Logfile for bbregister Tue Sep 10 18:31:50 EDT 2019 setenv SUBJECTS_DIR /media/sda1/nmrclass/tutorial_data/buckner_data/tutorial_subjs cd /media/sda1/nmrclass/tutorial_data_Sep_2019_rev3/buckner_data/tutorial_subjs/multimodal/fmri/fbirn-101 /media/sda1/nmrclass/freesurfer/bin/bbregister --mov template.nii --bold --s fbirn-anat-101.v6 --lta register.lta $Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $ Linux fsuser3-G5-5587 4.15.0-47-generic #50-Ubuntu SMP Wed Mar 13 10:44:52 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /media/sda1/nmrclass/freesurfer mri_convert template.nii ./tmp.bbregister.9147/template.nii mri_convert.bin template.nii ./tmp.bbregister.9147/template.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from template.nii... TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.9973, -0.0712038, 0.0179835) j_ras = (0.0625429, -0.951817, -0.300222) k_ras = (0.038494, -0.298286, 0.9537) writing to ./tmp.bbregister.9147/template.nii... mri_coreg --s fbirn-anat-101.v6 --mov ./tmp.bbregister.9147/template.nii --regdat ./tmp.bbregister.9147/reg.init.dat --reg ./tmp.bbregister.9147/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 /media/sda1/nmrclass/tutorial_data_Sep_2019_rev3/buckner_data/tutorial_subjs/multimodal/fmri/fbirn-101 cmdline mri_coreg --s fbirn-anat-101.v6 --mov ./tmp.bbregister.9147/template.nii --regdat ./tmp.bbregister.9147/reg.init.dat --reg ./tmp.bbregister.9147/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass 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.9147/template.nii Reading in ref /media/sda1/nmrclass/tutorial_data/buckner_data/tutorial_subjs/fbirn-anat-101.v6/mri/brainmask.mgz Reading in and applying refmask /media/sda1/nmrclass/tutorial_data/buckner_data/tutorial_subjs/fbirn-anat-101.v6/mri/aparc+aseg.mgz Setting cras translation parameters to align centers Creating random numbers for coordinate dithering Performing intensity dithering Initial parameters 2.6420 4.4712 2.8057 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 = 9188.3330 mov gstd 0.9989 0.9989 0.0000 Smoothing mov refsat = 120.0000 ref gstd 1.8914 1.8914 1.8914 Smoothing ref COREGpreproc() done Testing if mov and target overlap Init cost -1.0219510155 nhits = 99666 out of 16777216, Percent Overlap: 38.0 Initial RefRAS-to-MovRAS 1.00000 0.00000 0.00000 2.64198; 0.00000 1.00000 0.00000 4.47124; 0.00000 0.00000 1.00000 2.80568; 0.00000 0.00000 0.00000 1.00000; Initial RefVox-to-MovVox 0.29012 -0.00523 -0.02071 -2.18271; -0.01819 0.08734 -0.27689 57.98804; -0.00962 -0.23842 -0.07457 58.13406; 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 4.64198 -7.52876 -27.19432 -12.00000 0.00000 0.00000 -1.0474506 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6 Starting OpenPowel2(), sep = 4 InitialCost -1.0646710396 #@# 4 188 4.64198 -7.52876 -27.19432 -12.00000 0.00000 0.00000 -1.0646710 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.064671 #@# 4 195 4.37555 -7.52876 -27.19432 -12.00000 0.00000 0.00000 -1.0646974 #@# 4 196 4.36555 -7.52876 -27.19432 -12.00000 0.00000 0.00000 -1.0646975 #@# 4 199 4.36555 -6.52876 -27.19432 -12.00000 0.00000 0.00000 -1.0648546 #@# 4 206 4.36555 -6.43440 -27.19432 -12.00000 0.00000 0.00000 -1.0648577 #@# 4 213 4.36555 -6.43440 -28.81236 -12.00000 0.00000 0.00000 -1.0681227 #@# 4 217 4.36555 -6.43440 -31.81884 -12.00000 0.00000 0.00000 -1.0718377 #@# 4 218 4.36555 -6.43440 -32.09125 -12.00000 0.00000 0.00000 -1.0718416 #@# 4 219 4.36555 -6.43440 -31.97443 -12.00000 0.00000 0.00000 -1.0718496 #@# 4 225 4.36555 -6.43440 -31.97443 -13.61803 0.00000 0.00000 -1.0738093 #@# 4 229 4.36555 -6.43440 -31.97443 -14.77059 0.00000 0.00000 -1.0743724 #@# 4 231 4.36555 -6.43440 -31.97443 -14.75690 0.00000 0.00000 -1.0743725 #@# 4 232 4.36555 -6.43440 -31.97443 -14.74690 0.00000 0.00000 -1.0743738 #@# 4 235 4.36555 -6.43440 -31.97443 -14.68400 0.00000 0.00000 -1.0743761 #@# 4 240 4.36555 -6.43440 -31.97443 -14.68400 1.00000 0.00000 -1.0745554 #@# 4 244 4.36555 -6.43440 -31.97443 -14.68400 0.61803 0.00000 -1.0745734 powell nthiter 1: fret = -1.074573 #@# 4 268 3.74751 -6.43440 -31.97443 -14.68400 0.61803 0.00000 -1.0746535 #@# 4 270 3.97154 -6.43440 -31.97443 -14.68400 0.61803 0.00000 -1.0746973 #@# 4 274 3.93151 -6.43440 -31.97443 -14.68400 0.61803 0.00000 -1.0746977 #@# 4 283 3.93151 -6.33797 -31.97443 -14.68400 0.61803 0.00000 -1.0747054 #@# 4 285 3.93151 -6.35450 -31.97443 -14.68400 0.61803 0.00000 -1.0747061 #@# 4 292 3.93151 -6.35450 -32.59246 -14.68400 0.61803 0.00000 -1.0750079 #@# 4 294 3.93151 -6.35450 -32.73393 -14.68400 0.61803 0.00000 -1.0750282 #@# 4 301 3.93151 -6.35450 -32.73393 -15.30203 0.61803 0.00000 -1.0751196 #@# 4 304 3.93151 -6.35450 -32.73393 -15.26493 0.61803 0.00000 -1.0751244 #@# 4 308 3.93151 -6.35450 -32.73393 -15.26493 1.61803 0.00000 -1.0753504 #@# 4 313 3.93151 -6.35450 -32.73393 -15.26493 1.42856 0.00000 -1.0753710 #@# 4 324 3.93151 -6.35450 -32.73393 -15.26493 1.42856 -0.15504 -1.0753804 #@# 4 326 3.93151 -6.35450 -32.73393 -15.26493 1.42856 -0.12375 -1.0753815 powell nthiter 2: fret = -1.075382 #@# 4 338 3.64816 -6.35450 -32.73393 -15.26493 1.42856 -0.13394 -1.0754611 #@# 4 340 3.65816 -6.35450 -32.73393 -15.26493 1.42856 -0.13394 -1.0754617 #@# 4 349 3.65816 -5.97253 -32.73393 -15.26493 1.42856 -0.13394 -1.0754925 #@# 4 350 3.65816 -6.09407 -32.73393 -15.26493 1.42856 -0.13394 -1.0754931 #@# 4 351 3.65816 -6.04078 -32.73393 -15.26493 1.42856 -0.13394 -1.0754975 #@# 4 352 3.65816 -6.03078 -32.73393 -15.26493 1.42856 -0.13394 -1.0754987 #@# 4 361 3.65816 -6.03078 -32.89619 -15.26493 1.42856 -0.13394 -1.0755194 #@# 4 374 3.65816 -6.03078 -32.89619 -15.34426 1.42856 -0.13394 -1.0755213 #@# 4 383 3.65816 -6.03078 -32.89619 -15.34426 1.81053 -0.13394 -1.0755492 #@# 4 384 3.65816 -6.03078 -32.89619 -15.34426 1.70963 -0.13394 -1.0755496 #@# 4 385 3.65816 -6.03078 -32.89619 -15.34426 1.75357 -0.13394 -1.0755532 #@# 4 387 3.65816 -6.03078 -32.89619 -15.34426 1.73933 -0.13394 -1.0755546 #@# 4 395 3.65816 -6.03078 -32.89619 -15.34426 1.73933 -0.05832 -1.0755554 #@# 4 396 3.65816 -6.03078 -32.89619 -15.34426 1.73933 -0.07556 -1.0755566 #@# 4 397 3.65816 -6.03078 -32.89619 -15.34426 1.73933 -0.09211 -1.0755575 powell nthiter 3: fret = -1.075557 #@# 4 406 3.50882 -6.03078 -32.89619 -15.34426 1.73933 -0.09211 -1.0755762 #@# 4 407 3.51882 -6.03078 -32.89619 -15.34426 1.73933 -0.09211 -1.0755763 #@# 4 415 3.51882 -6.04078 -32.89619 -15.34426 1.73933 -0.09211 -1.0755774 #@# 4 429 3.51882 -6.04078 -32.88539 -15.34426 1.73933 -0.09211 -1.0755796 #@# 4 446 3.51882 -6.04078 -32.88539 -15.34426 1.90300 -0.09211 -1.0755804 #@# 4 447 3.51882 -6.04078 -32.88539 -15.34426 1.84210 -0.09211 -1.0755812 #@# 4 457 3.51882 -6.04078 -32.88539 -15.34426 1.84210 0.03080 -1.0755816 #@# 4 458 3.51882 -6.04078 -32.88539 -15.34426 1.84210 -0.02186 -1.0755818 #@# 4 461 3.51882 -6.04078 -32.88539 -15.34426 1.84210 -0.03211 -1.0755820 Powell done niters total = 3 OptTimeSec 11.2 sec OptTimeMin 0.19 min nEvals 461 Final parameters 3.51882076 -6.04077721 -32.88538742 -15.34426022 1.84209991 -0.03211052 Final cost -1.075582031551656 --------------------------------- mri_coreg utimesec 51.358970 mri_coreg stimesec 0.119997 mri_coreg ru_maxrss 424528 mri_coreg ru_ixrss 0 mri_coreg ru_idrss 0 mri_coreg ru_isrss 0 mri_coreg ru_minflt 125539 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 0 mri_coreg ru_nivcsw 28 Final RefRAS-to-MovRAS 0.99948 -0.00056 0.03215 3.51882; 0.00905 0.96435 -0.26448 -6.04078; -0.03085 0.26464 0.96385 -32.88539; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox 0.29032 -0.00119 -0.01843 -3.24076; -0.01837 0.01036 -0.29014 75.60376; -0.00159 -0.24984 -0.00882 42.43341; 0.00000 0.00000 0.00000 1.00000; Final parameters 3.5188 -6.0408 -32.8854 -15.3443 1.8421 -0.0321 nhits = 99025 out of 16777216, Percent Overlap: 37.8 mri_coreg RunTimeSec 51.5 sec To check run: tkregisterfv --mov ./tmp.bbregister.9147/template.nii --targ /media/sda1/nmrclass/tutorial_data/buckner_data/tutorial_subjs/fbirn-anat-101.v6/mri/brainmask.mgz --reg ./tmp.bbregister.9147/mri_coreg.lta --s fbirn-anat-101.v6 --surfs mri_coreg done mri_segreg --mov ./tmp.bbregister.9147/template.nii --init-reg ./tmp.bbregister.9147/reg.init.dat --out-reg ./tmp.bbregister.9147/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 /media/sda1/nmrclass/tutorial_data/buckner_data/tutorial_subjs cd /media/sda1/nmrclass/tutorial_data_Sep_2019_rev3/buckner_data/tutorial_subjs/multimodal/fmri/fbirn-101 mri_segreg --mov ./tmp.bbregister.9147/template.nii --init-reg ./tmp.bbregister.9147/reg.init.dat --out-reg ./tmp.bbregister.9147/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 fsuser3-G5-5587 machine x86_64 user nmrclass movvol ./tmp.bbregister.9147/template.nii regfile ./tmp.bbregister.9147/reg.init.dat subject fbirn-anat-101.v6 dof 6 outregfile ./tmp.bbregister.9147/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 1568518980 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99798 0.06335 -0.00411 2.03254; 0.00635 -0.03529 0.99936 -33.51446; -0.06316 0.99737 0.03562 -18.69974; 