Logfile for bbregister Sun Mar 27 21:40:38 EDT 2016 setenv SUBJECTS_DIR /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects cd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01 /usr/local/freesurfer/dev/bin/bbregister --s fsf01anat --init-coreg --6 --bold --mov bold/001/template.nii.gz --reg bold/001/register.dof6.dat --lta bold/001/register.dof6.lta --init-reg-out bold/001/init.register.dof6.dat $Id: bbregister,v 1.74 2016/02/17 21:07:31 greve Exp $ Linux transfer 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer/dev mri_convert bold/001/template.nii.gz bold/001/tmp.bbregister.7323/template.nii mri_convert.bin bold/001/template.nii.gz bold/001/tmp.bbregister.7323/template.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from bold/001/template.nii.gz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.973976, -0.226651) k_ras = (-2.36491e-18, -0.226651, 0.973976) writing to bold/001/tmp.bbregister.7323/template.nii... mri_coreg --s fsf01anat --mov bold/001/tmp.bbregister.7323/template.nii --regdat bold/001/tmp.bbregister.7323/reg.init.dat --reg bold/001/tmp.bbregister.7323/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 freadFloat: fread failed $Id: mri_coreg.c,v 1.26 2016/01/20 23:42:39 greve Exp $ cwd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01 cmdline mri_coreg --s fsf01anat --mov bold/001/tmp.bbregister.7323/template.nii --regdat bold/001/tmp.bbregister.7323/reg.init.dat --reg bold/001/tmp.bbregister.7323/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 sysname Linux hostname transfer machine x86_64 user zkaufman 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 Reading in mov bold/001/tmp.bbregister.7323/template.nii Reading in ref /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/brainmask.mgz freadFloat: fread failed Reading in and applying refmask /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/aparc+aseg.mgz Setting cras translation parameters to align centers Creating random numbers for coordinate dithering Performing intensity dithering Initial parameters -6.0223 -45.2577 79.2380 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 = 1714.3334 mov gstd 0.9989 0.9989 0.0000 Smoothing mov refsat = 118.0000 ref gstd 1.8914 1.8914 1.8914 Smoothing ref COREGpreproc() done Testing if mov and target overlap Init cost -1.0211907209 nhits = 106280 out of 16777216, Percent Overlap: 40.5 Initial RefRAS-to-MovRAS 1.00000 0.00000 0.00000 -6.02228; 0.00000 1.00000 0.00000 -45.25770; 0.00000 0.00000 1.00000 79.23798; 0.00000 0.00000 0.00000 1.00000; Initial RefVox-to-MovVox 0.29091 -0.00000 -0.00000 -5.59091; -0.00000 0.06593 -0.28334 59.21896; 0.00000 -0.19480 -0.04533 45.11600; 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 -6.02228 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0504159 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6 Starting OpenPowel2(), sep = 4 InitialCost -1.0719541311 #@# 4 188 -6.02228 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0719541 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.071954 #@# 4 193 -6.64031 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0719982 #@# 4 195 -6.42368 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0720158 #@# 4 198 -6.36391 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0720164 #@# 4 201 -6.34980 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0720165 #@# 4 205 -6.34980 -36.87573 49.23798 4.00000 0.00000 0.00000 -1.0744008 #@# 4 208 -6.34980 -40.53706 49.23798 4.00000 0.00000 0.00000 -1.0759999 #@# 4 210 -6.34980 -39.59051 49.23798 4.00000 0.00000 0.00000 -1.0763069 #@# 