Logfile for bbregister Sun Mar 27 21:47:05 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/003/template.nii.gz --reg bold/003/register.dof6.dat --lta bold/003/register.dof6.lta --init-reg-out bold/003/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/003/template.nii.gz bold/003/tmp.bbregister.9239/template.nii mri_convert.bin bold/003/template.nii.gz bold/003/tmp.bbregister.9239/template.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from bold/003/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/003/tmp.bbregister.9239/template.nii... mri_coreg --s fsf01anat --mov bold/003/tmp.bbregister.9239/template.nii --regdat bold/003/tmp.bbregister.9239/reg.init.dat --reg bold/003/tmp.bbregister.9239/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/003/tmp.bbregister.9239/template.nii --regdat bold/003/tmp.bbregister.9239/reg.init.dat --reg bold/003/tmp.bbregister.9239/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/003/tmp.bbregister.9239/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 = 1708.3334 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 -1.0202975942 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 -1.0499788 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6 Starting OpenPowel2(), sep = 4 InitialCost -1.0710277557 #@# 4 188 -6.02228 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0710278 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.071028 #@# 4 191 -7.64031 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0713971 #@# 4 192 -7.20970 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0714792 #@# 4 196 -7.17804 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0714808 #@# 4 202 -7.16804 -36.87573 49.23798 4.00000 0.00000 0.00000 -1.0740036 #@# 4 205 -7.16804 -40.14709 49.23798 4.00000 0.00000 0.00000 -1.0760239 #@# 4 207 -7.16804 -39.66540 49.23798 4.00000 0.00000 0.00000 -1.0760907 #@# 4 209 -7.16804 -39.69576 49.23798 4.00000 0.00000 0.00000 -1.0760912 #@# 4 211 -7.16804 -39.71626 49.23798 4.00000 0.00000 0.00000 -1.0760921 #@# 4 214 -7.16804 -39.72625 49.23798 4.00000 0.00000 0.00000 -1.0760937 #@# 4 217 -7.16804 -39.72625 47.61994 4.00000 0.00000 0.00000 -1.0762608 #@# 4 218 -7.16804 -39.72625 48.27965 4.00000 0.00000 0.00000 -1.0763843 #@# 4 222 -7.16804 -39.72625 48.26255 4.00000 0.00000 0.00000 -1.0763875 #@# 4 227 -7.16804 -39.72625 48.19618 4.00000 0.00000 0.00000 -1.0763898 #@# 4 228 -7.16804 -39.72625 48.20618 4.00000 0.00000 0.00000 -1.0763899 #@# 4 233 -7.16804 -39.72625 48.20618 3.38197 0.00000 0.00000 -1.0765280 #@# 4 235 -7.16804 -39.72625 48.20618 3.55769 0.00000 0.00000 -1.0765572 #@# 4 236 -7.16804 -39.72625 48.20618 3.56769 0.00000 0.00000 -1.0765582 #@# 4 238 -7.16804 -39.72625 48.20618 3.57769 0.00000 0.00000 -1.0765584 #@# 4 246 -7.16804 -39.72625 48.20618 3.57769 -0.26120 0.00000 -1.0765694 #@# 4 251 -7.16804 -39.72625 48.20618 3.57769 -0.28120 0.00000 -1.0765697 #@# 4 257 -7.16804 -39.72625 48.20618 3.57769 -0.28120 -0.61803 -1.0767374 #@# 4 259 -7.16804 -39.72625 48.20618 3.57769 -0.28120 -0.46037 -1.0767633 #@# 4 261 -7.16804 -39.72625 48.20618 3.57769 -0.28120 -0.49442 -1.0767654 #@# 4 264 -7.16804 -39.72625 48.20618 3.57769 -0.28120 -0.48413 -1.0767661 powell nthiter 1: fret = -1.076766 #@# 4 273 -7.02185 -39.72625 48.20618 3.57769 -0.28120 -0.48413 -1.0767806 #@# 4 274 -7.03185 -39.72625 48.20618 3.57769 -0.28120 -0.48413 -1.0767807 #@# 4 275 -7.04185 -39.72625 48.20618 3.57769 -0.28120 -0.48413 -1.0767813 #@# 4 284 -7.04185 -39.89198 48.20618 3.57769 -0.28120 -0.48413 -1.0767962 #@# 4 287 -7.04185 -39.90197 48.20618 3.57769 -0.28120 -0.48413 -1.0767970 #@# 4 292 -7.04185 -39.90197 47.58815 3.57769 -0.28120 -0.48413 -1.0768745 #@# 4 299 -7.04185 -39.90197 47.60170 3.57769 -0.28120 -0.48413 -1.0768762 #@# 4 305 -7.04185 -39.90197 47.60170 2.95966 -0.28120 -0.48413 -1.0769082 #@# 4 307 -7.04185 -39.90197 47.60170 3.23260 -0.28120 -0.48413 -1.0769733 #@# 4 308 -7.04185 -39.90197 47.60170 3.24260 -0.28120 -0.48413 -1.0769756 #@# 4 310 -7.04185 -39.90197 47.60170 3.28445 -0.28120 -0.48413 -1.0769801 #@# 4 330 -7.04185 -39.90197 47.60170 3.28445 -0.28120 -0.56028 -1.0769842 #@# 4 331 -7.04185 -39.90197 47.60170 3.28445 -0.28120 -0.54787 -1.0769848 #@# 4 333 -6.91566 -40.07769 46.99722 2.99120 -0.28120 -0.61160 -1.0771338 #@# 4 336 -6.71148 -40.36202 46.01915 2.51671 -0.28120 -0.71472 -1.0771655 #@# 4 337 -6.78855 -40.25469 46.38836 2.69583 -0.28120 -0.67579 -1.0771891 #@# 4 341 -6.77987 -40.26678 46.34677 2.67565 -0.28120 -0.68018 -1.0771896 #@# 4 342 -6.78113 -40.26502 46.35282 2.67858 -0.28120 -0.67954 -1.0771897 #@# 4 343 -6.78285 -40.26263 46.36103 2.68257 -0.28120 -0.67868 -1.0771898 #@# 4 344 -6.78503 -40.25960 46.37147 2.68763 -0.28120 -0.67757 -1.0771900 powell nthiter 2: fret = -1.077190 #@# 4 353 -6.77503 -40.25960 46.37147 2.68763 -0.28120 -0.67757 -1.0771902 #@# 4 364 -6.77503 -40.16743 46.37147 2.68763 -0.28120 -0.67757 -1.0771923 #@# 4 374 -6.77503 -40.16743 46.75343 2.68763 -0.28120 -0.67757 -1.0772008 #@# 4 375 -6.77503 -40.16743 46.58694 2.68763 -0.28120 -0.67757 -1.0772063 #@# 4 376 -6.77503 -40.16743 46.60578 2.68763 -0.28120 -0.67757 -1.0772073 #@# 4 378 -6.77503 -40.16743 46.61578 2.68763 -0.28120 -0.67757 -1.0772086 #@# 4 386 -6.77503 -40.16743 46.61578 2.68763 -0.28120 -0.77400 -1.0772150 #@# 4 398 -6.77503 -40.16743 46.61578 2.68763 -0.37044 -0.77400 -1.0772165 #@# 4 401 -6.77503 -40.16743 46.61578 2.68763 -0.31161 -0.77400 -1.0772182 #@# 4 408 -6.72683 -40.23455 46.38489 2.57562 -0.31161 -0.79835 -1.0772325 Powell done niters total = 2 OptTimeSec 18.1 sec OptTimeMin 0.30 min nEvals 412 Final parameters -6.72682571 -40.23455048 46.38489151 2.57562280 -0.31161472 -0.79834813 Final cost -1.077232506625936 --------------------------------- mri_coreg utimesec 107.507656 mri_coreg stimesec 0.536918 mri_coreg ru_maxrss 422120 mri_coreg ru_ixrss 0 mri_coreg ru_idrss 0 mri_coreg ru_isrss 0 mri_coreg