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 1.061064 1 -25.0 -25.0 25.0 1.058317 2 -25.0 25.0 -25.0 1.051092 3 -25.0 25.0 25.0 1.080429 4 25.0 -25.0 -25.0 1.101676 5 25.0 -25.0 25.0 1.065998 6 25.0 25.0 -25.0 1.035197 7 25.0 25.0 25.0 1.063983 REL: 8 0.641948 8.517755 1.064719 rel = 0.602927 Initial costs ---------------- Number of surface hits 3116 WM Intensity 5593.9856 +/- 863.8422 Ctx Intensity 5715.9534 +/- 1063.5233 Pct Contrast 1.4123 +/- 15.7364 Cost 0.6419 RelCost 0.6029 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 1.1213 1.1213 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 1.1016 1.1016 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 1.0455 1.0455 0.0 5 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 4.0000 1.0340 1.0340 0.0 6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.9820 0.9820 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.9759 0.9759 0.0 34 -4.0000 -4.0000 0.0000 -4.0000 4.0000 0.0000 0.9726 0.9726 0.0 39 -4.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.9412 0.9412 0.0 61 -4.0000 -4.0000 4.0000 -4.0000 4.0000 0.0000 0.9387 0.9387 0.0 117 -4.0000 0.0000 0.0000 0.0000 -4.0000 -4.0000 0.9154 0.9154 0.0 120 -4.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.9034 0.9034 0.0 282 0.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.8676 0.8676 0.0 283 0.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.8211 0.8211 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.6419 0.6419 0.0 Brute Force -------------------------- Min cost was 0.641948 Number of iterations 729 Search time 0.772000 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 = 0.641948 7 -0.120 0.000 0.000 0.000 0.000 0.000 0.6412679660 8 -0.154 0.000 0.000 0.000 0.000 0.000 0.6411270499 13 -0.164 0.000 0.000 0.000 0.000 0.000 0.6411258264 15 -0.160 0.000 0.000 0.000 0.000 0.000 0.6411236695 20 -0.160 -1.618 0.000 0.000 0.000 0.000 0.6317669894 21 -0.160 -0.930 0.000 0.000 0.000 0.000 0.6168585078 25 -0.160 -0.819 0.000 0.000 0.000 0.000 0.6163175397 26 -0.160 -0.811 0.000 0.000 0.000 0.000 0.6163103158 27 -0.160 -0.800 0.000 0.000 0.000 0.000 0.6162987967 31 -0.160 -0.797 0.000 0.000 0.000 0.000 0.6162941050 32 -0.160 -0.795 0.000 0.000 0.000 0.000 0.6162928970 34 -0.160 -0.796 0.000 0.000 0.000 0.000 0.6162926463 42 -0.160 -0.796 0.092 0.000 0.000 0.000 0.6159561440 45 -0.160 -0.796 0.090 0.000 0.000 0.000 0.6159557547 47 -0.160 -0.796 0.088 0.000 0.000 0.000 0.6159557099 55 -0.160 -0.796 0.088 0.167 0.000 0.000 0.6151476070 56 -0.160 -0.796 0.088 0.164 0.000 0.000 0.6151404831 58 -0.160 -0.796 0.088 0.155 0.000 0.000 0.6151296952 59 -0.160 -0.796 0.088 0.153 0.000 0.000 0.6151293685 61 -0.160 -0.796 0.088 0.152 0.000 0.000 0.6151293603 70 -0.160 -0.796 0.088 0.152 -0.096 0.000 0.6148195329 72 -0.160 -0.796 0.088 0.152 -0.077 0.000 0.6147862184 74 -0.160 -0.796 0.088 0.152 -0.073 0.000 0.6147833932 77 -0.160 -0.796 0.088 0.152 -0.072 0.000 0.6147833328 85 -0.160 -0.796 0.088 0.152 -0.072 -0.253 0.6139427690 86 -0.160 -0.796 0.088 0.152 -0.072 -0.220 