4 211 -6.34980 -39.48524 49.23798 4.00000 0.00000 0.00000 -1.0763090 #@# 4 212 -6.34980 -39.50470 49.23798 4.00000 0.00000 0.00000 -1.0763118 #@# 4 221 -6.34980 -39.50470 49.14936 4.00000 0.00000 0.00000 -1.0763154 #@# 4 222 -6.34980 -39.50470 49.13935 4.00000 0.00000 0.00000 -1.0763171 #@# 4 231 -6.34980 -39.50470 49.13935 3.38197 0.00000 0.00000 -1.0764904 #@# 4 233 -6.34980 -39.50470 49.13935 3.49223 0.00000 0.00000 -1.0765028 #@# 4 234 -6.34980 -39.50470 49.13935 3.52561 0.00000 0.00000 -1.0765045 #@# 4 236 -6.34980 -39.50470 49.13935 3.51561 0.00000 0.00000 -1.0765049 #@# 4 237 -6.34980 -39.50470 49.13935 3.50561 0.00000 0.00000 -1.0765057 #@# 4 244 -6.34980 -39.50470 49.13935 3.50561 0.13342 0.00000 -1.0765141 #@# 4 246 -6.34980 -39.50470 49.13935 3.50561 0.11799 0.00000 -1.0765142 #@# 4 254 -6.34980 -39.50470 49.13935 3.50561 0.11799 -0.18203 -1.0765320 #@# 4 257 -6.34980 -39.50470 49.13935 3.50561 0.11799 -0.17203 -1.0765326 #@# 4 265 -6.37596 -39.84391 49.13148 3.46613 0.12741 -0.18577 -1.0765558 #@# 4 266 -6.37268 -39.80144 49.13247 3.47107 0.12623 -0.18405 -1.0765580 powell nthiter 1: fret = -1.076558 #@# 4 274 -6.38890 -39.80144 49.13247 3.47107 0.12623 -0.18405 -1.0765586 #@# 4 275 -6.41432 -39.80144 49.13247 3.47107 0.12623 -0.18405 -1.0765587 #@# 4 278 -6.43432 -39.80144 49.13247 3.47107 0.12623 -0.18405 -1.0765595 #@# 4 296 -6.43432 -39.80144 48.51443 3.47107 0.12623 -0.18405 -1.0766954 #@# 4 298 -6.43432 -39.80144 48.53483 3.47107 0.12623 -0.18405 -1.0766957 #@# 4 299 -6.43432 -39.80144 48.54483 3.47107 0.12623 -0.18405 -1.0766963 #@# 4 308 -6.43432 -39.80144 48.54483 2.85304 0.12623 -0.18405 -1.0767852 #@# 4 310 -6.43432 -39.80144 48.54483 3.05311 0.12623 -0.18405 -1.0768225 #@# 4 311 -6.43432 -39.80144 48.54483 3.07104 0.12623 -0.18405 -1.0768234 #@# 4 320 -6.43432 -39.80144 48.54483 3.07104 -0.03917 -0.18405 -1.0768281 #@# 4 321 -6.43432 -39.80144 48.54483 3.07104 -0.04917 -0.18405 -1.0768285 #@# 4 324 -6.43432 -39.80144 48.54483 3.07104 -0.06163 -0.18405 -1.0768286 #@# 4 325 -6.43432 -39.80144 48.54483 3.07104 -0.07163 -0.18405 -1.0768287 #@# 4 334 -6.45092 -40.01678 48.53983 3.04597 -0.08174 -0.19277 -1.0768327 #@# 4 335 -6.44572 -39.94929 48.54139 3.05382 -0.08361 -0.19004 -1.0768330 #@# 4 337 -6.54164 -40.39388 47.94343 2.60204 -0.28521 -0.20804 -1.0770371 #@# 4 340 -6.69684 -41.11325 46.97591 1.87103 -0.61140 -0.23718 -1.0771599 #@# 4 346 -6.67134 -40.99509 47.13483 1.99110 -0.55782 -0.23240 -1.0771701 #@# 4 347 -6.66953 -40.98666 47.14616 1.99966 -0.55400 -0.23205 -1.0771704 powell nthiter 2: fret = -1.077170 #@# 4 355 -6.28756 -40.98666 47.14616 1.99966 -0.55400 -0.23205 -1.0771829 #@# 4 356 -6.45323 -40.98666 47.14616 1.99966 -0.55400 -0.23205 -1.0771980 #@# 4 357 -6.44323 -40.98666 47.14616 1.99966 -0.55400 -0.23205 -1.0771983 #@# 4 367 -6.43213 -40.98666 47.14616 1.99966 -0.55400 -0.20730 -1.0772012 #@# 4 369 -6.43213 -40.98666 47.14616 1.99966 -0.55400 -0.19130 -1.0772020 #@# 4 370 -6.43213 -40.98666 47.14616 1.99966 -0.55400 -0.18130 -1.0772022 #@# 4 377 -6.38192 -40.33559 47.16128 2.07545 -0.57209 -0.15493 -1.0773158 #@# 4 381 -6.37151 -40.20062 47.16441 2.09116 -0.57584 -0.14946 -1.0773164 #@# 4 382 -6.37504 -40.24644 47.16335 2.08583 -0.57456 -0.15132 -1.0773177 #@# 4 383 -6.37832 -40.28891 47.16236 2.08089 -0.57338 -0.15304 -1.0773191 #@# 4 390 -6.37832 -40.28891 47.16236 2.19769 -0.57338 -0.15304 -1.0773278 #@# 4 400 -6.37832 -40.28891 47.16236 2.19769 -0.19142 -0.15304 -1.0773637 #@# 4 401 -6.37832 -40.28891 47.16236 2.19769 -0.01061 -0.15304 -1.0773693 #@# 4 402 -6.37832 -40.28891 47.16236 2.19769 