Logfile for bbregister Sun Mar 27 21:37:27 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/template.nii.gz --reg bold/register.dof6.dat --lta bold/register.dof6.lta --init-reg-out bold/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/template.nii.gz bold/tmp.bbregister.6365/template.nii mri_convert.bin bold/template.nii.gz bold/tmp.bbregister.6365/template.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from bold/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/tmp.bbregister.6365/template.nii... mri_coreg --s fsf01anat --mov bold/tmp.bbregister.6365/template.nii --regdat bold/tmp.bbregister.6365/reg.init.dat --reg bold/tmp.bbregister.6365/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/tmp.bbregister.6365/template.nii --regdat bold/tmp.bbregister.6365/reg.init.dat --reg bold/tmp.bbregister.6365/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/tmp.bbregister.6365/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 = 1823.3334 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 -1.0212885186 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 -1.0505087 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6 Starting OpenPowel2(), sep = 4 InitialCost -1.0720660686 #@# 4 188 -6.02228 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0720661 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.072066 #@# 4 193 -6.64031 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0720886 #@# 4 195 -6.38299 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0721114 #@# 4 197 -6.30410 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0721116 #@# 4 199 -6.33944 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0721121 #@# 4 204 -6.34944 -36.87573 49.23798 4.00000 0.00000 0.00000 -1.0743937 #@# 4 207 -6.34944 -40.01580 49.23798 4.00000 0.00000 0.00000 -1.0761501 #@# 4 209 -6.34944 -39.59603 49.23798 4.00000 0.00000 0.00000 -1.0762134 #@# 4 231 -6.34944 -39.59603 49.23798 3.38197 0.00000 0.00000 -1.0765741 #@# 4 233 -6.34944 -39.59603 49.23798 3.21876 0.00000 0.00000 -1.0765885 #@# 4 234 -6.34944 -39.59603 49.23798 3.22876 0.00000 0.00000 -1.0765890 #@# 4 235 -6.34944 -39.59603 49.23798 3.25060 0.00000 0.00000 -1.0765903 #@# 4 238 -6.34944 -39.59603 49.23798 3.24060 0.00000 0.00000 -1.0765922 #@# 4 244 -6.34944 -39.59603 49.23798 3.24060 0.38197 0.00000 -1.0765955 #@# 4 245 -6.34944 -39.59603 49.23798 3.24060 0.23124 0.00000 -1.0765957 #@# 4 246 -6.34944 -39.59603 49.23798 3.24060 0.29701 0.00000 -1.0765992 #@# 4 248 -6.34944 -39.59603 49.23798 3.24060 0.28701 0.00000 -1.0765996 #@# 4 250 -6.34944 -39.59603 49.23798 3.24060 0.27701 0.00000 -1.0766003 #@# 4 257 -6.34944 -39.59603 49.23798 3.24060 0.27701 -0.11474 -1.0766048 #@# 4 258 -6.34944 -39.59603 49.23798 3.24060 0.27701 -0.07780 -1.0766064 #@# 4 260 -6.34944 -39.59603 49.23798 3.24060 0.27701 -0.08780 -1.0766071 #@# 4 269 -6.37729 -39.96533 49.23798 3.17596 0.30059 -0.09528 -1.0766178 powell nthiter 1: fret = -1.076618 #@# 4 283 -6.38729 -39.96533 49.23798 3.17596 0.30059 -0.09528 -1.0766183 #@# 4 298 -6.38729 -39.96533 47.61994 3.17596 0.30059 -0.09528 -1.0766504 #@# 4 299 -6.38729 -39.96533 48.39967 3.17596 0.30059 -0.09528 -1.0768719 #@# 4 303 -6.38729 -39.96533 48.38255 