0.6138703844 87 -0.160 -0.796 0.088 0.152 -0.072 -0.193 0.6137521935 88 -0.160 -0.796 0.088 0.152 -0.072 -0.119 0.6136906359 89 -0.160 -0.796 0.088 0.152 -0.072 -0.145 0.6136191704 90 -0.160 -0.796 0.088 0.152 -0.072 -0.151 0.6136148951 100 -0.169 -0.843 0.093 0.160 -0.076 -0.160 0.6135198692 102 -0.167 -0.828 0.092 0.158 -0.075 -0.157 0.6134930019 104 -0.166 -0.828 0.092 0.158 -0.074 -0.157 0.6134929847 powell nthiter 1: fret = 0.613493 114 -0.173 -0.828 0.092 0.158 -0.074 -0.157 0.6134877920 116 -0.177 -0.828 0.092 0.158 -0.074 -0.157 0.6134872974 127 -0.175 -0.828 0.092 0.158 -0.074 -0.186 0.6134764691 128 -0.175 -0.828 0.092 0.158 -0.074 -0.174 0.6134587671 130 -0.175 -0.828 0.092 0.158 -0.074 -0.175 0.6134584829 141 -0.175 -0.828 0.024 0.158 -0.074 -0.175 0.6133459438 142 -0.175 -0.828 0.034 0.158 -0.074 -0.175 0.6133227154 143 -0.175 -0.828 0.046 0.158 -0.074 -0.175 0.6133199823 144 -0.175 -0.828 0.041 0.158 -0.074 -0.175 0.6133123788 145 -0.175 -0.828 0.040 0.158 -0.074 -0.175 0.6133120376 154 -0.175 -0.828 0.040 0.152 -0.074 -0.175 0.6133050939 155 -0.175 -0.828 0.040 0.149 -0.074 -0.175 0.6133048340 157 -0.175 -0.828 0.040 0.150 -0.074 -0.175 0.6133048215 167 -0.175 -0.828 0.040 0.150 -0.078 -0.175 0.6133025800 168 -0.175 -0.828 0.040 0.150 -0.079 -0.175 0.6133022515 179 -0.176 -0.836 0.041 0.152 -0.079 -0.177 0.6132993859 180 -0.176 -0.834 0.041 0.151 -0.079 -0.176 0.6132985430 181 -0.176 -0.833 0.041 0.151 -0.079 -0.176 0.6132983905 powell nthiter 2: fret = 0.613298 192 -0.168 -0.833 0.041 0.151 -0.079 -0.176 0.6132941749 193 -0.169 -0.833 0.041 0.151 -0.079 -0.176 0.6132939778 194 -0.170 -0.833 0.041 0.151 -0.079 -0.176 0.6132938795 195 -0.172 -0.833 0.041 0.151 -0.079 -0.176 0.6132936469 205 -0.172 -0.833 0.041 0.151 -0.079 -0.180 0.6132908324 229 -0.172 -0.833 0.041 0.150 -0.079 -0.181 0.6132897576 230 -0.172 -0.833 0.041 0.146 -0.079 -0.181 0.6132883078 241 -0.172 -0.833 0.041 0.146 -0.077 -0.181 0.6132875438 251 -0.173 -0.839 0.042 0.148 -0.078 -0.182 0.6132858384 252 -0.173 -0.837 0.041 0.147 -0.078 -0.182 0.6132856061 253 -0.173 -0.838 0.041 0.147 -0.078 -0.182 0.6132854544 Powell done niters = 2 Computing relative cost 0 -25.0 -25.0 -25.0 1.050630 1 -25.0 -25.0 25.0 1.061290 2 -25.0 25.0 -25.0 1.057676 3 -25.0 25.0 25.0 1.078722 4 25.0 -25.0 -25.0 1.101915 5 25.0 -25.0 25.0 1.076953 6 25.0 25.0 -25.0 1.025027 7 25.0 25.0 25.0 1.061982 REL: 8 0.613285 8.514197 1.064275 rel = 0.576247 Number of iterations 2 Min cost was 0.613285 Number of FunctionCalls 254 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.275000 sec Parameters at optimum (transmm) -0.17306 -0.83828 0.04138 Parameters at optimum (rotdeg) 0.14739 -0.07783 -0.18176 Final costs ---------------- Number of surface hits 3116 WM Intensity 5569.3731 +/- 895.2983 Ctx Intensity 5711.1310 +/- 1095.3170 Pct Contrast 1.6601 +/- 16.2420 Cost 0.6133 RelCost 0.6029 Reg at min cost was 0.99808 0.06187 -0.00099 1.77882; 0.00335 -0.03805 0.99927 -34.31088; -0.06179 0.99736 0.03819 -18.74174; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to ./tmp.bbregister.9147/bbr.pass1.dat, type = 14 Original Reg 0.99798 0.06335 -0.00411 2.03254; 0.00635 -0.03529 0.99936 -33.51446; -0.06316 0.99737 0.03562 -18.69974; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00010 0.00148 -0.00312 0.25372; 0.00300 0.00276 0.00009 0.79642; -0.00137 0.00001 -0.00257 0.04200; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.778942 Computing change in rh position Surface-RMS-Diff-mm 0.864619 0.162017 1.233052 mri_segreg done mri_segreg --mov ./tmp.bbregister.9147/template.nii --init-reg ./tmp.bbregister.9147/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.9147/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 /media/sda1/nmrclass/tutorial_data/buckner_data/tutorial_subjs cd /media/sda1/nmrclass/tutorial_data_Sep_2019_rev3/buckner_data/tutorial_subjs/multimodal/fmri/fbirn-101 mri_segreg --mov ./tmp.bbregister.9147/template.nii --init-reg ./tmp.bbregister.9147/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.9147/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass movvol ./tmp.bbregister.9147/template.nii regfile ./tmp.bbregister.9147/bbr.pass1.dat subject fbirn-anat-101.v6 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 1568661312 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99808 0.06187 -0.00099 1.77882; 0.00335 -0.03805 0.99927 -34.31088; -0.06179 0.99736 0.03819 -18.74174; 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 1.040631 1 -25.0 -25.0 25.0 1.072279 2 -25.0 25.0 -25.0 1.066360 3 -25.0 25.0 25.0 1.064630 4 25.0 -25.0 -25.0 1.075448 5 25.0 -25.0 25.0 1.053625 6 25.0 25.0 -25.0 1.037239 7 25.0 25.0 25.0 1.068295 REL: 8 0.616721 8.478506 1.059813 rel = 0.581914 Initial costs ---------------- Number of surface hits 312585 WM Intensity 5569.1229 +/- 900.7761 Ctx Intensity 5719.9846 +/- 1101.3010 Pct Contrast 1.7245 +/- 16.0717 Cost 0.6167 RelCost 0.5819 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.6146 0.6146 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.6145 0.6145 0.0 9 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 -0.1000 0.6145 0.6145 0.0 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.6140 0.6140 0.0 30 -0.1000 -0.1000 0.0000 -0.1000 0.0000 -0.1000 0.6138 0.6138 0.0 255 0.0000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.6138 0.6138 0.0 273 0.0000 -0.1000 0.0000 -0.1000 0.0000 -0.1000 0.6135 0.6135 0.0 282 0.0000 -0.1000 0.0000 0.0000 0.0000 -0.1000 0.6135 0.6135 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.6133 0.6133 0.0 589 0.1000 0.0000 -0.1000 0.1000 0.0000 0.0000 0.6132 0.6132 0.0 590 0.1000 0.0000 -0.1000 0.1000 0.0000 0.1000 0.6132 0.6132 0.0 592 0.1000 0.0000 -0.1000 0.1000 0.1000 0.0000 0.6129 0.6129 0.0 Brute Force -------------------------- Min cost was 0.612920 Number of iterations 729 Search time 0.776000 sec Parameters at best (transmm, rotdeg) 0.100 0.000 -0.100 0.100 0.100 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0.1 1 0 2 -0.1 3 0.1 4 0.1 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000000 