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Dear Douglas,
I could not locate the log file, so I re-ran it, then copied all outputs here below.
bbregister --mov sess01/rest/template.nii.gz --bold --s bw083 --lta register.dof6.lta tmp ./tmp.bbregister.19439 Log file is register.dof6.dat.log Fri Sep 18 12:21:38 EDT 2020
setenv SUBJECTS_DIR /home1/am2359/fs6_data/app_large/ cd /home1/wz273/fmri_study/bw083 /home1/am2359/freesurfer_6/bin/bbregister --mov sess01/rest/template.nii.gz --bold --s bw083 --lta register.dof6.lta
$Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $ Linux piscespet.med.yale.edu 3.10.0-693.el7.x86_64 #1 SMP Tue Aug 22 21:09:27 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /home1/am2359/freesurfer_6 mri_convert sess01/rest/template.nii.gz ./tmp.bbregister.19439/template.nii mri_convert.bin sess01/rest/template.nii.gz ./tmp.bbregister.19439/template.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from sess01/rest/template.nii.gz... TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -1, 0) k_ras = (-0, -0, 1) writing to ./tmp.bbregister.19439/template.nii... mri_coreg --s bw083 --mov ./tmp.bbregister.19439/template.nii --regdat ./tmp.bbregister.19439/reg.init.dat --reg ./tmp.bbregister.19439/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01
$Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $ cwd /home1/wz273/fmri_study/bw083 cmdline mri_coreg --s bw083 --mov ./tmp.bbregister.19439/template.nii --regdat ./tmp.bbregister.19439/reg.init.dat --reg ./tmp.bbregister.19439/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 sysname Linux hostname piscespet.med.yale.edu machine x86_64 user wz273 dof 6 nsep 1 cras0 1 ftol 0.000100 linmintol 0.010000 bf 1 bflim 30.000000 bfnsamp 30 SmoothRef 0 SatPct 99.990000 MovOOB 0 optschema 1 Reading in mov ./tmp.bbregister.19439/template.nii Reading in ref /home1/am2359/fs6_data/app_large//bw083/mri/brainmask.mgz Reading in and applying refmask /home1/am2359/fs6_data/app_large//bw083/mri/aparc+aseg.mgz Setting cras translation parameters to align centers Creating random numbers for coordinate dithering Performing intensity dithering Initial parameters -0.4685 18.9454 -9.7070 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 = 2370.0000 mov gstd 1.0950 1.0950 1.1040 Smoothing mov refsat = 115.0000 ref gstd 1.8914 1.8914 1.8914 Smoothing ref COREGpreproc() done Testing if mov and target overlap Init cost -1.0252158306 nhits = 95459 out of 16777216, Percent Overlap: 36.4 Initial RefRAS-to-MovRAS 1.00000 0.00000 0.00000 -0.46851; 0.00000 1.00000 0.00000 18.94542; 0.00000 0.00000 1.00000 -9.70697; 0.00000 0.00000 0.00000 1.00000; Initial RefVox-to-MovVox -0.30189 0.00000 0.00000 69.99056; 0.00000 -0.30189 0.00000 66.99056; 0.00000 0.00000 0.30303 -15.13636; 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 -2.46851 24.94542 -7.70697 4.00000 4.00000 0.00000 -1.0183038 Turning MovOOB back off after brute force search
--------------------------------- Init Powel Params dof = 6 Starting OpenPowel2(), sep = 4 InitialCost -1.0265861750 #@# 4 188 -2.46851 24.94542 -7.70697 4.00000 4.00000 0.00000 -1.0265862 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.026586 #@# 4 195 -2.68711 24.94542 -7.70697 4.00000 4.00000 0.00000 -1.0265906 #@# 4 204 -2.68711 25.32738 -7.70697 4.00000 4.00000 0.00000 -1.0265933 #@# 4 205 -2.68711 25.19589 -7.70697 4.00000 4.00000 0.00000 -1.0265936 #@# 4 213 -2.68711 25.19589 -9.32500 4.00000 4.00000 0.00000 -1.0266647 #@# 4 221 -2.68711 25.19589 -9.27640 4.00000 4.00000 0.00000 -1.0266656 #@# 4 225 -2.68711 25.19589 -9.27640 5.00000 4.00000 0.00000 -1.0267084 #@# 4 228 -2.68711 25.19589 -9.27640 5.61803 4.00000 0.00000 -1.0267122 #@# 4 230 -2.68711 25.19589 -9.27640 5.38185 4.00000 0.00000 -1.0267199 #@# 4 232 -2.68711 25.19589 -9.27640 5.39601 4.00000 0.00000 -1.0267202 #@# 4 235 -2.68711 25.19589 -9.27640 5.40803 4.00000 0.00000 -1.0267205 #@# 4 241 -2.68711 25.19589 -9.27640 5.40803 3.38197 0.00000 -1.0267299 #@# 4 243 -2.68711 25.19589 -9.27640 5.40803 3.40654 0.00000 -1.0267303 #@# 4 245 -2.68711 25.19589 -9.27640 5.40803 3.47386 0.00000 -1.0267310 #@# 4 247 -2.68711 25.19589 -9.27640 5.40803 3.50348 0.00000 -1.0267314 #@# 4 259 -2.68711 25.19589 -9.27640 5.40803 3.49348 -0.01692 -1.0267320 #@# 4 260 -2.68711 25.19589 -9.27640 5.40803 3.49348 -0.03438 -1.0267322 #@# 4 262 -2.90572 25.44636 -10.84584 6.81606 2.98696 -0.06877 -1.0267975 #@# 4 267 -3.04083 25.60116 -11.81580 7.68627 2.67391 -0.09002 -1.0267996 powell nthiter 1: fret = -1.026800 #@# 4 282 -3.28654 25.60116 -11.81580 7.68627 2.67391 -0.09002 -1.0268101 #@# 4 283 -3.31173 25.60116 -11.81580 7.68627 2.67391 -0.09002 -1.0268105 #@# 4 290 -3.30173 23.98313 -11.81580 7.68627 2.67391 -0.09002 -1.0268387 #@# 4 291 -3.30173 24.53065 -11.81580 7.68627 2.67391 -0.09002 -1.0268476 #@# 4 295 -3.30173 24.44049 -11.81580 7.68627 2.67391 -0.09002 -1.0268492 #@# 4 296 -3.30173 24.43049 -11.81580 7.68627 2.67391 -0.09002 -1.0268493 #@# 4 298 -3.30173 24.42049 -11.81580 7.68627 2.67391 -0.09002 -1.0268494 #@# 4 304 -3.30173 24.42049 -11.81580 7.68627 2.67391 -0.70805 -1.0268533 #@# 4 306 -3.30173 24.42049 -11.81580 7.68627 2.67391 -0.44235 -1.0268584 #@# 4 308 -3.30173 24.42049 -11.81580 7.68627 2.67391 -0.46235 -1.0268586 #@# 4 309 -3.30173 24.42049 -11.81580 7.68627 2.67391 -0.55620 -1.0268593 #@# 4 314 -3.30173 24.42049 -11.81580 8.68627 2.67391 -0.54620 -1.0268656 #@# 4 327 -3.30173 24.42049 -11.81580 8.66627 1.05588 -0.54620 -1.0268992 #@# 4 330 -3.30173 24.42049 -11.81580 8.66627 0.05588 -0.54620 -1.0269008 #@# 4 332 -3.30173 24.42049 -11.81580 8.66627 0.35911 -0.54620 -1.0269036 #@# 4 333 -3.30173 24.42049 -11.81580 8.66627 0.50673 -0.54620 -1.0269041 #@# 4 343 -3.38523 24.51616 -12.41527 9.20409 0.31325 -0.55933 -1.0269070 #@# 4 344 -3.35567 24.48229 -12.20306 9.01370 0.38174 -0.55468 -1.0269073 #@# 4 346 -3.33506 24.45868 -12.05514 8.88100 0.42948 -0.55144 -1.0269080 #@# 4 352 -3.98301 23.72148 -14.83387 12.35396 -2.63452 -1.06851 -1.0269804 #@# 4 357 -4.38347 23.26586 -16.55123 14.50037 -4.52817 -1.38807 -1.0269905 #@# 4 360 -4.47800 23.15830 -16.95664 15.00707 -4.97520 -1.46351 -1.0269907 #@# 4 361 -4.43413 23.20822 -16.76848 14.77190 -4.76772 -1.42849 -1.0269977 powell nthiter 2: fret = -1.026998 #@# 4 365 -3.43413 23.20822 -16.76848 14.77190 -4.76772 -1.42849 -1.0270245 #@# 4 369 -3.81609 23.20822 -16.76848 14.77190 -4.76772 -1.42849 -1.0270305 #@# 4 372 -3.84033 23.20822 -16.76848 14.77190 -4.76772 -1.42849 -1.0270308 #@# 4 382 -3.77524 23.14511 -16.37301 14.41710 -4.64009 -1.41983 -1.0270345 #@# 4 383 -3.78122 23.15195 -16.41588 14.45557 -4.65393 -1.42077 -1.0270361 #@# 4 385 -3.78753 23.15918 -16.46120 14.49623 -4.66855 -1.42176 -1.0270364 #@# 4 386 -3.78971 23.16168 -16.47690 14.51031 -4.67362 -1.42210 -1.0270369 #@# 4 390 -3.78971 23.16168 -16.47690 14.51031 -4.67362 -3.04014 -1.0270855 #@# 4 391 -3.78971 23.16168 -16.47690 14.51031 -4.67362 -2.93216 -1.0270857 #@# 4 396 -3.78971 23.16168 -16.47690 14.51031 -4.67362 -2.97340 -1.0270864 #@# 4 401 -3.78971 23.16168 -16.47690 15.51031 -4.67362 -2.96340 -1.0270867 #@# 4 402 -3.78971 23.16168 -16.47690 17.12834 -4.67362 -2.96340 -1.0272329 #@# 4 403 -3.78971 23.16168 -16.47690 19.74637 -4.67362 -2.96340 -1.0273694 #@# 4 404 -3.78971 23.16168 -16.47690 21.32888 -4.67362 -2.96340 -1.0274194 #@# 4 409 -3.78971 23.16168 -16.47690 21.09202 -4.67362 -2.96340 -1.0274218 #@# 4 412 -3.78971 23.16168 -16.47690 21.13144 -4.67362 -2.96340 -1.0274227 #@# 4 416 -3.78971 23.16168 -16.47690 21.13144 -3.67362 -2.96340 -1.0274307 #@# 4 421 -3.78971 23.16168 -16.47690 21.13144 -3.66362 -2.96340 -1.0274314 #@# 4 424 -3.78971 23.16168 -16.47690 21.13144 -3.60999 -2.96340 -1.0274322 #@# 4 426 -3.78971 23.16168 -16.47690 21.13144 -3.59282 -2.96340 -1.0274324 #@# 4 429 -4.43766 22.42448 -19.25563 24.60441 -6.65681 -3.48047 -1.0274658 #@# 4 433 -4.19017 22.70607 -18.19425 23.27785 -5.48647 -3.28297 -1.0274745 #@# 4 435 -4.03721 22.88010 -17.53828 22.45800 -4.76316 -3.16090 -1.0274837 #@# 4 442 -4.03073 22.88747 -17.51049 22.42327 -4.73252 -3.15573 -1.0274842 #@# 4 443 -4.72640 