0.03750 -0.15304 -1.0773698 #@# 4 408 -6.47424 -40.73350 46.56440 1.74590 -0.16410 -0.17105 -1.0774988 #@# 4 417 -6.47180 -40.72219 46.57962 1.75740 -0.15897 -0.17059 -1.0774992 #@# 4 419 -6.47276 -40.72663 46.57364 1.75288 -0.16099 -0.17077 -1.0774993 powell nthiter 3: fret = -1.077499 #@# 4 427 -6.49168 -40.72663 46.57364 1.75288 -0.16099 -0.17077 -1.0775008 #@# 4 445 -6.46515 -40.38260 46.58163 1.79293 -0.17054 -0.15683 -1.0775325 #@# 4 448 -6.46187 -40.34013 46.58261 1.79787 -0.17172 -0.15511 -1.0775337 #@# 4 459 -6.46187 -40.34013 46.58261 1.81916 -0.17172 -0.15511 -1.0775342 #@# 4 468 -6.46187 -40.34013 46.58261 1.81916 -0.22158 -0.15511 -1.0775393 #@# 4 469 -6.46187 -40.34013 46.58261 1.81916 -0.43860 -0.15511 -1.0775400 #@# 4 470 -6.46187 -40.34013 46.58261 1.81916 -0.33451 -0.15511 -1.0775418 #@# 4 471 -6.46187 -40.34013 46.58261 1.81916 -0.34451 -0.15511 -1.0775422 #@# 4 475 -6.55779 -40.78473 45.98465 1.36737 -0.54610 -0.17312 -1.0775452 #@# 4 479 -6.52115 -40.61491 46.21305 1.53994 -0.46910 -0.16624 -1.0775739 #@# 4 483 -6.51923 -40.60601 46.22501 1.54897 -0.46507 -0.16588 -1.0775740 #@# 4 484 -6.51721 -40.59665 46.23761 1.55849 -0.46082 -0.16550 -1.0775748 #@# 4 485 -6.51596 -40.59086 46.24539 1.56437 -0.45820 -0.16527 -1.0775765 Powell done niters total = 3 OptTimeSec 24.2 sec OptTimeMin 0.40 min nEvals 486 Final parameters -6.51596308 -40.59085846 46.24539185 1.56437409 -0.45819777 -0.16526955 Final cost -1.077576544779150 --------------------------------- mri_coreg utimesec 113.811697 mri_coreg stimesec 0.634903 mri_coreg ru_maxrss 422120 mri_coreg ru_ixrss 0 mri_coreg ru_idrss 0 mri_coreg ru_isrss 0 mri_coreg ru_minflt 266590 mri_coreg ru_majflt 0 mri_coreg ru_nswap 0 mri_coreg ru_inblock 0 mri_coreg ru_oublock 0 mri_coreg ru_msgsnd 0 mri_coreg ru_msgrcv 0 mri_coreg ru_nsignals 0 mri_coreg ru_nvcsw 48 mri_coreg ru_nivcsw 233 Final RefRAS-to-MovRAS 0.99996 -0.00288 -0.00800 -6.51596; 0.00310 0.99962 0.02730 -40.59086; 0.00792 -0.02732 0.99960 46.24539; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox 0.29090 -0.00233 0.00084 -5.27552; 0.00140 0.07364 -0.28143 58.99800; -0.00140 -0.19348 -0.05064 38.90063; 0.00000 0.00000 0.00000 1.00000; Final parameters -6.5160 -40.5909 46.2454 1.5644 -0.4582 -0.1653 nhits = 106066 out of 16777216, Percent Overlap: 40.5 mri_coreg RunTimeSec 114.5 sec To check run: tkregisterfv --mov bold/001/tmp.bbregister.7323/template.nii --targ /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/brainmask.mgz --reg bold/001/tmp.bbregister.7323/mri_coreg.lta --s fsf01anat --surfs mri_coreg done mri_segreg --mov bold/001/tmp.bbregister.7323/template.nii --init-reg bold/001/tmp.bbregister.7323/reg.init.dat --out-reg bold/001/tmp.bbregister.7323/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 1.112 2014/02/25 19:06:37 greve Exp $ setenv SUBJECTS_DIR /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects cd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01 mri_segreg --mov bold/001/tmp.bbregister.7323/template.nii --init-reg bold/001/tmp.bbregister.7323/reg.init.dat --out-reg bold/001/tmp.bbregister.7323/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 transfer machine x86_64 user zkaufman movvol bold/001/tmp.bbregister.7323/template.nii regfile bold/001/tmp.bbregister.7323/reg.init.dat subject fsf01anat dof 6 outregfile bold/001/tmp.bbregister.7323/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 1459133830 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99996 -0.00288 -0.00800 0.79362; 0.00701 -0.25318 0.96739 -37.62688; 0.00482 0.96742 0.25315 -1.99570; 