3.17596 0.30059 -0.09528 -1.0768723 #@# 4 304 -6.38729 -39.96533 48.36356 3.17596 0.30059 -0.09528 -1.0768774 #@# 4 307 -6.38729 -39.96533 48.34749 3.17596 0.30059 -0.09528 -1.0768780 #@# 4 308 -6.38729 -39.96533 48.33749 3.17596 0.30059 -0.09528 -1.0768782 #@# 4 313 -6.38729 -39.96533 48.33749 2.55793 0.30059 -0.09528 -1.0771557 #@# 4 316 -6.38729 -39.96533 48.33749 2.53099 0.30059 -0.09528 -1.0771587 #@# 4 327 -6.38729 -39.96533 48.33749 2.53099 0.13331 -0.09528 -1.0771602 #@# 4 328 -6.38729 -39.96533 48.33749 2.53099 0.17348 -0.09528 -1.0771612 #@# 4 329 -6.38729 -39.96533 48.33749 2.53099 0.19911 -0.09528 -1.0771617 #@# 4 332 -6.38729 -39.96533 48.33749 2.53099 0.18911 -0.09528 -1.0771620 #@# 4 339 -6.40911 -40.25465 48.33749 2.48034 0.20758 -0.10113 -1.0771667 #@# 4 340 -6.40108 -40.14819 48.33749 2.49898 0.20078 -0.09898 -1.0771717 #@# 4 341 -6.39781 -40.10480 48.33749 2.50657 0.19801 -0.09810 -1.0771728 #@# 4 343 -6.44618 -40.61357 47.43700 1.77254 0.11902 -0.10840 -1.0776173 #@# 4 346 -6.52444 -41.43678 45.97999 0.58486 -0.00880 -0.12506 -1.0779318 #@# 4 354 -6.52554 -41.44830 45.95959 0.56824 -0.01059 -0.12529 -1.0779326 #@# 4 355 -6.52602 -41.45339 45.95059 0.56090 -0.01138 -0.12539 -1.0779327 powell nthiter 2: fret = -1.077933 #@# 4 381 -6.51602 -41.45339 45.33255 0.56090 -0.01138 -0.12539 -1.0781561 #@# 4 384 -6.51602 -41.45339 45.29290 0.56090 -0.01138 -0.12539 -1.0781580 #@# 4 385 -6.51602 -41.45339 45.28108 0.56090 -0.01138 -0.12539 -1.0781593 #@# 4 394 -6.46746 -40.80951 45.28108 0.67360 -0.05249 -0.11236 -1.0783229 #@# 4 395 -6.46302 -40.75062 45.28108 0.68391 -0.05625 -0.11117 -1.0783257 #@# 4 396 -6.45898 -40.69698 45.28108 0.69330 -0.05967 -0.11008 -1.0783294 #@# 4 400 -6.45570 -40.65359 45.28108 0.70090 -0.06244 -0.10921 -1.0783297 #@# 4 405 -6.45570 -40.65359 45.28108 0.70090 -0.68048 -0.10921 -1.0783579 #@# 4 407 -6.45570 -40.65359 45.28108 0.70090 -0.49850 -0.10921 -1.0783703 #@# 4 417 -6.47418 -40.84793 44.93712 0.42052 -0.52868 -0.11314 -1.0784123 #@# 4 418 -6.48349 -40.94590 44.76371 0.27916 -0.54389 -0.11512 -1.0784197 #@# 4 421 -6.48229 -40.93325 44.78611 0.29742 -0.54193 -0.11487 -1.0784198 powell nthiter 3: fret = -1.078420 #@# 4 439 -6.49229 -40.93325 44.78611 0.29742 -0.54193 -0.03213 -1.0784249 #@# 4 440 -6.49229 -40.93325 44.78611 0.29742 -0.54193 -0.04305 -1.0784262 #@# 4 441 -6.49229 -40.93325 44.78611 0.29742 -0.54193 -0.06127 -1.0784266 #@# 4 459 -6.48520 -40.83922 44.78611 0.31388 -0.54793 -0.05937 -1.0784274 #@# 4 479 -6.48980 -40.88761 44.70045 0.24406 -0.55544 -0.06035 -1.0784291 #@# 4 481 -6.48818 -40.87054 44.73068 0.26870 -0.55279 -0.06001 -1.0784304 Powell done niters total = 3 OptTimeSec 24.2 sec OptTimeMin 0.40 min nEvals 483 Final parameters -6.48817730 -40.87053680 44.73067856 0.26869830 -0.55279166 -0.06000530 Final cost -1.078430418798719 --------------------------------- mri_coreg utimesec 113.939678 mri_coreg stimesec 0.579911 mri_coreg ru_maxrss 422124 mri_coreg ru_ixrss 0 mri_coreg ru_idrss 0 mri_coreg ru_isrss 0 mri_coreg ru_minflt 265510 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 129 mri_coreg ru_nivcsw 218 Final RefRAS-to-MovRAS 0.99995 -0.00105 -0.00965 -6.48818; 0.00109 0.99999 0.00469 -40.87054; 