ru_minflt 239950 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 47 mri_coreg ru_nivcsw 123 Final RefRAS-to-MovRAS 0.99989 -0.01393 -0.00544 -6.72683; 0.01416 0.99889 0.04494 -40.23455; 0.00481 -0.04501 0.99897 46.38489; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox 0.29088 -0.00158 0.00405 -5.50132; 0.00433 0.07860 -0.28006 57.90867; -0.00029 -0.19256 -0.05405 38.90065; 0.00000 0.00000 0.00000 1.00000; Final parameters -6.7268 -40.2346 46.3849 2.5756 -0.3116 -0.7983 nhits = 105924 out of 16777216, Percent Overlap: 40.4 mri_coreg RunTimeSec 108.1 sec To check run: tkregisterfv --mov bold/003/tmp.bbregister.9239/template.nii --targ /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/brainmask.mgz --reg bold/003/tmp.bbregister.9239/mri_coreg.lta --s fsf01anat --surfs mri_coreg done mri_segreg --mov bold/003/tmp.bbregister.9239/template.nii --init-reg bold/003/tmp.bbregister.9239/reg.init.dat --out-reg bold/003/tmp.bbregister.9239/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/003/tmp.bbregister.9239/template.nii --init-reg bold/003/tmp.bbregister.9239/reg.init.dat --out-reg bold/003/tmp.bbregister.9239/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/003/tmp.bbregister.9239/template.nii regfile bold/003/tmp.bbregister.9239/reg.init.dat subject fsf01anat dof 6 outregfile bold/003/tmp.bbregister.9239/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 1459445017 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99989 -0.01393 -0.00544 -0.16222; 0.00147 -0.27024 0.96279 -38.51289; 0.01488 0.96269 0.27019 -2.32548; 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 1.064490 1 -25.0 -25.0 25.0 1.053749 2 -25.0 25.0 -25.0 1.068206 3 -25.0 25.0 25.0 1.069813 4 25.0 -25.0 -25.0 1.061733 5 25.0 -25.0 25.0 1.041060 6 25.0 25.0 -25.0 1.037284 7 25.0 25.0 25.0 1.063876 REL: 8 0.712841 8.460211 1.057526 rel = 0.674065 Initial costs ---------------- Number of surface hits 3040 WM Intensity 848.1464 +/- 206.9645 Ctx Intensity 853.5742 +/- 234.8119 Pct Contrast -1.0428 +/- 20.9501 Cost 0.7128 RelCost 0.6741 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 1.0661 1.0661 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 1.0498 1.0498 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 1.0052 1.0052 0.0 5 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 4.0000 0.9773 0.9773 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.9715 0.9715 0.0 8 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 4.0000 0.9548 0.9548 0.0 18 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 -4.0000 0.9470 0.9470 0.0 30 -4.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.9254 0.9254 0.0 34 -4.0000 -4.0000 0.0000 -4.0000 4.0000 0.0000 0.9160 0.9160 0.0 40 -4.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.8973 0.8973 0.0 273 0.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.8276 0.8276 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.7740 0.7740 0.0 282 0.