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 1.091030 1 -25.0 -25.0 25.0 1.054789 2 -25.0 25.0 -25.0 1.072374 3 -25.0 25.0 25.0 1.071854 4 25.0 -25.0 -25.0 1.053108 5 25.0 -25.0 25.0 1.051902 6 25.0 25.0 -25.0 1.032281 7 25.0 25.0 25.0 1.064927 REL: 8 0.741129 8.492266 1.061533 rel = 0.698168 Initial costs ---------------- Number of surface hits 3040 WM Intensity 855.3245 +/- 209.5971 Ctx Intensity 857.9055 +/- 239.0958 Pct Contrast -1.3471 +/- 21.9053 Cost 0.7411 RelCost 0.6982 WARNING: initial G-W contrast is negative, but expecting positive. If the mov data has a T1 contrast, re-run with --T1 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 1.0755 1.0755 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 1.0380 1.0380 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 1.0152 1.0152 0.0 5 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 4.0000 1.0011 1.0011 0.0 6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 1.0006 1.0006 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.9613 0.9613 0.0 18 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 -4.0000 0.9509 0.9509 0.0 30 -4.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.9324 0.9324 0.0 34 -4.0000 -4.0000 0.0000 -4.0000 4.0000 0.0000 0.9215 0.9215 0.0 40 -4.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.9087 0.9087 0.0 273 0.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.8170 0.8170 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.7728 0.7728 0.0 282 0.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.7334 0.7334 0.0 283 0.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.6066 0.6066 0.0 Brute Force -------------------------- Min cost was 0.606586 Number of iterations 729 Search time 1.390000 sec Parameters at best (transmm, rotdeg) 0.000 -4.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 -4 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 = 0.606586 7 0.066 -4.000 0.000 0.000 0.000 0.000 0.6062284744 9 0.078 -4.000 0.000 0.000 0.000 0.000 0.6062084021 11 0.077 -4.000 0.000 0.000 0.000 0.000 0.6062080631 14 0.077 -3.000 0.000 0.000 0.000 0.000 0.5911750249 20 0.077 -2.999 0.000 0.000 0.000 0.000 0.5911741576 21 0.077 -2.990 0.000 0.000 0.000 0.000 0.5911666665 23 0.077 -2.986 0.000 0.000 0.000 0.000 0.5911666121 24 0.077 -2.988 0.000 0.000 0.000 0.000 0.5911665914 25 0.077 -2.989 0.000 0.000 0.000 0.000 0.5911665783 32 0.077 -2.989 -0.081 0.000 0.000 0.000 0.5910502958 33 0.077 -2.989 -0.086 0.000 0.000 0.000 0.5910246040 34 0.077 -2.989 -0.289 0.000 0.000 0.000 0.5894910382 37 0.077 -2.989 -0.310 0.000 0.000 0.000 0.5894845029 38 0.077 -2.989 -0.301 0.000 0.000 0.000 0.5894757486 41 0.077 -2.989 -0.299 0.000 0.000 0.000 0.5894752072 47 0.077 -2.989 -0.299 -0.618 0.000 0.000 0.5840612358 48 0.077 -2.989 -0.299 -1.000 0.000 0.000 0.5837877173 49 0.077 -2.989 -0.299 -0.854 0.000 0.000 0.5832733231 50 0.077 -2.989 -0.299 -0.829 0.000 0.000 0.5832206346 52 0.077 -2.989 -0.299 -0.805 0.000 0.000 0.5831866416 54 0.077 -2.989 -0.299 -0.803 0.000 0.000 0.5831835268 56 0.077 -2.989 -0.299 -0.798 0.000 0.000 0.5831774762 66 0.077 -2.989 -0.299 -0.798 0.156 0.000 0.5824563477 67 0.077 -2.989 -0.299 -0.798 0.160 0.000 0.5824445317 69 0.077 -2.989 -0.299 -0.798 0.201 0.000 0.5823838314 73 0.077 -2.989 -0.299 -0.798 0.202 0.000 0.5823837361 82 0.077 -2.989 -0.299 -0.798 0.202 0.011 0.5823759210 83 0.077 -2.989 -0.299 -0.798 0.202 0.012 0.5823758510 powell nthiter 1: fret = 0.582376 92 0.208 -2.989 -0.299 -0.798 0.202 0.012 0.5817083693 93 0.224 -2.989 -0.299 -0.798 0.202 0.012 0.5816498022 109 0.224 -2.965 -0.299 -0.798 0.202 0.012 0.5815972125 