0.00964 -0.00470 0.99994 44.73068; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox 0.29090 -0.00281 0.00030 -5.20012; 0.00095 0.06726 -0.28303 59.97077; -0.00183 -0.19457 -0.04625 38.48653; 0.00000 0.00000 0.00000 1.00000; Final parameters -6.4882 -40.8705 44.7307 0.2687 -0.5528 -0.0600 nhits = 106099 out of 16777216, Percent Overlap: 40.5 mri_coreg RunTimeSec 114.6 sec To check run: tkregisterfv --mov bold/tmp.bbregister.6365/template.nii --targ /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/brainmask.mgz --reg bold/tmp.bbregister.6365/mri_coreg.lta --s fsf01anat --surfs mri_coreg done mri_segreg --mov bold/tmp.bbregister.6365/template.nii --init-reg bold/tmp.bbregister.6365/reg.init.dat --out-reg bold/tmp.bbregister.6365/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/tmp.bbregister.6365/template.nii --init-reg bold/tmp.bbregister.6365/reg.init.dat --out-reg bold/tmp.bbregister.6365/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/tmp.bbregister.6365/template.nii regfile bold/tmp.bbregister.6365/reg.init.dat subject fsf01anat dof 6 outregfile bold/tmp.bbregister.6365/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 1459543723 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99995 -0.00105 -0.00965 0.98232; 0.00914 -0.23123 0.97286 -37.86047; 0.00325 0.97290 0.23121 -1.62868; 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 1.083311 1 -25.0 -25.0 25.0 1.051309 2 -25.0 25.0 -25.0 1.054864 3 -25.0 25.0 25.0 1.081770 4 25.0 -25.0 -25.0 1.067926 5 25.0 -25.0 25.0 1.050873 6 25.0 25.0 -25.0 1.030024 7 25.0 25.0 25.0 1.084266 REL: 8 0.696003 8.504343 1.063043 rel = 0.654727 Initial costs ---------------- Number of surface hits 3040 WM Intensity 858.6377 +/- 209.8749 Ctx Intensity 868.9119 +/- 243.4205 Pct Contrast -0.6755 +/- 22.6146 Cost 0.6960 RelCost 0.6547 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 1.0629 1.0629 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 1.0062 1.0062 0.0 5 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 4.0000 0.9908 0.9908 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.9492 0.9492 0.0 18 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 -4.0000 0.9448 0.9448 0.0 30 -4.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.9355 0.9355 0.0 31 -4.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.9241 0.9241 0.0 33 -4.0000 -4.0000 0.0000 -4.0000 4.0000 -4.0000 0.9222 0.9222 0.0 34 -4.0000 -4.0000 0.0000 -4.0000 4.0000 0.0000 0.9048 0.9048 0.0 40 -4.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.8986 0.8986 0.0 273 0.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.8425 0.8425 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.7947 0.7947 0.0 282 0.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.7454 0.7454 0.0 283 0.