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.7555 0.7555 0.0 283 0.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.6114 0.6114 0.0 Brute Force -------------------------- Min cost was 0.611427 Number of iterations 729 Search time 1.424000 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 = 0.611427 7 0.086 -4.000 0.000 0.000 0.000 0.000 0.6110832010 9 0.069 -4.000 0.000 0.000 0.000 0.000 0.6110689071 10 0.073 -4.000 0.000 0.000 0.000 0.000 0.6110668926 11 0.074 -4.000 0.000 0.000 0.000 0.000 0.6110667963 14 0.074 -3.000 0.000 0.000 0.000 0.000 0.5762751272 19 0.074 -2.780 0.000 0.000 0.000 0.000 0.5750879568 22 0.074 -2.766 0.000 0.000 0.000 0.000 0.5750816091 23 0.074 -2.768 0.000 0.000 0.000 0.000 0.5750813194 34 0.074 -2.769 -0.007 0.000 0.000 0.000 0.5750800698 36 0.074 -2.769 -0.005 0.000 0.000 0.000 0.5750795277 37 0.074 -2.769 -0.004 0.000 0.000 0.000 0.5750793737 45 0.074 -2.769 -0.004 -0.188 0.000 0.000 0.5731449330 46 0.074 -2.769 -0.004 -0.231 0.000 0.000 0.5730869485 47 0.074 -2.769 -0.004 -0.227 0.000 0.000 0.5730854129 48 0.074 -2.769 -0.004 -0.225 0.000 0.000 0.5730847681 59 0.074 -2.769 -0.004 -0.225 -0.068 0.000 0.5725784834 61 0.074 -2.769 -0.004 -0.225 -0.090 0.000 0.5725432845 62 0.074 -2.769 -0.004 -0.225 -0.092 0.000 0.5725428360 70 0.074 -2.769 -0.004 -0.225 -0.092 -0.283 0.5717403601 71 0.074 -2.769 -0.004 -0.225 -0.092 -0.279 0.5717324154 73 0.074 -2.769 -0.004 -0.225 -0.092 -0.259 0.5717052529 74 0.074 -2.769 -0.004 -0.225 -0.092 -0.247 0.5716930073 77 0.074 -2.769 -0.004 -0.225 -0.092 -0.245 0.5716893200 78 0.074 -2.769 -0.004 -0.225 -0.092 -0.243 0.5716861491 powell nthiter 1: fret = 0.571686 101 0.075 -2.769 -0.004 -0.225 -0.092 -0.243 0.5716853711 102 0.086 -2.769 -0.004 -0.225 -0.092 -0.243 0.5716718018 105 0.106 -2.769 -0.004 -0.225 -0.092 -0.243 0.5716494029 107 0.110 -2.769 -0.004 -0.225 -0.092 -0.243 0.5716479167 108 0.111 -2.769 -0.004 -0.225 -0.092 -0.243 0.5716477313 109 0.114 -2.769 -0.004 -0.225 -0.092 -0.243 0.5716473342 111 0.113 -2.769 -0.004 -0.225 -0.092 -0.243 0.5716471628 136 0.113 -2.769 0.052 -0.225 -0.092 -0.243 0.5715540922 140 0.113 -2.769 0.049 -0.225 -0.092 -0.243 0.5715535052 150 0.113 -2.769 0.048 -0.250 -0.092 -0.243 0.5714838203 151 0.113 -2.769 0.048 -0.252 -0.092 -0.243 0.5714830893 159 0.113 -2.769 0.048 -0.252 -0.126 -0.243 0.5710646421 161 0.113 -2.769 0.048 -0.252 -0.170 -0.243 0.5710512642 162 0.113 -2.769 0.048 -0.252 -0.149 -0.243 0.5709812709 176 0.113 -2.771 0.048 -0.251 -0.149 -0.242 0.5709718280 powell nthiter 2: fret = 0.570972 191 0.112 -2.771 0.048 -0.251 -0.149 -0.242 0.5709712708 212 0.112 -2.771 0.016 -0.251 -0.149 -0.242 0.5709397252 215 0.112 -2.771 0.020 -0.251 -0.149 -0.242 0.5709384474 217 0.112 -2.771 0.019 -0.251 -0.149 -0.242 0.5709383487 218 0.112 -2.771 0.018 -0.251 -0.149 -0.242 0.5709382848 226 0.112 -2.771 0.018 -0.290 -0.149 -0.242 0.5709004748 230 0.112 -2.771 0.018 -0.291 -0.149 -0.242 0.5708999470 232 0.112 -2.771 