21.31625 -22.96585 35.96554 -9.89452 -5.76002 -1.0275375 #@# 4 449 -4.46067 21.91640 -20.88209 30.79285 -7.92281 -4.76527 -1.0275429 #@# 4 450 -4.57922 21.64866 -21.81171 33.10054 -8.80245 -5.20906 -1.0275702 #@# 4 451 -4.58748 21.63000 -21.87650 33.26138 -8.86376 -5.23999 -1.0275749 #@# 4 452 -4.64054 21.51016 -22.29259 34.29428 -9.25747 -5.43863 -1.0275828 #@# 4 453 -4.62498 21.54530 -22.17058 33.99140 -9.14202 -5.38038 -1.0275872 powell nthiter 3: fret = -1.027587 #@# 4 457 -3.62498 21.54530 -22.17058 33.99140 -9.14202 -5.38038 -1.0276059 #@# 4 461 -4.00695 21.54530 -22.17058 33.99140 -9.14202 -5.38038 -1.0276169 #@# 4 463 -3.93946 21.54530 -22.17058 33.99140 -9.14202 -5.38038 -1.0276175 #@# 4 465 -3.96273 21.54530 -22.17058 33.99140 -9.14202 -5.38038 -1.0276176 #@# 4 467 -3.95273 21.54530 -22.17058 33.99140 -9.14202 -5.38038 -1.0276177 #@# 4 477 -3.94716 21.53891 -22.13055 33.95549 -9.12910 -5.37950 -1.0276185 #@# 4 506 -3.94934 21.54141 -22.14625 33.96957 -8.75220 -5.38985 -1.0276223 #@# 4 509 -3.94934 21.54141 -22.14625 33.96957 -8.76580 -5.38985 -1.0276226 #@# 4 520 -3.96666 21.50230 -22.28206 34.30672 -8.89431 -5.45469 -1.0276333 Powell done niters total = 3 OptTimeSec 22.5 sec OptTimeMin 0.38 min nEvals 522 Final parameters -3.96666241 21.50229645 -22.28206444 34.30671692 -8.89431286 -5.45468521 Final cost -1.027633299797374
--------------------------------- mri_coreg utimesec 107.537083 mri_coreg stimesec 0.472004 mri_coreg ru_maxrss 420284 mri_coreg ru_ixrss 0 mri_coreg ru_idrss 0 mri_coreg ru_isrss 0 mri_coreg ru_minflt 559397 mri_coreg ru_majflt 0 mri_coreg ru_nswap 0 mri_coreg ru_inblock 0 mri_coreg ru_oublock 16 mri_coreg ru_msgsnd 0 mri_coreg ru_msgrcv 0 mri_coreg ru_nsignals 0 mri_coreg ru_nvcsw 39 mri_coreg ru_nivcsw 228 Final RefRAS-to-MovRAS 0.98350 -0.09392 -0.15461 -3.96666; 0.16527 0.81401 0.55685 21.50230; 0.07356 -0.57321 0.81610 -22.28206; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox -0.29691 0.02835 0.04668 60.85724; -0.04989 -0.24574 -0.16810 86.71729; 0.02229 -0.17370 0.24730 7.53311; 0.00000 0.00000 0.00000 1.00000; Final parameters -3.9667 21.5023 -22.2821 34.3067 -8.8943 -5.4547 nhits = 95350 out of 16777216, Percent Overlap: 36.4 mri_coreg RunTimeSec 108.0 sec To check run: tkregisterfv --mov ./tmp.bbregister.19439/template.nii --targ /home1/am2359/fs6_data/app_large//bw083/mri/brainmask.mgz --reg ./tmp.bbregister.19439/mri_coreg.lta --s bw083 --surfs
mri_coreg done
mri_segreg --mov ./tmp.bbregister.19439/template.nii --init-reg ./tmp.bbregister.19439/reg.init.dat --out-reg ./tmp.bbregister.19439/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.113 2016/05/10 03:23:20 greve Exp $ setenv SUBJECTS_DIR /home1/am2359/fs6_data/app_large/ cd /home1/wz273/fmri_study/bw083 mri_segreg --mov ./tmp.bbregister.19439/template.nii --init-reg ./tmp.bbregister.19439/reg.init.dat --out-reg ./tmp.bbregister.19439/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 piscespet.med.yale.edu machine x86_64 user wz273 movvol ./tmp.bbregister.19439/template.nii regfile ./tmp.bbregister.19439/reg.init.dat subject bw083 dof 6 outregfile ./tmp.bbregister.19439/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 1600690048 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg -0.98350 -0.15461 0.09392 -1.51302; -0.07356 0.81610 0.57321 -13.83544; -0.16527 0.55685 -0.81401 5.43526; 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 0.976224 1 -25.0 -25.0 25.0 0.979283 2 -25.0 25.0 -25.0 1.003892 3 -25.0 25.0 25.0 1.004795 4 25.0 -25.0 -25.0 1.044749 5 25.0 -25.0 25.0 1.075405 6 25.0 25.0 -25.0 1.031226 7 25.0 25.0 25.0 1.024298 REL: 8 1.045017 8.139873 1.017484 rel = 1.02706 Initial costs ---------------- Number of surface hits 2333 WM Intensity 772.5130 +/- 434.3440 Ctx Intensity 764.3172 +/- 439.8091 Pct Contrast -2.3927 +/- 26.8390 Cost 1.0450 RelCost 1.0271