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.6102 0.6102 0.0 Brute Force -------------------------- Min cost was 0.610218 Number of iterations 729 Search time 1.399000 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 = 0.610218 6 0.382 -4.000 0.000 0.000 0.000 0.000 0.6088949457 8 0.276 -4.000 0.000 0.000 0.000 0.000 0.6088196475 9 0.315 -4.000 0.000 0.000 0.000 0.000 0.6087799486 11 0.341 -4.000 0.000 0.000 0.000 0.000 0.6087733692 12 0.329 -4.000 0.000 0.000 0.000 0.000 0.6087612813 14 0.324 -4.000 0.000 0.000 0.000 0.000 0.6087549140 20 0.324 -3.000 0.000 0.000 0.000 0.000 0.5746081690 30 0.324 -3.021 0.000 0.000 0.000 0.000 0.5745843566 31 0.324 -3.034 0.000 0.000 0.000 0.000 0.5745490332 34 0.324 -3.036 0.000 0.000 0.000 0.000 0.5745438653 36 0.324 -3.037 0.000 0.000 0.000 0.000 0.5745411536 43 0.324 -3.037 -0.139 0.000 0.000 0.000 0.5745334091 44 0.324 -3.037 -0.071 0.000 0.000 0.000 0.5745215456 45 0.324 -3.037 -0.078 0.000 0.000 0.000 0.5745187304 46 0.324 -3.037 -0.096 0.000 0.000 0.000 0.5745154637 47 0.324 -3.037 -0.098 0.000 0.000 0.000 0.5745153552 49 0.324 -3.037 -0.099 0.000 0.000 0.000 0.5745153198 57 0.324 -3.037 -0.100 -0.201 0.000 0.000 0.5741958771 58 0.324 -3.037 -0.100 -0.168 0.000 0.000 0.5741640610 62 0.324 -3.037 -0.100 -0.169 0.000 0.000 0.5741637986 69 0.324 -3.037 -0.100 -0.169 0.382 0.000 0.5691101744 70 0.324 -3.037 -0.100 -0.169 0.459 0.000 0.5687130027 72 0.324 -3.037 -0.100 -0.169 0.443 0.000 0.5686866622 73 0.324 -3.037 -0.100 -0.169 0.444 0.000 0.5686864233 74 0.324 -3.037 -0.100 -0.169 0.445 0.000 0.5686863014 88 0.324 -3.037 -0.100 -0.169 0.445 0.027 0.5686260322 103 0.321 -3.045 -0.099 -0.167 0.441 0.027 0.5686241973 105 0.322 -3.043 -0.100 -0.168 0.443 0.027 0.5686235116 106 0.322 -3.042 -0.100 -0.168 0.443 0.027 0.5686234854 107 0.323 -3.041 -0.100 -0.168 0.443 0.027 0.5686229253 powell nthiter 1: fret = 0.568623 115 0.188 -3.041 -0.100 -0.168 0.443 0.027 0.5680738566 116 0.201 -3.041 -0.100 -0.168 0.443 0.027 0.5679567597 117 0.236 -3.041 -0.100 -0.168 0.443 0.027 0.5678070430 119 0.238 -3.041 -0.100 -0.168 0.443 0.027 0.5678052689 120 0.240 -3.041 -0.100 -0.168 0.443 0.027 0.5678035783 122 0.244 -3.041 -0.100 -0.168 0.443 0.027 0.5678028566 123 0.243 -3.041 -0.100 -0.168 0.443 0.027 0.5678027463 131 0.243 -3.041 -0.100 -0.168 0.443 0.114 0.5676332257 134 0.243 -3.041 -0.100 -0.168 0.443 0.108 0.5676315694 136 0.243 -3.041 -0.100 -0.168 0.443 0.107 0.5676315551 147 0.243 -3.041 -0.106 -0.168 0.443 0.107 0.5676297126 148 0.243 -3.041 -0.107 -0.168 0.443 0.107 0.5676291650 149 0.243 -3.041 -0.119 -0.168 0.443 0.107 0.5676270460 150 0.243 -3.041 -0.116 -0.168 0.443 0.107 0.5676261695 151 0.243 -3.041 -0.115 -0.168 0.443 0.107 0.5676260540 159 0.243 -3.041 -0.115 -0.029 0.443 0.107 0.5666409292 160 0.243 -3.041 -0.115 0.008 0.443 0.107 0.5666355895 161 0.243 -3.041 -0.115 -0.008 0.443 0.107 0.5666240413 164 0.243 -3.041 -0.115 -0.007 0.443 0.107 0.5666240305 172 0.243 -3.041 -0.115 -0.007 0.404 0.107 0.5665818302 173 0.243 -3.041 -0.115 -0.007 0.407 0.107 0.5665814958 174 0.243 -3.041 -0.115 -0.007 0.408 0.107 0.5665813884 189 0.244 -3.038 -0.115 -0.008 0.409 0.107 0.5665780062 190 0.246 -3.032 -0.116 -0.009 0.412 0.107 0.5665745281 193 0.246 -3.031 -0.116 -0.009 0.412 0.107 0.5665742939 powell nthiter 2: fret = 0.566574 201 0.150 -3.031 -0.116 -0.009 0.412 0.107 0.5665409139 202 0.194 -3.031 -0.116 -0.009 0.412 0.107 0.5663031664 203 0.197 -3.031 -0.116 -0.009 0.412 0.107 0.5662995016 204 0.206 -3.031 -0.116 -0.009 0.412 0.107 0.5662934947 206 0.205 -3.031 -0.116 -0.009 0.412 0.107 0.5662931920 214 0.205 -3.031 -0.116 -0.009 0.412 0.098 