111 0.224 -2.967 -0.299 -0.798 0.202 0.012 0.5815971409 118 0.224 -2.967 0.083 -0.798 0.202 0.012 0.5779825349 119 0.224 -2.967 0.125 -0.798 0.202 0.012 0.5776512064 120 0.224 -2.967 0.345 -0.798 0.202 0.012 0.5774362066 121 0.224 -2.967 0.254 -0.798 0.202 0.012 0.5767839647 123 0.224 -2.967 0.253 -0.798 0.202 0.012 0.5767838318 131 0.224 -2.967 0.253 -0.934 0.202 0.012 0.5767136750 132 0.224 -2.967 0.253 -0.882 0.202 0.012 0.5766593687 133 0.224 -2.967 0.253 -0.880 0.202 0.012 0.5766570831 134 0.224 -2.967 0.253 -0.849 0.202 0.012 0.5766276192 139 0.224 -2.967 0.253 -0.848 0.202 0.012 0.5766269157 141 0.224 -2.967 0.253 -0.847 0.202 0.012 0.5766264777 148 0.224 -2.967 0.253 -0.847 0.273 0.012 0.5761817590 149 0.224 -2.967 0.253 -0.847 0.302 0.012 0.5761157809 150 0.224 -2.967 0.253 -0.847 0.317 0.012 0.5761107539 151 0.224 -2.967 0.253 -0.847 0.313 0.012 0.5761103305 161 0.224 -2.967 0.253 -0.847 0.313 -0.237 0.5753880894 162 0.224 -2.967 0.253 -0.847 0.313 -0.219 0.5753198208 163 0.224 -2.967 0.253 -0.847 0.313 -0.162 0.5750734898 164 0.224 -2.967 0.253 -0.847 0.313 -0.095 0.5750461053 165 0.224 -2.967 0.253 -0.847 0.313 -0.122 0.5750031327 166 0.224 -2.967 0.253 -0.847 0.313 -0.124 0.5750020595 168 0.224 -2.967 0.253 -0.847 0.313 -0.126 0.5750019348 powell nthiter 2: fret = 0.575002 179 0.245 -2.967 0.253 -0.847 0.313 -0.126 0.5749931670 180 0.236 -2.967 0.253 -0.847 0.313 -0.126 0.5749865621 181 0.237 -2.967 0.253 -0.847 0.313 -0.126 0.5749863135 190 0.238 -2.585 0.253 -0.847 0.313 -0.126 0.5737294716 191 0.238 -2.613 0.253 -0.847 0.313 -0.126 0.5733581688 192 0.238 -2.741 0.253 -0.847 0.313 -0.126 0.5731019269 194 0.238 -2.702 0.253 -0.847 0.313 -0.126 0.5729946273 195 0.238 -2.696 0.253 -0.847 0.313 -0.126 0.5729917427 196 0.238 -2.694 0.253 -0.847 0.313 -0.126 0.5729915673 204 0.238 -2.694 0.170 -0.847 0.313 -0.126 0.5729650848 205 0.238 -2.694 0.208 -0.847 0.313 -0.126 0.5727941122 206 0.238 -2.694 0.210 -0.847 0.313 -0.126 0.5727918004 207 0.238 -2.694 0.215 -0.847 0.313 -0.126 0.5727903233 208 0.238 -2.694 0.214 -0.847 0.313 -0.126 0.5727902177 218 0.238 -2.694 0.214 -0.885 0.313 -0.126 0.5727347502 219 0.238 -2.694 0.214 -0.873 0.313 -0.126 0.5727215961 221 0.238 -2.694 0.214 -0.870 0.313 -0.126 0.5727215641 224 0.238 -2.694 0.214 -0.871 0.313 -0.126 0.5727213214 225 0.238 -2.694 0.214 -0.872 0.313 -0.126 0.5727212996 233 0.238 -2.694 0.214 -0.872 0.380 -0.126 0.5725384737 235 0.238 -2.694 0.214 -0.872 0.359 -0.126 0.5724816420 244 0.238 -2.694 0.214 -0.872 0.359 -0.244 0.5722659064 245 0.238 -2.694 0.214 -0.872 0.359 -0.220 0.5721382936 247 0.238 -2.694 0.214 -0.872 0.359 -0.210 0.5721288352 248 0.238 -2.694 0.214 -0.872 0.359 -0.211 0.5721285019 249 0.238 -2.694 0.214 -0.872 0.359 -0.212 0.5721284982 powell nthiter 3: fret = 0.572128 261 0.251 -2.694 0.214 -0.872 0.359 -0.212 0.5721268545 262 0.245 -2.694 0.214 -0.872 0.359 -0.212 0.5721263911 263 0.247 -2.694 0.214 -0.872 0.359 -0.212 0.5721261892 273 0.247 -2.686 0.214 -0.872 0.359 -0.212 0.5721196467 274 0.247 -2.685 0.214 -0.872 0.359 -0.212 0.5721194444 275 0.247 -2.684 0.214 -0.872 0.359 -0.212 0.5721194427 284 0.247 -2.684 0.189 -0.872 0.359 -0.212 0.5720285823 286 0.247 -2.684 0.188 -0.872 0.359 -0.212 0.5720282467 287 0.247 -2.684 0.187 -0.872 0.359 -0.212 0.5720281917 297 0.247 -2.684 0.187 -0.896 0.359 -0.212 0.5719820945 299 0.247 -2.684 0.187 -0.894 0.359 -0.212 0.5719819454 311 0.247 -2.684 0.187 -0.894 0.369 -0.212 0.5719638925 312 0.247 -2.684 0.187 -0.894 0.370 -0.212 0.5719635060 313 0.247 -2.684 0.187 -0.894 0.371 -0.212 0.5719633947 324 0.247 -2.684 