0.018 -0.294 -0.149 -0.242 0.5708994141 233 0.112 -2.771 0.018 -0.295 -0.149 -0.242 0.5708993348 244 0.112 -2.771 0.018 -0.295 -0.155 -0.242 0.5708983296 245 0.112 -2.771 0.018 -0.295 -0.152 -0.242 0.5708972395 259 0.112 -2.777 0.018 -0.294 -0.152 -0.241 0.5708932587 260 0.112 -2.775 0.018 -0.294 -0.152 -0.241 0.5708779739 powell nthiter 3: fret = 0.570878 272 0.113 -2.775 0.018 -0.294 -0.152 -0.241 0.5708765324 273 0.114 -2.775 0.018 -0.294 -0.152 -0.241 0.5708752883 294 0.114 -2.775 0.012 -0.294 -0.152 -0.241 0.5708694707 295 0.114 -2.775 0.006 -0.294 -0.152 -0.241 0.5708683940 296 0.114 -2.775 0.008 -0.294 -0.152 -0.241 0.5708681606 304 0.114 -2.775 0.008 -0.309 -0.152 -0.241 0.5708675109 305 0.114 -2.775 0.008 -0.302 -0.152 -0.241 0.5708647982 307 0.114 -2.775 0.008 -0.303 -0.152 -0.241 0.5708647687 320 0.114 -2.775 0.008 -0.303 -0.154 -0.241 0.5708639190 321 0.114 -2.775 0.008 -0.303 -0.155 -0.241 0.5708638899 335 0.114 -2.776 0.008 -0.303 -0.155 -0.241 0.5708613627 Powell done niters = 3 Computing relative cost 0 -25.0 -25.0 -25.0 1.035794 1 -25.0 -25.0 25.0 1.061384 2 -25.0 25.0 -25.0 1.067881 3 -25.0 25.0 25.0 1.084840 4 25.0 -25.0 -25.0 1.045115 5 25.0 -25.0 25.0 1.043826 6 25.0 25.0 -25.0 1.005493 7 25.0 25.0 25.0 1.033448 REL: 8 0.570861 8.377779 1.047222 rel = 0.545119 Number of iterations 3 Min cost was 0.570861 Number of FunctionCalls 337 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.659000 sec Parameters at optimum (transmm) 0.11433 -2.77582 0.00807 Parameters at optimum (rotdeg) -0.30293 -0.15539 -0.24108 Final costs ---------------- Number of surface hits 3040 WM Intensity 815.0247 +/- 221.7895 Ctx Intensity 841.8167 +/- 253.2951 Pct Contrast 1.1337 +/- 22.0110 Cost 0.5709 RelCost 0.6741 Reg at min cost was 0.99984 -0.01766 -0.00210 -0.20423; -0.00266 -0.26507 0.96423 -41.29947; 0.01759 0.96407 0.26508 -2.11419; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/003/tmp.bbregister.9239/bbr.pass1.dat, type = 14 Original Reg 0.99989 -0.01393 -0.00544 -0.16222; 0.00147 -0.27024 0.96279 -38.51289; 0.01488 0.96269 0.27019 -2.32548; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00005 0.00373 -0.00334 0.04201; 0.00413 -0.00517 -0.00143 2.78658; -0.00270 -0.00137 0.00511 -0.21129; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 2.726874 Computing change in rh position Surface-RMS-Diff-mm 2.836810 0.269703 3.367713 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/003/tmp.bbregister.9239/template.nii --init-reg bold/003/tmp.bbregister.9239/bbr.pass1.dat --out-reg bold/003/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/003/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/003/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/003/tmp.bbregister.9239/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/003/tmp.bbregister.9239/template.nii --init-reg bold/003/tmp.bbregister.9239/bbr.pass1.dat --out-reg