0.5662739078 215 0.205 -3.031 -0.116 -0.009 0.412 0.021 0.5662487535 217 0.205 -3.031 -0.116 -0.009 0.412 0.052 0.5662394047 218 0.205 -3.031 -0.116 -0.009 0.412 0.048 0.5662380703 219 0.205 -3.031 -0.116 -0.009 0.412 0.043 0.5662366346 221 0.205 -3.031 -0.116 -0.009 0.412 0.041 0.5662361231 222 0.205 -3.031 -0.116 -0.009 0.412 0.040 0.5662359616 223 0.205 -3.031 -0.116 -0.009 0.412 0.038 0.5662358682 231 0.205 -3.031 -0.113 -0.009 0.412 0.038 0.5662227771 232 0.205 -3.031 -0.063 -0.009 0.412 0.038 0.5661138356 235 0.205 -3.031 -0.070 -0.009 0.412 0.038 0.5661103308 236 0.205 -3.031 -0.071 -0.009 0.412 0.038 0.5661102844 249 0.205 -3.031 -0.072 0.091 0.412 0.038 0.5659033885 251 0.205 -3.031 -0.072 0.059 0.412 0.038 0.5658567785 252 0.205 -3.031 -0.072 0.061 0.412 0.038 0.5658565120 262 0.205 -3.031 -0.072 0.061 0.398 0.038 0.5658481006 264 0.205 -3.031 -0.072 0.061 0.404 0.038 0.5658320693 273 0.218 -2.992 -0.076 0.054 0.422 0.039 0.5657713063 274 0.216 -2.997 -0.075 0.055 0.419 0.039 0.5657109693 276 0.215 -3.002 -0.075 0.056 0.417 0.039 0.5657084187 277 0.215 -3.001 -0.075 0.055 0.418 0.039 0.5657057140 278 0.215 -3.000 -0.075 0.055 0.418 0.039 0.5657034651 279 0.216 -2.999 -0.075 0.055 0.419 0.039 0.5657016512 280 0.185 -2.967 -0.035 0.119 0.425 -0.030 0.5655312015 powell nthiter 3: fret = 0.565702 341 0.201 -2.999 -0.051 0.072 0.404 0.012 0.5655245601 344 0.201 -2.999 -0.051 0.072 0.399 0.012 0.5655244770 346 0.201 -2.999 -0.051 0.072 0.401 0.012 0.5655209827 348 0.201 -2.999 -0.051 0.072 0.400 0.012 0.5655202100 357 0.202 -2.996 -0.051 0.071 0.402 0.012 0.5655033387 358 0.204 -2.991 -0.052 0.071 0.404 0.013 0.5654914325 360 0.203 -2.993 -0.052 0.071 0.403 0.013 0.5654874315 powell nthiter 4: fret = 0.565487 374 0.204 -2.993 -0.052 0.071 0.403 0.013 0.5654870053 382 0.204 -2.993 -0.052 0.071 0.403 0.009 0.5654826995 384 0.204 -2.993 -0.052 0.071 0.403 0.007 0.5654818649 395 0.204 -2.993 -0.046 0.071 0.403 0.007 0.5654803965 406 0.204 -2.993 -0.047 0.085 0.403 0.007 0.5654715163 407 0.204 -2.993 -0.047 0.083 0.403 0.007 0.5654712014 417 0.204 -2.993 -0.047 0.083 0.402 0.007 0.5654697103 429 0.205 -2.991 -0.047 0.083 0.403 0.007 0.5654611619 430 0.206 -2.986 -0.048 0.082 0.405 0.007 0.5654397630 Powell done niters = 4 Computing relative cost 0 -25.0 -25.0 -25.0 1.046751 1 -25.0 -25.0 25.0 1.049925 2 -25.0 25.0 -25.0 1.073495 3 -25.0 25.0 25.0 1.083916 4 25.0 -25.0 -25.0 1.047432 5 25.0 -25.0 25.0 1.043519 6 25.0 25.0 -25.0 1.023743 7 25.0 25.0 25.0 1.041117 REL: 8 0.565440 8.409899 1.051237 rel = 0.53788 Number of iterations 4 Min cost was 0.565440 Number of FunctionCalls 435 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.832000 sec Parameters at optimum (transmm) 0.20611 -2.98644 -0.04755 Parameters at optimum (rotdeg) 0.08215 0.40505 0.00728 Final costs ---------------- Number of surface hits 3040 WM Intensity 823.4812 +/- 226.6387 Ctx Intensity 852.8414 +/- 261.7289 Pct Contrast 1.3812 +/- 22.7389 Cost 0.5654 RelCost 0.6547 Reg at min cost was 0.99995 0.00586 -0.00813 1.18132; 0.00927 -0.23262 0.97252 -40.84442; -0.00381 0.97255 0.23266 -1.73742; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/tmp.bbregister.6365/bbr.pass1.dat, type = 14 Original Reg 