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 1.0307 1.0307 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 1.0022 1.0022 0.0 30 -4.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.9884 0.9884 0.0 110 -4.0000 0.0000 0.0000 -4.0000 -4.0000 4.0000 0.9870 0.9870 0.0 245 0.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.9864 0.9864 0.0 272 0.0000 -4.0000 0.0000 -4.0000 -4.0000 4.0000 0.9806 0.9806 0.0 297 0.0000 -4.0000 4.0000 -4.0000 -4.0000 -4.0000 0.9601 0.9601 0.0 310 0.0000 -4.0000 4.0000 0.0000 0.0000 0.0000 0.9588 0.9588 0.0 320 0.0000 -4.0000 4.0000 4.0000 0.0000 4.0000 0.9556 0.9556 0.0 556 4.0000 -4.0000 4.0000 0.0000 4.0000 0.0000 0.9547 0.9547 0.0 Brute Force -------------------------- Min cost was 0.954746 Number of iterations 729 Search time 2.140000 sec Parameters at best (transmm, rotdeg) 4.000 -4.000 4.000 0.000 4.000 0.000 --------------------------------------------
Starting Powell Minimization Init Powel Params dof = 6 0 4 1 -4 2 4 3 0 4 4 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000100 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.954746 6 4.382 -4.000 4.000 0.000 4.000 0.000 0.9512990769 8 4.368 -4.000 4.000 0.000 4.000 0.000 0.9511437808 9 4.228 -4.000 4.000 0.000 4.000 0.000 0.9486753931 12 4.230 -4.000 4.000 0.000 4.000 0.000 0.9486606621 13 4.235 -4.000 4.000 0.000 4.000 0.000 0.9486592558 15 4.233 -4.000 4.000 0.000 4.000 0.000 0.9486580431 25 4.233 -4.008 4.000 0.000 4.000 0.000 0.9485942569 27 4.233 -4.015 4.000 0.000 4.000 0.000 0.9485718320 29 4.233 -4.017 4.000 0.000 4.000 0.000 0.9485709411 38 4.233 -4.017 3.945 0.000 4.000 0.000 0.9482605458 41 4.233 -4.017 3.952 0.000 4.000 0.000 0.9482173486 42 4.233 -4.017 3.954 0.000 4.000 0.000 0.9482169108 56 4.233 -4.017 3.954 0.002 4.000 0.000 0.9482072562 57 4.233 -4.017 3.954 0.004 4.000 0.000 0.9482009567 64 4.233 -4.017 3.954 0.004 3.382 0.000 0.9469640908 70 4.233 -4.017 3.954 0.004 3.369 0.000 0.9469362941 71 4.233 -4.017 3.954 0.004 3.370 0.000 0.9469359407 72 4.233 -4.017 3.954 0.004 3.371 0.000 0.9469355408 88 4.233 -4.017 3.954 0.004 3.371 -0.002 0.9469345111 89 4.233 -4.017 3.954 0.004 3.371 -0.003 0.9469344112 powell nthiter 1: fret = 0.946934 97 4.615 -4.017 3.954 0.004 3.371 -0.003 0.9468082455 106 4.618 -4.017 3.954 0.004 3.371 -0.003 0.9468054888 114 4.618 -3.635 3.954 0.004 3.371 -0.003 0.9449685836 117 4.618 -3.641 3.954 0.004 3.371 -0.003 0.9449607516 120 4.618 -3.642 3.954 0.004 3.371 -0.003 0.9449604930 123 4.618 -3.642 4.954 0.004 3.371 -0.003 0.9426541219 128 4.618 -3.642 4.983 0.004 3.371 -0.003 0.9422949870 130 4.618 -3.642 5.080 0.004 3.371 -0.003 0.9413800509 132 4.618 -3.642 5.085 0.004 3.371 -0.003 0.9413692528 133 4.618 -3.642 5.091 0.004 3.371 -0.003 0.9413598503 136 4.618 -3.642 5.092 0.004 3.371 -0.003 0.9413594257 146 4.618 -3.642 5.092 -0.086 3.371 -0.003 0.9407155776 149 4.618 -3.642 5.092 -0.084 3.371 -0.003 0.9407130012 150 4.618 -3.642 5.092 -0.079 3.371 -0.003 0.9407082031 159 4.618 -3.642 5.092 -0.080 3.753 -0.003 0.9395560154 163 4.618 -3.642 5.092 -0.080 3.762 -0.003 0.9395439153 165 4.618 -3.642 5.092 -0.080 3.766 -0.003 0.9395438000 167 4.618 -3.642 5.092 -0.080 3.764 -0.003 0.9395437802 168 4.618 -3.642 5.092 -0.080 3.763 -0.003 0.9395433730 175 4.618 -3.642 5.092 -0.080 3.763 0.131 0.9379560300 177 4.618 -3.642 5.092 -0.080 3.763 0.114 0.9379116254 179 4.618 -3.642 5.092 -0.080 3.763 0.118 0.9379083919 powell nthiter 2: fret = 0.937908 187 4.000 -3.642 5.092 -0.080 3.763 0.118 0.9376519663 188 3.618 -3.642 5.092 -0.080 3.763 0.118 0.9355117452 194 3.586 -3.642 5.092 -0.080 3.763 0.118 0.9350993095 196 3.589 -3.642 5.092 -0.080 3.763 0.118 0.9350945939 198 3.590 -3.642 5.092 -0.080 3.763 0.118 0.9350942020 208 3.590 -3.620 5.092 -0.080 3.763 0.118 0.9349253267 209 3.590 -3.617 5.092 -0.080 3.763 0.118 0.9349118705 210 3.590 -3.607 5.092 -0.080 3.763 0.118 0.9348896806 212 3.590 -3.602 5.092 -0.080 3.763 0.118 0.9348859613 213 3.590 -3.601 5.092 -0.080 3.763 0.118 0.9348859612 214 3.590 -3.600 5.092 -0.080 3.763 0.118 0.9348846395 215 3.590 -3.598 5.092 -0.080 3.763 0.118 0.9348821352 225 3.590 -3.598 5.102 -0.080 3.763 0.118 0.9348283470 227 3.590 -3.598 5.104 -0.080 3.763 0.118 0.9348273644 237 3.590 -3.598 5.104 -0.129 3.763 0.118 0.9347884269 