0.187 -0.894 0.371 -0.215 0.5719596491 326 0.247 -2.684 0.187 -0.894 0.371 -0.219 0.5719594195 330 0.256 -2.674 0.161 -0.916 0.383 -0.226 0.5719197605 336 0.252 -2.678 0.171 -0.907 0.378 -0.224 0.5719164947 337 0.254 -2.676 0.167 -0.911 0.380 -0.225 0.5719163309 338 0.253 -2.677 0.168 -0.909 0.379 -0.224 0.5719163070 339 0.253 -2.677 0.168 -0.909 0.379 -0.224 0.5719162257 341 0.253 -2.677 0.168 -0.910 0.379 -0.224 0.5719161766 344 0.253 -2.677 0.168 -0.910 0.379 -0.224 0.5719161519 powell nthiter 4: fret = 0.571916 353 0.261 -2.677 0.168 -0.910 0.379 -0.224 0.5719063789 365 0.260 -2.687 0.168 -0.910 0.379 -0.224 0.5718940157 368 0.260 -2.688 0.168 -0.910 0.379 -0.224 0.5718939767 388 0.260 -2.688 0.168 -0.908 0.379 -0.224 0.5718927247 390 0.260 -2.688 0.168 -0.907 0.379 -0.224 0.5718925026 400 0.260 -2.688 0.168 -0.907 0.377 -0.224 0.5718906748 402 0.260 -2.688 0.168 -0.907 0.378 -0.224 0.5718905732 409 0.261 -2.687 0.163 -0.911 0.380 -0.226 0.5718875429 411 0.261 -2.687 0.163 -0.910 0.380 -0.226 0.5718875190 413 0.261 -2.687 0.164 -0.910 0.379 -0.225 0.5718873484 414 0.261 -2.687 0.164 -0.910 0.379 -0.226 0.5718871917 Powell done niters = 4 Computing relative cost 0 -25.0 -25.0 -25.0 1.046795 1 -25.0 -25.0 25.0 1.059148 2 -25.0 25.0 -25.0 1.058524 3 -25.0 25.0 25.0 1.068570 4 25.0 -25.0 -25.0 1.050597 5 25.0 -25.0 25.0 1.058344 6 25.0 25.0 -25.0 1.008646 7 25.0 25.0 25.0 1.039732 REL: 8 0.571887 8.390356 1.048795 rel = 0.545281 Number of iterations 4 Min cost was 0.571887 Number of FunctionCalls 417 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.799000 sec Parameters at optimum (transmm) 0.26102 -2.68671 0.16381 Parameters at optimum (rotdeg) -0.91016 0.37946 -0.22558 Final costs ---------------- Number of surface hits 3040 WM Intensity 823.1487 +/- 219.0824 Ctx Intensity 850.7398 +/- 251.0629 Pct Contrast 1.2975 +/- 21.2306 Cost 0.5719 RelCost 0.6982 Reg at min cost was 0.99999 0.00261 -0.00260 0.89712; 0.00314 -0.23779 0.97131 -40.34334; -0.00192 0.97131 0.23780 -1.23918; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/001/tmp.bbregister.7323/bbr.pass1.dat, type = 14 Original Reg 0.99996 -0.00288 -0.00800 0.79362; 0.00701 -0.25318 0.96739 -37.62688; 0.00482 0.96742 0.25315 -1.99570; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00003 -0.00550 -0.00540 -0.10350; 0.00386 -0.01539 -0.00392 2.71645; 0.00673 -0.00390 0.01535 -0.75653; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 2.828482 Computing change in rh position Surface-RMS-Diff-mm 2.899287 0.678971 4.298419 WARNING: initial G-W contrast was negative, but expected positive. If the mov data has a T1 contrast, re-run with --T1 mri_segreg done mri_segreg --mov bold/001/tmp.bbregister.7323/template.nii --init-reg bold/001/tmp.bbregister.7323/bbr.pass1.dat --out-reg bold/001/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/001/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/001/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/001/tmp.bbregister.7323/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.112 2014/02/25 19:06:37 greve Exp $ setenv SUBJECTS_DIR /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects cd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01 mri_segreg --mov bold/001/tmp.bbregister.7323/template.nii --init-reg bold/001/tmp.bbregister.7323/bbr.pass1.dat --out-reg bold/001/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/001/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/001/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/001/tmp.bbregister.7323/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname transfer machine x86_64 user zkaufman movvol bold/001/tmp.bbregister.7323/template.nii regfile bold/001/tmp.bbregister.7323/bbr.pass1.dat subject fsf01anat dof 6 outregfile bold/001/register.dof6.