bold/003/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/003/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/003/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/003/tmp.bbregister.9239/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/003/tmp.bbregister.9239/template.nii regfile bold/003/tmp.bbregister.9239/bbr.pass1.dat subject fsf01anat dof 6 outregfile bold/003/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 1460084016 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99984 -0.01766 -0.00210 -0.20423; -0.00266 -0.26507 0.96423 -41.29947; 0.01759 0.96407 0.26508 -2.11419; 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 1.037860 1 -25.0 -25.0 25.0 1.050974 2 -25.0 25.0 -25.0 1.056127 3 -25.0 25.0 25.0 1.065740 4 25.0 -25.0 -25.0 1.029204 5 25.0 -25.0 25.0 1.033160 6 25.0 25.0 -25.0 1.018567 7 25.0 25.0 25.0 1.056295 REL: 8 0.586631 8.347926 1.043491 rel = 0.562182 Initial costs ---------------- Number of surface hits 304441 WM Intensity 817.0696 +/- 218.7005 Ctx Intensity 843.7289 +/- 248.8705 Pct Contrast 1.3464 +/- 21.8518 Cost 0.5866 RelCost 0.5622 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.5742 0.5742 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.5735 0.5735 0.0 2 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.5733 0.5733 0.0 5 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1000 0.5729 0.5729 0.0 11 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.1000 0.5729 0.5729 0.0 13 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.5727 0.5727 0.0 14 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.1000 0.5727 0.5727 0.0 24 -0.1000 -0.1000 -0.1000 0.1000 0.1000 -0.1000 0.5725 0.5725 0.0 25 -0.1000 -0.1000 -0.1000 0.1000 0.1000 0.0000 0.5725 0.5725 0.0 41 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.1000 0.5723 0.5723 0.0 85 -0.1000 0.0000 -0.1000 -0.1000 0.0000 0.0000 0.5720 0.5720 0.0 86 -0.1000 0.0000 -0.1000 -0.1000 0.0000 0.1000 0.5719 0.5719 0.0 93 -0.1000 0.0000 -0.1000 0.0000 0.0000 -0.1000 0.5718 0.5718 0.0 94 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.0000 0.5716 0.5716 0.0 105 -0.1000 0.0000 -0.1000 0.1000 0.1000 -0.1000 0.5715 0.5715 0.0 121 -0.1000 0.0000 0.0000 0.0000 0.0000 0.0000 0.5714 0.5714 0.0 186 -0.1000 0.1000 -0.1000 0.1000 0.1000 -0.1000 0.5713 0.5713 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.5709 0.5709 0.0 Brute Force -------------------------- Min cost was 0.570861 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 = 0.586631 7 -0.084 0.000 0.000 0.000 0.000 0.000 0.5864572238 8 -0.086 0.000 0.000 0.000 0.000 0.000 0.5864550790 10 -0.135 0.000 0.000 0.000 0.000 0.000 0.5864488077 11 -0.114 0.000 0.000 0.000 0.000 0.000 0.5864396257 20 -0.114 0.135 0.000 0.000 0.000 0.000 0.5860444851 21 -0.114 0.137 0.000 0.000 0.000 0.000 0.5860433769 22 -0.114 0.148 0.000 0.000 0.000 0.000 0.5860424187 24 -0.114 0.144 0.000 0.000 0.000 0.000 0.5860420319 33 -0.114 0.143 -0.167 0.000 0.000 0.000 0.5854810982 35 -0.114 0.143 -0.172 0.000 0.000 0.000 