238 3.590 -3.598 5.104 -0.110 3.763 0.118 0.9346813233 239 3.590 -3.598 5.104 -0.106 3.763 0.118 0.9346717784 240 3.590 -3.598 5.104 -0.100 3.763 0.118 0.9346696567 242 3.590 -3.598 5.104 -0.102 3.763 0.118 0.9346680988 244 3.590 -3.598 5.104 -0.101 3.763 0.118 0.9346680773 255 3.590 -3.598 5.104 -0.101 3.718 0.118 0.9342960311 257 3.590 -3.598 5.104 -0.101 3.712 0.118 0.9342815437 258 3.590 -3.598 5.104 -0.101 3.710 0.118 0.9342792214 270 3.590 -3.598 5.104 -0.101 3.710 0.120 0.9342757380 271 3.590 -3.598 5.104 -0.101 3.710 0.123 0.9342745332 272 3.590 -3.598 5.104 -0.101 3.710 0.122 0.9342744871 powell nthiter 3: fret = 0.934274 286 3.561 -3.598 5.104 -0.101 3.710 0.122 0.9337162985 287 3.557 -3.598 5.104 -0.101 3.710 0.122 0.9336765121 289 3.552 -3.598 5.104 -0.101 3.710 0.122 0.9336716076 290 3.554 -3.598 5.104 -0.101 3.710 0.122 0.9336688928 302 3.554 -3.596 5.104 -0.101 3.710 0.122 0.9336674900 303 3.554 -3.593 5.104 -0.101 3.710 0.122 0.9336625651 304 3.554 -3.589 5.104 -0.101 3.710 0.122 0.9336590760 305 3.554 -3.588 5.104 -0.101 3.710 0.122 0.9336588101 306 3.554 -3.587 5.104 -0.101 3.710 0.122 0.9336577260 315 3.554 -3.587 5.108 -0.101 3.710 0.122 0.9336553495 327 3.554 -3.587 5.108 -0.144 3.710 0.122 0.9333997662 328 3.554 -3.587 5.108 -0.145 3.710 0.122 0.9333973747 330 3.554 -3.587 5.108 -0.151 3.710 0.122 0.9333919496 343 3.554 -3.587 5.108 -0.151 3.669 0.122 0.9328387268 349 3.554 -3.587 5.108 -0.151 3.668 0.122 0.9328386315 356 3.554 -3.587 5.108 -0.151 3.668 0.135 0.9327202194 359 3.554 -3.587 5.108 -0.151 3.668 0.140 0.9327151408 360 3.554 -3.587 5.108 -0.151 3.668 0.139 0.9327147582 362 3.517 -3.575 5.111 -0.200 3.627 0.157 0.9320743512 369 3.511 -3.574 5.112 -0.208 3.620 0.160 0.9320598489 371 3.512 -3.574 5.112 -0.207 3.621 0.159 0.9320591370 375 3.512 -3.574 5.112 -0.207 3.621 0.159 0.9320591163 376 3.512 -3.574 5.112 -0.207 3.621 0.159 0.9320589071 powell nthiter 4: fret = 0.932059 388 3.512 -3.574 5.112 -0.207 3.621 0.161 0.9320588040 398 3.512 -3.549 5.112 -0.207 3.621 0.161 0.9319102940 399 3.512 -3.529 5.112 -0.207 3.621 0.161 0.9318656898 404 3.512 -3.528 5.112 -0.207 3.621 0.161 0.9318638816 429 3.512 -3.528 5.113 -0.206 3.621 0.161 0.9318603233 440 3.512 -3.528 5.113 -0.206 3.644 0.161 0.9316556370 441 3.512 -3.528 5.113 -0.206 3.646 0.161 0.9316542901 442 3.512 -3.528 5.113 -0.206 3.647 0.161 0.9316542769 450 3.506 -3.526 5.113 -0.215 3.640 0.164 0.9316451534 451 3.506 -3.526 5.113 -0.213 3.641 0.163 0.9316445317 452 3.507 -3.526 5.113 -0.213 3.641 0.163 0.9316440100 457 3.508 -3.527 5.113 -0.212 3.642 0.163 0.9316436241 powell nthiter 5: fret = 0.931644 470 3.508 -3.527 5.113 -0.212 3.642 0.170 0.9316051408 473 3.508 -3.527 5.113 -0.212 3.642 0.171 0.9316016612 474 3.508 -3.527 5.113 -0.212 3.642 0.172 0.9316006077 498 3.508 -3.527 5.110 -0.212 3.642 0.172 0.9315992943 524 3.508 -3.527 5.111 -0.212 3.643 0.172 0.9315964957 525 3.508 -3.527 5.111 -0.212 3.647 0.172 0.9315911629 542 3.508 -3.527 5.111 -0.212 3.647 0.172 0.9315909776 543 3.508 -3.527 5.111 -0.212 3.647 0.172 0.9315907573 544 3.508 -3.527 5.111 -0.212 3.647 0.172 0.9315906514 Powell done niters = 5 Computing relative cost 0 -25.0 -25.0 -25.0 0.978878 1 -25.0 -25.0 25.0 1.023023 2 -25.0 25.0 -25.0 1.016793 3 -25.0 25.0 25.0 1.030374 4 25.0 -25.0 -25.0 1.032237 5 25.0 -25.0 25.0 1.051317 6 25.0 25.0 -25.0 1.022404 7 25.0 25.0 25.0 0.957293 REL: 8 0.931591 8.112318 1.014040 rel = 0.918692 Number of iterations 5 Min cost was 0.931591 Number of FunctionCalls 546 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 1.649000 sec Parameters at optimum (transmm) 3.50765 -3.52661 5.11115 Parameters at optimum (rotdeg) -0.21173 3.64684 0.17215 Final costs ---------------- Number of surface hits 2284 WM Intensity 716.1340 +/- 398.4948 Ctx Intensity 719.8314 +/- 406.4317 Pct Contrast -0.2661 +/- 28.0351 Cost 0.9316 RelCost 1.0271 Reg at min cost was -0.99178 -0.12153 0.04010 2.38817; -0.07715 0.81779 0.57032 -17.34529; -0.10211 0.56254 -0.82044 10.68263; 0.00000 0.00000 0.00000 1.00000;