0.99995 -0.00105 -0.00965 0.98232; 0.00914 -0.23123 0.97286 -37.86047; 0.00325 0.97290 0.23121 -1.62868; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00000 -0.00691 -0.00152 -0.19900; -0.00012 0.00139 0.00033 2.98394; 0.00706 0.00035 -0.00146 0.10874; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 3.002696 Computing change in rh position Surface-RMS-Diff-mm 3.006413 0.085604 3.234398 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/tmp.bbregister.6365/template.nii --init-reg bold/tmp.bbregister.6365/bbr.pass1.dat --out-reg bold/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/tmp.bbregister.6365/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/tmp.bbregister.6365/template.nii --init-reg bold/tmp.bbregister.6365/bbr.pass1.dat --out-reg bold/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/tmp.bbregister.6365/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/tmp.bbregister.6365/template.nii regfile bold/tmp.bbregister.6365/bbr.pass1.dat subject fsf01anat dof 6 outregfile bold/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 1459147969 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99995 0.00586 -0.00813 1.18132; 0.00927 -0.23262 0.97252 -40.84442; -0.00381 0.97255 0.23266 -1.73742; 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 1.033917 1 -25.0 -25.0 25.0 1.054409 2 -25.0 25.0 -25.0 1.061950 3 -25.0 25.0 25.0 1.071155 4 25.0 -25.0 -25.0 1.042408 5 25.0 -25.0 25.0 1.034931 6 25.0 25.0 -25.0 1.033287 7 25.0 25.0 25.0 1.061837 REL: 8 0.572625 8.393893 1.049237 rel = 0.545754 Initial costs ---------------- Number of surface hits 304441 WM Intensity 824.7969 +/- 224.4640 Ctx Intensity 853.3974 +/- 259.6470 Pct Contrast 1.3784 +/- 23.5542 Cost 0.5726 RelCost 0.5458 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.5700 0.5700 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.5694 0.5694 0.0 2 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.5684 0.5684 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.5679 0.5679 0.0 5 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1000 0.5676 0.5676 0.0 14 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.1000 0.5673 0.5673 0.0 85 -0.1000 0.0000 -0.1000 -0.1000 0.0000 0.0000 0.5669 0.5669 0.0 92 -0.1000 0.0000 -0.1000 0.0000 -0.1000 0.1000 0.5665 0.5665 0.0 94 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.0000 0.5662 0.5662 0.0 95 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.1000 0.5661 0.5661 0.0 185 -0.1000 0.1000 -0.1000 0.1000 0.0000 0.1000 0.5659 0.5659 0.0 187 -0.1000 0.1000 -0.1000 0.1000 0.1000 0.0000 0.5658 0.5658 0.0 334 0.0000 0.0000 -0.1000 0.0000 -0.1000 0.0000 0.5655 0.5655 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.5654 0.5654 0.0 427 0.0000 0.1000 -0.1000 0.1000 0.0000 0.0000 0.5654 0.5654 0.0 Brute Force -------------------------- Min cost was 0.565439 Number of iterations 729 Search time 1.400000 sec Parameters at best (transmm, rotdeg) 0.000 0.100 -0.100 0.100 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0.1 2 -0.1 3 0.1 4 0 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000000 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.574334 7 -0.152 0.100 -0.100 0.100 0.000 0.000 0.5740838514 8 -0.115 