0.5854804344 37 -0.114 0.143 -0.173 0.000 0.000 0.000 0.5854804221 42 -0.114 0.143 -0.173 -0.618 0.000 0.000 0.5849595337 44 -0.114 0.143 -0.173 -0.335 0.000 0.000 0.5835658191 45 -0.114 0.143 -0.173 -0.333 0.000 0.000 0.5835656485 46 -0.114 0.143 -0.173 -0.331 0.000 0.000 0.5835653514 50 -0.114 0.143 -0.173 -0.324 0.000 0.000 0.5835652076 51 -0.114 0.143 -0.173 -0.327 0.000 0.000 0.5835651162 52 -0.114 0.143 -0.173 -0.328 0.000 0.000 0.5835650546 60 -0.114 0.143 -0.173 -0.328 0.004 0.000 0.5835583925 61 -0.114 0.143 -0.173 -0.328 0.032 0.000 0.5835332284 63 -0.114 0.143 -0.173 -0.328 0.034 0.000 0.5835331527 69 -0.114 0.143 -0.173 -0.328 0.035 0.000 0.5835329896 76 -0.114 0.143 -0.173 -0.328 0.035 -0.082 0.5834538650 80 -0.114 0.143 -0.173 -0.328 0.035 -0.083 0.5834537841 powell nthiter 1: fret = 0.583454 88 -0.078 0.143 -0.173 -0.328 0.035 -0.083 0.5834342311 89 -0.084 0.143 -0.173 -0.328 0.035 -0.083 0.5834334407 98 -0.083 0.253 -0.173 -0.328 0.035 -0.083 0.5832112554 99 -0.083 0.249 -0.173 -0.328 0.035 -0.083 0.5832101233 100 -0.083 0.244 -0.173 -0.328 0.035 -0.083 0.5832092276 102 -0.083 0.245 -0.173 -0.328 0.035 -0.083 0.5832091998 111 -0.083 0.246 -0.167 -0.328 0.035 -0.083 0.5832083397 120 -0.083 0.246 -0.166 -0.383 0.035 -0.083 0.5831861851 121 -0.083 0.246 -0.166 -0.366 0.035 -0.083 0.5831809294 123 -0.083 0.246 -0.166 -0.369 0.035 -0.083 0.5831808315 134 -0.083 0.246 -0.166 -0.370 0.029 -0.083 0.5831798754 143 -0.083 0.246 -0.166 -0.370 0.030 -0.091 0.5831790286 144 -0.083 0.246 -0.166 -0.370 0.030 -0.092 0.5831788717 158 -0.079 0.260 -0.165 -0.376 0.029 -0.093 0.5831763662 powell nthiter 2: fret = 0.583176 170 -0.084 0.259 -0.165 -0.375 0.029 -0.093 0.5831749836 171 -0.088 0.259 -0.165 -0.375 0.029 -0.093 0.5831748069 172 -0.087 0.259 -0.165 -0.375 0.029 -0.093 0.5831747961 180 -0.086 0.259 -0.165 -0.375 0.029 -0.092 0.5831746524 190 -0.086 0.259 -0.167 -0.375 0.029 -0.092 0.5831741571 191 -0.086 0.259 -0.172 -0.375 0.029 -0.092 0.5831736691 193 -0.086 0.259 -0.171 -0.375 0.029 -0.092 0.5831735941 203 -0.086 0.259 -0.170 -0.377 0.029 -0.092 0.5831734131 212 -0.086 0.259 -0.170 -0.377 0.030 -0.092 0.5831734022 220 -0.083 0.266 -0.169 -0.380 0.030 -0.093 0.5831726812 powell nthiter 3: fret = 0.583173 238 -0.084 0.267 -0.169 -0.380 0.029 -0.093 0.5831723398 239 -0.090 0.267 -0.169 -0.380 0.029 -0.093 0.5831719801 241 -0.088 0.267 -0.169 -0.380 0.029 -0.093 0.5831718957 250 -0.087 0.267 -0.169 -0.380 0.029 -0.092 0.5831718312 251 -0.087 0.267 -0.169 -0.380 0.029 -0.090 0.5831716930 258 -0.087 0.267 -0.169 -0.380 0.029 -0.091 0.5831716275 266 -0.087 0.267 -0.174 -0.380 0.029 -0.091 0.5831712317 268 -0.087 0.267 -0.173 -0.380 0.029 -0.091 0.5831711905 276 -0.087 0.267 -0.173 -0.389 0.029 -0.091 0.5831710092 277 -0.087 0.267 -0.173 -0.385 0.029 -0.091 0.5831708236 278 -0.087 0.267 -0.173 -0.386 0.029 -0.091 0.5831707726 295 -0.086 0.270 -0.173 -0.387 0.029 -0.091 0.5831700523 296 -0.085 0.274 -0.173 -0.389 