0 -25.0 0.996570 5 25.0 -25.0 25.0 1.013790 6 25.0 25.0 -25.0 1.019291 7 25.0 25.0 25.0 0.997010 REL: 8 0.992716 8.085243 1.010655 rel = 0.982249 Initial costs ---------------- Number of surface hits 217062 WM Intensity 1.0207 +/- 66.4680 Ctx Intensity 0.6763 +/- 67.6458 Pct Contrast 0.2042 +/- 37022.6160 Cost 0.9927 RelCost 0.9822 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.9277 0.9277 0.0 11 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.1000 0.9231 0.9231 0.0 20 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 0.1000 0.9125 0.9125 0.0 97 -0.1000 0.0000 -0.1000 0.0000 0.1000 0.0000 0.9089 0.9089 0.0 191 -0.1000 0.1000 0.0000 -0.1000 -0.1000 0.1000 0.9035 0.9035 0.0 200 -0.1000 0.1000 0.0000 0.0000 -0.1000 0.1000 0.9014 0.9014 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.8996 0.8996 0.0 437 0.0000 0.1000 0.0000 -0.1000 0.0000 0.1000 0.8995 0.8995 0.0 446 0.0000 0.1000 0.0000 0.0000 0.0000 0.1000 0.8988 0.8988 0.0 680 0.1000 0.1000 0.0000 -0.1000 0.0000 0.1000 0.8968 0.8968 0.0 Brute Force -------------------------- Min cost was 0.896793 Number of iterations 729 Search time 0.793000 sec Parameters at best (transmm, rotdeg) 0.100 0.100 0.000 -0.100 0.000 0.100 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0.1 1 0.1 2 0 3 -0.1 4 0 5 0.1 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000000 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.991463 2 1.100 0.100 0.000 -0.100 0.000 0.100 0.9892236634 7 0.934 0.100 0.000 -0.100 0.000 0.100 0.9885273524 10 0.960 0.100 0.000 -0.100 0.000 0.100 0.9881859643 19 0.960 -1.518 0.000 -0.100 0.000 0.100 0.9768393282 24 0.960 -1.694 0.000 -0.100 0.000 0.100 0.9766226362 25 0.960 -1.656 0.000 -0.100 0.000 0.100 0.9765878831 28 0.960 -1.652 0.000 -0.100 0.000 0.100 0.9764930207 37 0.960 -1.652 0.382 -0.100 0.000 0.100 0.9759870729 39 0.960 -1.652 0.341 -0.100 0.000 0.100 0.9751066777 41 0.960 -1.652 0.339 -0.100 0.000 0.100 0.9750643231 44 0.960 -1.652 0.338 -0.100 0.000 0.100 0.9750574008 45 0.960 -1.652 0.337 -0.100 0.000 0.100 0.9750529124 77 0.960 -1.652 0.337 -0.100 0.002 0.100 0.9750459816 93 0.960 -1.652 0.337 -0.100 0.002 0.098 0.9750063396 powell nthiter 1: fret = 0.975006 114 0.960 -1.557 0.337 -0.100 0.002 0.098 0.9745597920 116 0.960 -1.563 0.337 -0.100 0.002 0.098 0.9744961475 179 0.960 -1.563 0.337 -0.100 0.002 0.099 0.9744866583 powell nthiter 2: fret = 0.974487 207 0.960 -1.556 0.337 -0.100 0.002 0.099 0.9744373103 240 0.960 -1.556 0.337 -0.105 0.002 0.099 0.9744237161 242 0.960 -1.556 0.337 -0.106 0.002 0.099 0.9743806947 244 0.960 -1.556 0.337 -0.107 0.002 0.099 0.9743663600 272 0.960 -1.556 0.337 -0.107 0.002 0.101 0.9743601040 powell nthiter 3: fret = 0.974360 333 0.960 -1.556 0.337 -0.106 0.002 0.101 0.9743119255 349 0.960 -1.556 0.337 -0.106 0.001 0.101 0.9742451923 powell nthiter 4: fret = 0.974245 Powell done niters = 4 Computing relative cost 0 -25.0 -25.0 -25.0 1.010977 1 -25.0 -25.0 25.0 1.004096 2 -25.0 25.0 -25.0 1.007800 3 -25.0 25.0 25.0 1.021635 4 25.0 -25.0 -25.0 1.009474 5 25.0 -25.0 25.0 1.018382 6 25.0 25.0 -25.0 1.017655 7 25.0 25.0 25.0 0.993856 REL: 8 0.974245 8.083876 1.010484 rel = 0.964137 Number of iterations 4 Min cost was 0.974245 Number of FunctionCalls 456 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 29.506000 sec Parameters at optimum (transmm) 0.95981 -1.55605 0.33749 Parameters at optimum (rotdeg) -0.10595 0.00100 0.10074 Final costs ---------------- Number of surface hits 213655 WM Intensity 0.3418 +/- 66.4362 Ctx Intensity 1.4199 +/- 69.0641 Pct Contrast 311.4196 +/- 106112.3993 Cost 0.9742 RelCost 0.9822 Reg at min cost was 0.93724 -0.34121 0.07185 -1.78888; -0.10100 -0.06843 0.99253 -17.17917; 0.33375 0.93749 0.09859 -5.32500; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to register.dat, type = 14 Original Reg 0.93705 -0.34135 0.07360 -2.77606; -0.10327 -0.06956 0.99222 -15.60777; 0.33357 0.93736 0.10043 -5.69140; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00018 -0.00014 0.00174 -0.98718; -0.00226 -0.00113 -0.00031 1.57140; -0.00017 -0.00013 0.00184 -0.36641; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 1.916261 Computing change in rh position Surface-RMS-Diff-mm 1.865498 0.084069 2.051020 mri_segreg done MinCost: 0.974245 0.341775 1.419948 311.419604 Cleaning up Started at Thu Nov 21 15:56:33 EST 2019 Ended at Thu Nov 21 15:58:12 EST 2019 BBR-Run-Time-Sec 99 bbregister Done To check results, run: tkregisterfv --mov pa0292_S004_bis_matrix_new_1_preprocessed_output_crop.nii.gz --reg register.dat --surfs