0.100 -0.100 0.100 0.000 0.000 0.5740361834 9 -0.108 0.100 -0.100 0.100 0.000 0.000 0.5740341107 11 -0.107 0.100 -0.100 0.100 0.000 0.000 0.5740340539 18 -0.107 0.482 -0.100 0.100 0.000 0.000 0.5732433597 19 -0.107 0.333 -0.100 0.100 0.000 0.000 0.5728437757 20 -0.107 0.342 -0.100 0.100 0.000 0.000 0.5728343078 21 -0.107 0.357 -0.100 0.100 0.000 0.000 0.5728218038 24 -0.107 0.374 -0.100 0.100 0.000 0.000 0.5728191235 25 -0.107 0.369 -0.100 0.100 0.000 0.000 0.5728180167 26 -0.107 0.368 -0.100 0.100 0.000 0.000 0.5728179701 35 -0.107 0.367 0.282 0.100 0.000 0.000 0.5724629506 36 -0.107 0.367 0.110 0.100 0.000 0.000 0.5717696334 37 -0.107 0.367 0.111 0.100 0.000 0.000 0.5717693458 38 -0.107 0.367 0.117 0.100 0.000 0.000 0.5717690940 40 -0.107 0.367 0.115 0.100 0.000 0.000 0.5717688895 47 -0.107 0.367 0.115 -0.518 0.000 0.000 0.5621395859 49 -0.107 0.367 0.115 -0.592 0.000 0.000 0.5619647560 52 -0.107 0.367 0.115 -0.591 0.000 0.000 0.5619646731 60 -0.107 0.367 0.115 -0.591 -0.083 0.000 0.5617906006 61 -0.107 0.367 0.115 -0.591 -0.076 0.000 0.5617872865 62 -0.107 0.367 0.115 -0.591 -0.073 0.000 0.5617867623 71 -0.107 0.367 0.115 -0.591 -0.073 -0.227 0.5612106612 powell nthiter 1: fret = 0.561211 87 -0.173 0.367 0.115 -0.591 -0.073 -0.227 0.5611533745 88 -0.156 0.367 0.115 -0.591 -0.073 -0.227 0.5611454858 89 -0.155 0.367 0.115 -0.591 -0.073 -0.227 0.5611454157 90 -0.154 0.367 0.115 -0.591 -0.073 -0.227 0.5611454088 99 -0.154 0.484 0.115 -0.591 -0.073 -0.227 0.5608218206 101 -0.154 0.493 0.115 -0.591 -0.073 -0.227 0.5608209513 103 -0.154 0.490 0.115 -0.591 -0.073 -0.227 0.5608204314 112 -0.154 0.489 0.140 -0.591 -0.073 -0.227 0.5608048442 121 -0.154 0.489 0.139 -0.655 -0.073 -0.227 0.5607661379 122 -0.154 0.489 0.139 -0.637 -0.073 -0.227 0.5607644810 123 -0.154 0.489 0.139 -0.643 -0.073 -0.227 0.5607631156 124 -0.154 0.489 0.139 -0.645 -0.073 -0.227 0.5607630528 132 -0.154 0.489 0.139 -0.645 -0.109 -0.227 0.5607085328 134 -0.154 0.489 0.139 -0.645 -0.112 -0.227 0.5607080568 143 -0.154 0.489 0.139 -0.645 -0.112 -0.260 0.5606905357 144 -0.154 0.489 0.139 -0.645 -0.112 -0.266 0.5606903635 150 -0.154 0.489 0.139 -0.645 -0.112 -0.270 0.5606902735 152 -0.154 0.489 0.139 -0.645 -0.112 -0.268 0.5606902497 powell nthiter 2: fret = 0.560690 160 -0.188 0.489 0.139 -0.645 -0.112 -0.268 0.5606870293 161 -0.173 0.489 0.139 -0.645 -0.112 -0.268 0.5606806368 170 -0.173 0.506 0.139 -0.645 -0.112 -0.268 0.5606800873 171 -0.173 0.498 0.139 -0.645 -0.112 -0.268 0.5606791202 181 -0.173 0.499 0.127 -0.645 -0.112 -0.268 0.5606763680 191 -0.173 0.499 0.129 -0.642 -0.112 -0.268 0.5606760673 192 -0.173 0.499 0.129 -0.640 -0.112 -0.268 0.5606760156 193 -0.173 0.499 0.129 -0.639 -0.112 -0.268 0.5606757540 198 -0.173 0.499 0.129 -0.635 -0.112 -0.268 0.5606754372 207 -0.173 0.499 0.129 -0.635 -0.117 -0.268 0.5606750492 217 -0.173 0.499 0.129 -0.635 -0.117 -0.272 0.5606739954 218 -0.173 0.499 0.129 -0.635 -0.117 -0.279 0.5606734052 powell nthiter 3: fret = 0.560673 229 -0.174 0.499 0.129 -0.635 -0.117 -0.280 0.5606732722 230 -0.175 0.499 0.129 -0.635 -0.117 -0.280 0.5606732242 239 -0.175 0.497 0.129 -0.635 -0.117 -0.280 0.5606729538 241 -0.175 0.493 0.129 -0.635 -0.117 -0.280 0.5606727874 242 -0.175 0.492 0.129 -0.635 -0.117 -0.280 0.5606727718 243 -0.175 0.491 0.129 -0.635 -0.117 -0.280 0.5606727681 269 -0.175 0.491 0.129 -0.628 -0.117 -0.280 0.5606705370 270 -0.175 0.491 0.129 -0.625 -0.117 -0.280 0.5606704198 271 -0.175 0.491 0.129 -0.626 -0.117 -0.280 0.5606703453 279 -0.175 0.491 0.129 -0.626 -0.118 -0.280 0.5606702392 280 -0.175 0.491 0.129 -0.626 -0.119 -0.280 0.5606699522 286 -0.175 0.491 0.129 -0.626 -0.121 -0.280 0.5606698293 powell nthiter 4: fret = 0.560670 305 -0.176 0.491 0.129 -0.626 -0.121 -0.280 0.5606697719 306 -0.177 0.491 0.129 -0.626 -0.121 -0.280 0.5606697693 317 -0.178 0.486 0.129 -0.626 -0.121 -0.280 0.5606697219 318 -0.178 0.489 0.129 -0.626 -0.121 -0.280 0.5606695357 powell nthiter 5: fret = 0.560670 Powell done niters = 5 Computing relative cost 0 -25.0 -25.0 -25.0 1.035909 1 -25.0 -25.0 25.0 1.053714 2 -25.0 25.0 -25.0 1.061847 3 -25.0 25.0 25.0 1.073981 4 25.0 -25.0 -25.0 1.048710 5 25.0 -25.0 25.0 1.040168 6 25.0 25.0 -25.0 1.030810 7 25.0 25.0 25.0 1.063426 REL: 8 0.560670 8.408567 1.051071 rel = 0.533427 Number of iterations 5 Min cost was 0.560670 Number of FunctionCalls 419 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 50.472000 sec Parameters at optimum (transmm) -0.17708 0.48899 0.12883 Parameters at optimum (rotdeg) -0.62551 -0.12050 -0.28116 Final costs ---------------- Number of surface hits 304441 WM Intensity 828.8717 +/- 218.1828 Ctx Intensity 860.1954 +/- 253.4915 Pct Contrast 1.7561 +/- 22.8229 Cost 0.5607 RelCost 0.5458 Reg at min cost was 0.99999 0.00272 -0.00381 0.80644; 0.00432 -0.22201 0.97504 -40.37728; -0.00180 0.97504 0.22201 -1.16010; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/register.dof6.dat, type = 14 Original Reg 0.99995 0.00586 -0.00813 1.18132; 0.00927 -0.23262 0.97252 -40.84442; -0.00381 0.97255 0.23266 -1.73742; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00004 0.00314 -0.00432 0.37489; 0.00495 -0.01062 -0.00251 -0.46714; -0.00200 -0.00249 0.01065 -0.57732; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.738681 Computing change in rh position Surface-RMS-Diff-mm 0.710759 0.368009 1.646569 mri_segreg done MinCost: 0.560670 828.871695 860.195415 1.756131 tkregister2_cmdl --mov bold/template.nii.gz --reg bold/register.dof6.dat --noedit --ltaout bold/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/template.nii.gz reg file bold/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 -------- 0.99999 0.00272 -0.00381 0.80644; 0.00432 -0.22201 0.97504 -40.37728; -0.00180 0.97504 0.22201 -1.16010; 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/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 -------- 0.99999 0.00272 -0.00381 0.80644; 0.00432 -0.22201 0.97504 -40.37728; -0.00180 0.97504 0.22201 -1.16010; 0.00000 0.00000 0.00000 1.00000; Determinant -1 subject = fsf01anat RegMat --------------------------- 0.99999 0.00272 -0.00381 0.80644; 0.00432 -0.22201 0.97504 -40.37728; -0.00180 0.97504 0.22201 -1.16010; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Sun Mar 27 21:37:27 EDT 2016 Ended at Sun Mar 27 21:40:38 EDT 2016 BBR-Run-Time-Sec 191 bbregister Done To check results, run: tkregister2 --mov bold/template.nii.gz --reg bold/register.dof6.dat --surf