Writing optimal reg to ./tmp.bbregister.19439/bbr.pass1.dat, type = 14 Original Reg -0.98350 -0.15461 0.09392 -1.51302; -0.07356 0.81610 0.57321 -13.83544; -0.16527 0.55685 -0.81401 5.43526; 0.00000 0.00000 0.00000 1.00000;
Original Reg - Optimal Reg 0.00828 -0.03308 0.05381 -3.90119; 0.00359 -0.00169 0.00289 3.50985; -0.06316 -0.00569 0.00643 -5.24737; 0.00000 0.00000 0.00000 0.00000;
Computing change in lh position LH rmsDiffMean 5.155253 Computing change in rh position Surface-RMS-Diff-mm 6.525376 1.641230 10.263662
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 ./tmp.bbregister.19439/template.nii --init-reg ./tmp.bbregister.19439/bbr.pass1.dat --out-reg register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost register.dof6.dat.mincost --dof 6 --nmax 36 --param register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg ./tmp.bbregister.19439/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.113 2016/05/10 03:23:20 greve Exp $ setenv SUBJECTS_DIR /home1/am2359/fs6_data/app_large/ cd /home1/wz273/fmri_study/bw083 mri_segreg --mov ./tmp.bbregister.19439/template.nii --init-reg ./tmp.bbregister.19439/bbr.pass1.dat --out-reg register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost register.dof6.dat.mincost --dof 6 --nmax 36 --param register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg ./tmp.bbregister.19439/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname piscespet.med.yale.edu machine x86_64 user wz273 movvol ./tmp.bbregister.19439/template.nii regfile ./tmp.bbregister.19439/bbr.pass1.dat subject bw083 dof 6 outregfile 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 1600625371 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg -0.99178 -0.12153 0.04010 2.38817; -0.07715 0.81779 0.57032 -17.34529; -0.10211 0.56254 -0.82044 10.68263; 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 1.003990 1 -25.0 -25.0 25.0 1.015713 2 -25.0 25.0 -25.0 0.997144 3 -25.0 25.0 25.0 1.017487 4 25.0 -25.0 -25.0 1.042784 5 25.0 -25.0 25.0 1.040891 6 25.0 25.0 -25.0 0.998860 7 25.0 25.0 25.0 1.002158 REL: 8 0.988304 8.119027 1.014878 rel = 0.973815 Initial costs ---------------- Number of surface hits 230028 WM Intensity 720.1549 +/- 397.4066 Ctx Intensity 720.9233 +/- 409.0205 Pct Contrast -1.4558 +/- 28.2880 Cost 0.9883 RelCost 0.9738
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 -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.9397 0.9397 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.9362 0.9362 0.0 10 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.0000 0.9339 0.9339 0.0 19 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 0.0000 0.9324 0.9324 0.0 46 -0.1000 -0.1000 0.0000 0.1000 -0.1000 0.0000 0.9319 0.9319 0.0 118 -0.1000 0.0000 0.0000 0.0000 -0.1000 0.0000 0.9318 0.9318 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.9316 0.9316 0.0 Brute Force -------------------------- Min cost was 0.931591 Number of iterations 729 Search time 1.822000 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 = 0.988304 2 1.000 0.000 0.000 0.000 0.000 0.000 0.9834619527 5 1.618 0.000 0.000 0.000 0.000 0.000 0.9823316804 7 1.579 0.000 0.000 0.000 0.000 0.000 0.9823280001 8 1.585 0.000 0.000 0.000 0.000 0.000 0.9823261252 9 1.595 0.000 0.000 0.000 0.000 0.000 0.9823231784 11 1.596 0.000 0.000 0.000 0.000 0.000 0.9823228788 12 1.598 0.000 0.000 0.000 0.000 0.000 0.9823226827 14 1.599 0.000 0.000 0.000 0.000 0.000 0.9823226297 16 1.599 1.000 0.000 0.000 0.000 0.000 0.9789579729 19 1.599 1.618 0.000 0.000 0.000 0.000 0.9784029645 21 1.599 1.441 0.000 0.000 0.000 0.000 0.9782539321 24 1.599 1.453 0.000 0.000 0.000 0.000 0.9782470182 25 1.599 1.456 0.000 0.000 0.000 0.000 0.9782349437 26 1.599 1.462 0.000 0.000 0.000 0.000 0.9782309273 29 1.599 1.464 0.000 0.000 0.000 0.000 0.9782289369 38 1.599 1.464 -0.045 0.000 0.000 0.000 0.9782151613 39 1.599 1.464 -0.088 0.000 0.000 0.000 0.9781824978 40 1.599 1.464 -0.138 0.000 0.000 0.000 0.9781785431 41 1.599 1.464 -0.119 0.000 0.000 0.000 0.9781765589 45 1.599 1.464 -0.118 0.000 0.000 0.000 0.9781765244 53 1.599 