0.029 -0.092 0.5831694443 307 -0.087 0.281 -0.176 -0.398 0.029 -0.090 0.5831671965 314 -0.087 0.282 -0.177 -0.399 0.029 -0.090 0.5831669310 316 -0.087 0.282 -0.177 -0.399 0.029 -0.090 0.5831668655 powell nthiter 4: fret = 0.583167 329 -0.096 0.282 -0.177 -0.399 0.029 -0.090 0.5831663616 331 -0.092 0.282 -0.177 -0.399 0.029 -0.090 0.5831660062 powell nthiter 5: fret = 0.583166 404 -0.092 0.282 -0.176 -0.399 0.029 -0.090 0.5831659980 Powell done niters = 5 Computing relative cost 0 -25.0 -25.0 -25.0 1.037328 1 -25.0 -25.0 25.0 1.053696 2 -25.0 25.0 -25.0 1.052743 3 -25.0 25.0 25.0 1.065192 4 25.0 -25.0 -25.0 1.030789 5 25.0 -25.0 25.0 1.033511 6 25.0 25.0 -25.0 1.016194 7 25.0 25.0 25.0 1.055953 REL: 8 0.583166 8.345408 1.043176 rel = 0.559029 Number of iterations 5 Min cost was 0.583166 Number of FunctionCalls 460 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 55.127000 sec Parameters at optimum (transmm) -0.09225 0.28190 -0.17709 Parameters at optimum (rotdeg) -0.39935 0.02875 -0.08970 Final costs ---------------- Number of surface hits 304441 WM Intensity 819.2719 +/- 215.1285 Ctx Intensity 846.2816 +/- 245.7675 Pct Contrast 1.3831 +/- 21.6201 Cost 0.5832 RelCost 0.5622 Reg at min cost was 0.99985 -0.01758 -0.00046 -0.36207; -0.00410 -0.25832 0.96605 -41.03093; 0.01710 0.96590 0.25835 -2.00327; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/003/register.dof6.dat, type = 14 Original Reg 0.99984 -0.01766 -0.00210 -0.20423; -0.00266 -0.26507 0.96423 -41.29947; 0.01759 0.96407 0.26508 -2.11419; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00000 -0.00008 -0.00164 0.15784; 0.00144 -0.00675 -0.00183 -0.26854; 0.00048 -0.00183 0.00673 -0.11092; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.434600 Computing change in rh position Surface-RMS-Diff-mm 0.417951 0.186093 0.922594 mri_segreg done MinCost: 0.583166 819.271929 846.281568 1.383141 tkregister2_cmdl --mov bold/003/template.nii.gz --reg bold/003/register.dof6.dat --noedit --ltaout bold/003/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/003/template.nii.gz reg file bold/003/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 -------- 0.99985 -0.01758 -0.00046 -0.36207; -0.00410 -0.25832 0.96605 -41.03093; 0.01710 0.96590 0.25835 -2.00327; 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/003/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 -------- 0.99985 -0.01758 -0.00046 -0.36207; -0.00410 -0.25832 0.96605 -41.03093; 0.01710 0.96590 0.25835 -2.00327; 0.00000 0.00000 0.00000 1.00000; Determinant -1 subject = fsf01anat RegMat --------------------------- 0.99985 -0.01758 -0.00046 -0.36207; -0.00410 -0.25832 0.96605 -41.03093; 0.01710 0.96590 0.25835 -2.00327; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Sun Mar 27 21:47:05 EDT 2016 Ended at Sun Mar 27 21:50:11 EDT 2016 BBR-Run-Time-Sec 186 bbregister Done To check results, run: tkregister2 --mov bold/003/template.nii.gz --reg bold/003/register.dof6.dat --surf