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 1459888130 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99999 0.00261 -0.00260 0.89712; 0.00314 -0.23779 0.97131 -40.34334; -0.00192 0.97131 0.23780 -1.23918; 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 1.041968 1 -25.0 -25.0 25.0 1.059150 2 -25.0 25.0 -25.0 1.061925 3 -25.0 25.0 25.0 1.067526 4 25.0 -25.0 -25.0 1.044055 5 25.0 -25.0 25.0 1.037784 6 25.0 25.0 -25.0 1.029330 7 25.0 25.0 25.0 1.059843 REL: 8 0.575895 8.401582 1.050198 rel = 0.548368 Initial costs ---------------- Number of surface hits 304441 WM Intensity 824.4612 +/- 216.4690 Ctx Intensity 852.2073 +/- 248.1521 Pct Contrast 1.4860 +/- 21.7327 Cost 0.5759 RelCost 0.5484 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.5758 0.5758 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.5754 0.5754 0.0 2 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.5750 0.5750 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.5749 0.5749 0.0 5 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1000 0.5741 0.5741 0.0 32 -0.1000 -0.1000 0.0000 -0.1000 0.0000 0.1000 0.5738 0.5738 0.0 41 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.1000 0.5733 0.5733 0.0 121 -0.1000 0.0000 0.0000 0.0000 0.0000 0.0000 0.5730 0.5730 0.0 122 -0.1000 0.0000 0.0000 0.0000 0.0000 0.1000 0.5724 0.5724 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.5719 0.5719 0.0 Brute Force -------------------------- Min cost was 0.571887 Number of iterations 729 Search time 1.389000 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 = 0.575895 7 -0.179 0.000 0.000 0.000 0.000 0.000 0.5752653415 8 -0.169 0.000 0.000 0.000 0.000 0.000 0.5752605206 10 -0.167 0.000 0.000 0.000 0.000 0.000 0.5752604991 18 -0.167 -0.124 0.000 0.000 0.000 0.000 0.5749283431 20 -0.167 -0.123 0.000 0.000 0.000 0.000 0.5749282754 23 -0.167 -0.116 0.000 0.000 0.000 0.000 0.5749281752 24 -0.167 -0.118 0.000 0.000 0.000 0.000 0.5749281119 34 -0.167 -0.120 -0.066 0.000 0.000 0.000 0.5748104146 35 -0.167 -0.120 -0.067 0.000 0.000 0.000 0.5748102314 36 -0.167 -0.120 -0.069 0.000 0.000 0.000 0.5748101899 39 -0.167 -0.120 -0.068 0.000 0.000 0.000 0.5748101682 46 -0.167 -0.120 -0.068 0.066 0.000 0.000 0.5747279731 47 -0.167 -0.120 -0.068 0.065 0.000 0.000 0.5747277809 48 -0.167 -0.120 -0.068 0.062 0.000 0.000 0.5747273292 59 -0.167 -0.120 -0.068 0.060 -0.130 0.000 0.5742703125 60 -0.167 -0.120 -0.068 0.060 -0.126 0.000 0.5742702276 62 -0.167 -0.120 -0.068 0.060 -0.127 0.000 0.5742702108 70 -0.167 -0.120 -0.068 0.060 -0.127 -0.135 0.5740538576 72 -0.167 -0.120 -0.068 0.060 -0.127 -0.123 0.5740517557 73 -0.167 -0.120 -0.068 0.060 -0.127 -0.124 0.5740515949 powell nthiter 1: fret = 0.574052 83 -0.177 -0.120 -0.068 0.060 -0.127 -0.124 0.5740498590 85 -0.178 -0.120 -0.068 0.060 -0.127 -0.124 0.5740498430 87 -0.179 -0.120 -0.068 0.060 -0.127 -0.124 0.5740498351 97 -0.179 -0.146 -0.068 0.060 -0.127 -0.124 0.5740408555 99 -0.179 -0.141 -0.068 0.060 -0.127 -0.124 0.5740394896 100 -0.179 -0.139 -0.068 0.060 -0.127 -0.124 0.5740392308 103 -0.179 -0.138 -0.068 0.060 -0.127 -0.124 0.5740391210 111 -0.179 -0.138 -0.076 0.060 -0.127 -0.124 0.5740381369 112 -0.179 -0.138 -0.075 0.060 -0.127 -0.124 0.5740380875 121 -0.179 -0.138 -0.075 0.067 -0.127 -0.124 0.5740370003 130 -0.179 -0.138 -0.075 0.067 -0.147 -0.124 0.5740299009 131 -0.179 -0.138 -0.075 0.067 -0.143 -0.124 0.5740290835 132 -0.179 -0.138 -0.075 0.067 -0.142 -0.124 0.5740290639 142 -0.179 -0.138 -0.075 0.067 -0.142 -0.121 0.5740290133 powell nthiter 2: fret = 0.574029 153 -0.177 -0.138 -0.075 0.067 -0.142 -0.122 0.5740289562 165 -0.176 -0.141 -0.075 0.067 -0.142 -0.122 0.5740288872 167 -0.176 -0.140 -0.075 0.067 -0.142 -0.122 0.5740288792 175 -0.176 -0.140 -0.076 0.067 -0.142 -0.122 0.5740288603 202 -0.176 -0.140 -0.076 0.067 -0.142 -0.120 0.5740288189 powell nthiter 3: fret = 0.574029 218 -0.180 -0.140 -0.076 0.067 -0.142 -0.120 0.5740287982 220 -0.178 -0.140 -0.076 0.067 -0.142 -0.120 0.5740286976 230 -0.178 -0.141 -0.076 0.067 -0.142 -0.120 0.5740286646 powell nthiter 4: fret = 0.574029 Powell done niters = 4 Computing relative cost 0 -25.0 -25.0 -25.0 1.042605 1 -25.0 -25.0 25.0 1.059107 2 -25.0 25.0 -25.0 1.061220 3 -25.0 25.0 25.0 1.067018 4 25.0 -25.0 -25.0 1.041190 5 25.0 -25.0 25.0 1.038381 6 25.0 25.0 -25.0 1.026362 7 25.0 25.0 25.0 1.058163 REL: 8 0.574029 8.394046 1.049256 rel = 0.547082 Number of iterations 4 Min cost was 0.574029 Number of FunctionCalls 327 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 39.169000 sec Parameters at optimum (transmm) -0.17750 -0.14145 -0.07556 Parameters at optimum (rotdeg) 0.06718 -0.14231 -0.11978 Final costs ---------------- Number of surface hits 304441 WM Intensity 822.8239 +/- 217.8386 Ctx Intensity 850.7266 +/- 249.7037 Pct Contrast 1.4813 +/- 21.8878 Cost 0.5740 RelCost 0.5484 Reg at min cost was 1.00000 -0.00030 -0.00116 0.63848; 0.00106 -0.23893 0.97104 -40.48510; 0.00057 0.97104 0.23893 -1.35981; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/001/register.dof6.dat, type = 14 Original Reg 0.99999 0.00261 -0.00260 0.89712; 0.00314 -0.23779 0.97131 -40.34334; -0.00192 0.97131 0.23780 -1.23918; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00001 0.00291 -0.00144 0.25864; 0.00209 0.00114 0.00028 0.14176; -0.00249 0.00028 -0.00113 0.12063; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.268551 Computing change in rh position Surface-RMS-Diff-mm 0.278744 0.119083 0.560626 mri_segreg done MinCost: 0.574029 822.823927 850.726610 1.481314 tkregister2_cmdl --mov bold/001/template.nii.gz --reg bold/001/register.dof6.dat --noedit --ltaout bold/001/register.dof6.lta tkregister_tcl /usr/local/freesurfer/dev/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume bold/001/template.nii.gz reg file bold/001/register.dof6.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.131 2016/03/24 17:39:56 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- 1.00000 -0.00030 -0.00116 0.63848; 0.00106 -0.23893 0.97104 -40.48510; 0.00057 0.97104 0.23893 -1.35981; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: loading target /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/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 bold/001/template.nii.gz Tmov: -------------------- -3.43750 0.00000 0.00000 110.00000; 0.00000 0.00000 5.00000 -75.00000; 0.00000 -3.43750 0.00000 109.99999; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 1.00000 -0.00030 -0.00116 0.63848; 0.00106 -0.23893 0.97104 -40.48510; 0.00057 0.97104 0.23893 -1.35981; 0.00000 0.00000 0.00000 1.00000; Determinant -1 subject = fsf01anat RegMat --------------------------- 1.00000 -0.00030 -0.00116 0.63848; 0.00106 -0.23893 0.97104 -40.48510; 0.00057 0.97104 0.23893 -1.35981; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Sun Mar 27 21:40:38 EDT 2016 Ended at Sun Mar 27 21:43:35 EDT 2016 BBR-Run-Time-Sec 177 bbregister Done To check results, run: tkregister2 --mov bold/001/template.nii.gz --reg bold/001/register.dof6.dat --surf