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.617609 7 -0.181 0.000 -0.100 0.100 0.100 0.000 0.6155280927 9 -0.175 0.000 -0.100 0.100 0.100 0.000 0.6155277512 11 -0.177 0.000 -0.100 0.100 0.100 0.000 0.6155274730 20 -0.177 0.096 -0.100 0.100 0.100 0.000 0.6152918923 30 -0.177 0.095 -0.207 0.100 0.100 0.000 0.6150179509 32 -0.177 0.095 -0.201 0.100 0.100 0.000 0.6150171369 41 -0.177 0.095 -0.201 0.210 0.100 0.000 0.6147644087 42 -0.177 0.095 -0.201 0.208 0.100 0.000 0.6147638481 43 -0.177 0.095 -0.201 0.204 0.100 0.000 0.6147629786 54 -0.177 0.095 -0.201 0.204 -0.103 0.000 0.6136018002 55 -0.177 0.095 -0.201 0.204 -0.101 0.000 0.6136009678 56 -0.177 0.095 -0.201 0.204 -0.096 0.000 0.6136004739 57 -0.177 0.095 -0.201 0.204 -0.097 0.000 0.6136004296 65 -0.177 0.095 -0.201 0.204 -0.097 -0.104 0.6133606621 66 -0.177 0.095 -0.201 0.204 -0.097 -0.134 0.6133564866 67 -0.177 0.095 -0.201 0.204 -0.097 -0.123 0.6133550460 68 -0.177 0.095 -0.201 0.204 -0.097 -0.124 0.6133550448 69 -0.177 0.095 -0.201 0.204 -0.097 -0.125 0.6133550389 powell nthiter 1: fret = 0.613355 79 -0.166 0.095 -0.201 0.204 -0.097 -0.125 0.6133459421 80 -0.155 0.095 -0.201 0.204 -0.097 -0.125 0.6133439808 81 -0.158 0.095 -0.201 0.204 -0.097 -0.125 0.6133439203 90 -0.158 0.130 -0.201 0.204 -0.097 -0.125 0.6133052082 91 -0.158 0.135 -0.201 0.204 -0.097 -0.125 0.6133051605 92 -0.158 0.133 -0.201 0.204 -0.097 -0.125 0.6133050614 93 -0.158 0.132 -0.201 0.204 -0.097 -0.125 0.6133050603 100 -0.158 0.132 -0.270 0.204 -0.097 -0.125 0.6131634211 102 -0.158 0.132 -0.267 0.204 -0.097 -0.125 0.6131630430 104 -0.158 0.132 -0.266 0.204 -0.097 -0.125 0.6131630357 115 -0.158 0.132 -0.265 0.235 -0.097 -0.125 0.6131600858 116 -0.158 0.132 -0.265 0.222 -0.097 -0.125 0.6131555320 117 -0.158 0.132 -0.265 0.221 -0.097 -0.125 0.6131555249 125 -0.158 0.132 -0.265 0.221 -0.125 -0.125 0.6131463094 126 -0.158 0.132 -0.265 0.221 -0.117 -0.125 0.6131441892 136 -0.158 0.132 -0.265 0.221 -0.118 -0.146 0.6131416006 137 -0.158 0.132 -0.265 0.221 -0.118 -0.139 0.6131407119 powell nthiter 2: fret = 0.613141 148 -0.147 0.132 -0.265 0.221 -0.118 -0.139 0.6131368704 158 -0.146 0.143 -0.265 0.221 -0.118 -0.139 0.6131330787 159 -0.146 0.145 -0.265 0.221 -0.118 -0.139 0.6131330731 173 -0.146 0.146 -0.282 0.221 -0.118 -0.139 0.6131312896 174 -0.146 0.146 -0.275 0.221 -0.118 -0.139 0.6131293382 175 -0.146 0.146 -0.274 0.221 -0.118 -0.139 0.6131293304 184 -0.146 0.146 -0.274 0.222 -0.118 -0.139 0.6131293160 185 -0.146 0.146 -0.274 0.223 -0.118 -0.139 0.6131292106 196 -0.146 0.146 -0.274 0.223 -0.121 -0.139 0.6131288442 197 -0.146 0.146 -0.274 0.223 -0.122 -0.139 0.6131288396 powell nthiter 3: fret = 0.613129 219 -0.145 0.146 -0.274 0.223 -0.122 -0.139 0.6131288110 227 -0.145 0.148 -0.274 0.223 -0.122 -0.139 0.6131287626 242 -0.145 0.149 -0.276 0.223 -0.122 -0.139 0.6131287045 252 -0.145 0.149 -0.277 0.224 -0.122 -0.139 0.6131286757 262 -0.145 0.149 -0.277 0.224 -0.120 -0.139 0.6131286647 277 -0.145 0.149 -0.277 0.224 -0.120 -0.137 0.6131286211 powell nthiter 4: fret = 0.613129 298 -0.144 0.150 -0.277 0.224 -0.120 -0.136 0.6131286167 325 -0.144 0.150 -0.277 0.224 -0.121 -0.136 0.6131285922 326 -0.144 0.150 -0.277 0.224 -0.122 -0.136 0.6131285409 powell nthiter 5: fret = 0.613129 Powell done niters = 5 Computing relative cost 0 -25.0 -25.0 -25.0 1.042006 1 -25.0 -25.0 25.0 1.075599 2 -25.0 25.0 -25.0 1.066369 3 -25.0 25.0 25.0 1.063803 4 25.0 -25.0 -25.0 1.073425 5 25.0 -25.0 25.0 1.055532 6 25.0 25.0 -25.0 1.037564 7 25.0 25.0 25.0 1.067466 REL: 8 0.613129 8.481765 1.060221 rel = 0.578303 Number of iterations 5 Min cost was 0.613129 Number of FunctionCalls 395 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 20.923000 sec Parameters at optimum (transmm) -0.14389 0.14857 -0.27574 Parameters at optimum (rotdeg) 0.22347 -0.12080 -0.13797 Final costs ---------------- Number of surface hits 312585 WM Intensity 5567.5792 +/- 899.6342 Ctx Intensity 5718.1931 +/- 1104.2307 Pct Contrast 1.6981 +/- 16.2371 Cost 0.6131 RelCost 0.5819 Reg at min cost was 0.99822 0.05967 0.00133 1.59227; 0.00119 -0.04209 0.99911 -34.09323; -0.05967 0.99733 0.04208 -19.14736; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to register.dat, type = 14 Original Reg 0.99808 0.06187 -0.00099 1.77882; 0.00335 -0.03805 0.99927 -34.31088; -0.06179 0.99736 0.03819 -18.74174; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00013 0.00220 -0.00232 0.18655; 0.00216 0.00403 0.00016 -0.21765; -0.00212 0.00003 -0.00389 0.40563; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.465704 Computing change in rh position Surface-RMS-Diff-mm 0.396061 0.139087 0.691436 mri_segreg done MinCost: 0.613129 5567.579214 5718.193144 1.698091 tkregister2_cmdl --mov template.nii --reg register.dat --noedit --ltaout register.lta tkregister_tcl /media/sda1/nmrclass/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume template.nii reg file register.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 -------- 0.99822 0.05967 0.00133 1.59227; 0.00119 -0.04209 0.99911 -34.09323; -0.05967 0.99733 0.04208 -19.14736; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: loading target /media/sda1/nmrclass/tutorial_data/buckner_data/tutorial_subjs/fbirn-anat-101.v6/mri/orig.mgz 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 template.nii Tmov: -------------------- -3.43750 0.00000 0.00000 110.00000; 0.00000 0.00000 4.00000 -70.00000; 0.00000 -3.43750 0.00000 109.99999; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 0.99822 0.05967 0.00133 1.59227; 0.00119 -0.04209 0.99911 -34.09323; -0.05967 0.99733 0.04208 -19.14736; 0.00000 0.00000 0.00000 1.00000; Determinant -1 subject = fbirn-anat-101.v6 RegMat --------------------------- 0.99822 0.05967 0.00133 1.59227; 0.00119 -0.04209 0.99911 -34.09323; -0.05967 0.99733 0.04208 -19.14736; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Tue Sep 10 18:31:50 EDT 2019 Ended at Tue Sep 10 18:33:14 EDT 2019 BBR-Run-Time-Sec 84 bbregister Done To check results, run: tkregisterfv --mov template.nii --reg register.lta --surfs