1.464 -0.117 -0.189 0.000 0.000 0.9781198064 54 1.599 1.464 -0.117 -0.138 0.000 0.000 0.9781109229 56 1.599 1.464 -0.117 -0.160 0.000 0.000 0.9780802652 57 1.599 1.464 -0.117 -0.171 0.000 0.000 0.9780636692 61 1.599 1.464 -0.117 -0.169 0.000 0.000 0.9780619950 67 1.599 1.464 -0.117 -0.169 -0.618 0.000 0.9777996874 69 1.599 1.464 -0.117 -0.169 -0.383 0.000 0.9776007258 70 1.599 1.464 -0.117 -0.169 -0.373 0.000 0.9775678355 71 1.599 1.464 -0.117 -0.169 -0.231 0.000 0.9774495041 72 1.599 1.464 -0.117 -0.169 -0.276 0.000 0.9774302516 74 1.599 1.464 -0.117 -0.169 -0.274 0.000 0.9774301163 75 1.599 1.464 -0.117 -0.169 -0.273 0.000 0.9774300427 78 1.599 1.464 -0.117 -0.169 -0.271 1.000 0.9706728176 79 1.599 1.464 -0.117 -0.169 -0.271 2.618 0.9675929082 80 1.599 1.464 -0.117 -0.169 -0.271 2.322 0.9670326333 83 1.599 1.464 -0.117 -0.169 -0.271 2.129 0.9669859638 85 1.599 1.464 -0.117 -0.169 -0.271 2.010 0.9669627604 86 1.599 1.464 -0.117 -0.169 -0.271 1.937 0.9669371076 89 1.599 1.464 -0.117 -0.169 -0.271 1.920 0.9669157254 91 1.599 1.464 -0.117 -0.169 -0.271 1.922 0.9669123765 93 1.599 1.464 -0.117 -0.169 -0.271 1.921 0.9669119087 powell nthiter 1: fret = 0.966912 101 1.637 1.464 -0.117 -0.169 -0.271 1.921 0.9668923108 102 1.663 1.464 -0.117 -0.169 -0.271 1.921 0.9668595766 103 1.785 1.464 -0.117 -0.169 -0.271 1.921 0.9668482610 104 1.730 1.464 -0.117 -0.169 -0.271 1.921 0.9667790012 106 1.735 1.464 -0.117 -0.169 -0.271 1.921 0.9667789529 108 1.732 1.464 -0.117 -0.169 -0.271 1.921 0.9667786504 119 1.732 1.439 -0.117 -0.169 -0.271 1.921 0.9667597436 120 1.732 1.417 -0.117 -0.169 -0.271 1.921 0.9667469723 125 1.732 1.424 -0.117 -0.169 -0.271 1.921 0.9667416845 134 1.732 1.424 0.265 -0.169 -0.271 1.921 0.9666066490 135 1.732 1.424 0.147 -0.169 -0.271 1.921 0.9664752969 137 1.732 1.424 0.170 -0.169 -0.271 1.921 0.9664641413 138 1.732 1.424 0.177 -0.169 -0.271 1.921 0.9664600200 140 1.732 1.424 0.190 -0.169 -0.271 1.921 0.9664583762 141 1.732 1.424 0.187 -0.169 -0.271 1.921 0.9664575245 154 1.732 1.424 0.184 -0.197 -0.271 1.921 0.9664337772 158 1.732 1.424 0.184 -0.200 -0.271 1.921 0.9664288223 173 1.732 1.424 0.184 -0.200 -0.275 1.921 0.9664284618 175 1.732 1.424 0.184 -0.200 -0.276 1.921 0.9664283987 184 1.732 1.424 0.184 -0.200 -0.276 1.989 0.9663972197 187 1.732 1.424 0.184 -0.200 -0.276 1.990 0.9663971578 powell nthiter 2: fret = 0.966397 195 1.658 1.424 0.184 -0.200 -0.276 1.990 0.9663930974 196 1.692 1.424 0.184 -0.200 -0.276 1.990 0.9663807346 198 1.687 1.424 0.184 -0.200 -0.276 1.990 0.9663804957 201 1.683 1.424 0.184 -0.200 -0.276 1.990 0.9663803156 203 1.682 1.424 0.184 -0.200 -0.276 1.990 0.9663802989 210 1.682 1.545 0.184 -0.200 -0.276 1.990 0.9662792430 216 1.682 1.546 0.184 -0.200 -0.276 1.990 0.9662778601 225 1.682 1.546 0.174 -0.200 -0.276 1.990 0.9662708073 226 1.682 1.546 0.137 -0.200 -0.276 1.990 0.9662586856 227 1.682 1.546 0.135 -0.200 -0.276 1.990 0.9662574893 228 1.682 1.546 0.101 -0.200 -0.276 1.990 0.9662479789 230 1.682 1.546 0.112 -0.200 -0.276 1.990 0.9662458331 231 1.682 1.546 0.110 -0.200 -0.276 1.990 0.9662455471 232 1.682 1.546 0.109 -0.200 -0.276 1.990 0.9662455323 233 1.682 1.546 0.108 -0.200 -0.276 1.990 0.9662455107 246 1.682 1.546 0.108 -0.202 -0.276 1.990 0.9662432640 257 1.682 1.546 0.108 -0.202 -0.287 1.990 0.9662432272 258 1.682 1.546 0.108 -0.202 -0.282 1.990 0.9662418540 267 1.682 1.546 0.108 -0.202 -0.281 2.058 0.9662217827 270 1.682 1.546 0.108 -0.202 -0.281 2.056 0.9662108067 powell nthiter 3: fret = 0.966211 309 1.682 1.546 0.142 -0.202 -0.281 2.056 0.9662023097 313 1.682 1.546 0.162 -0.202 -0.281 2.056 0.9661968406 314 1.682 1.546 0.167 -0.202 -0.281 2.056 0.9661967651 315 1.682 1.546 0.165 -0.202 -0.281 2.056 0.9661967530 powell nthiter 4: fret = 0.966197 371 1.680 1.576 0.163 -0.202 -0.281 2.056 0.9661947694 377 1.680 1.572 0.163 -0.202 -0.281 2.056 0.9661928726 391 1.680 1.572 0.172 -0.202 -0.281 2.056 0.9661884836 393 1.680 1.572 0.175 -0.202 -0.281 2.056 0.9661884050 405 1.680 1.572 0.176 -0.205 -0.281 2.056 0.9661881833 407 1.680 1.572 0.176 -0.207 -0.281 2.056 0.9661854241 408 1.680 1.572 0.176 -0.208 -0.281 2.056 0.9661839461 420 1.680 1.572 0.176 -0.208 -0.280 2.056 0.9661834472 421 1.680 1.572 0.176 -0.208 -0.279 2.056 0.9661830363 422 1.680 1.572 0.176 -0.208 -0.278 2.056 0.9661826375 434 1.680 1.572 0.176 -0.208 -0.278 2.063 0.9661799503 436 1.680 1.572 0.176 -0.208 -0.278 2.062 0.9661799055 powell nthiter 5: fret = 0.966180 450 1.679 1.572 0.176 -0.208 -0.278 2.062 0.9661797382 451 1.678 1.572 0.176 -0.208 -0.278 2.062 0.9661797019 465 1.678 1.573 0.176 -0.208 -0.278 2.062 0.9661758493 477 1.678 1.573 0.173 -0.208 -0.278 2.062 0.9661752996 488 1.678 1.573 0.173 -0.213 -0.278 2.062 0.9661732040 490 1.678 1.573 0.173 -0.217 -0.278 2.062 0.9661728921 491 1.678 1.573 0.173 -0.215 -0.278 2.062 0.9661706333 502 1.678 1.573 0.173 -0.215 -0.273 2.062 0.9661701553 503 1.678 1.573 0.173 -0.215 -0.274 2.062 0.9661698107 504 1.678 1.573 0.173 -0.215 -0.275 2.062 0.9661697421 519 1.678 1.573 0.173 -0.215 -0.275 2.063 0.9661695820 powell nthiter 6: fret = 0.966170 533 1.680 1.573 0.173 -0.215 -0.275 2.063 0.9661695803 557 1.680 1.573 0.169 -0.215 -0.275 2.063 0.9661692986 559 1.680 1.573 0.170 -0.215 -0.275 2.063 0.9661692720 573 1.680 1.573 0.171 -0.216 -0.275 2.063 0.9661679613 583 1.680 1.573 0.171 -0.216 -0.274 2.063 0.9661678099 584 1.680 1.573 0.171 -0.216 -0.273 2.063 0.9661677945 powell nthiter 7: fret = 0.966168 659 1.681 1.573 0.171 -0.216 -0.272 2.063 0.9661677897 Powell done niters = 7 Computing relative cost 0 -25.0 -25.0 -25.0 1.008210 1 -25.0 -25.0 25.0 1.022474 2 -25.0 25.0 -25.0 0.993965 3 -25.0 25.0 25.0 1.008695 4 25.0 -25.0 -25.0 1.024113 5 25.0 -25.0 25.0 1.038158 6 25.0 25.0 -25.0 0.995725 7 25.0 25.0 25.0 1.016986 REL: 8 0.966168 8.108326 1.013541 rel = 0.95326 Number of iterations 7 Min cost was 0.966168 Number of FunctionCalls 675 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 59.925000 sec Parameters at optimum (transmm) 1.68075 1.57290 0.17126 Parameters at optimum (rotdeg) -0.21642 -0.27221 2.06313 Final costs ---------------- Number of surface hits 232599 WM Intensity 725.3020 +/- 402.1809 Ctx Intensity 727.5790 +/- 413.8297 Pct Contrast -0.9952 +/- 27.4467 Cost 0.9662 RelCost 0.9738 Reg at min cost was -0.98785 -0.15362 0.02356 4.63930; -0.11317 0.81491 0.56844 -15.63657; -0.10652 0.55886 -0.82239 10.93056; 0.00000 0.00000 0.00000 1.00000;
Writing optimal reg to register.dof6.dat, type = 14 Original Reg -0.99178 -0.12153 0.04010 2.38817; -0.07715 0.81779 0.57032 -17.34529; -0.10211 0.56254 -0.82044 10.68263; 0.00000 0.00000 0.00000 1.00000;
Original Reg - Optimal Reg -0.00393 0.03209 0.01654 -2.25113; 0.03602 0.00288 0.00189 -1.70873; 0.00442 0.00368 0.00195 -0.24793; 0.00000 0.00000 0.00000 0.00000;
Computing change in lh position LH rmsDiffMean 3.925438 Computing change in rh position Surface-RMS-Diff-mm 3.445047 1.317487 5.996321
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 MinCost: 0.966168 725.302002 727.578959 -0.995208 tkregister2_cmdl --mov sess01/rest/template.nii.gz --reg register.dof6.dat --noedit --ltaout register.dof6.lta tkregister_tcl /home1/am2359/freesurfer_6/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume sess01/rest/template.nii.gz reg file register.dof6.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- -0.98785 -0.15362 0.02356 4.63930; -0.11317 0.81491 0.56844 -15.63657; -0.10652 0.55886 -0.82239 10.93056; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: loading target /home1/am2359/fs6_data/app_large//bw083/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 sess01/rest/template.nii.gz Tmov: -------------------- -3.31250 0.00000 0.00000 106.00000; 0.00000 0.00000 3.30000 -79.20000; 0.00000 -3.31250 0.00000 96.06250; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- -0.98785 -0.15362 0.02356 4.63930; -0.11317 0.81491 0.56844 -15.63657; -0.10652 0.55886 -0.82239 10.93056; 0.00000 0.00000 0.00000 1.00000; Determinant 0.999999 subject = bw083 RegMat --------------------------- -0.98785 -0.15362 0.02356 4.63930; -0.11317 0.81491 0.56844 -15.63657; -0.10652 0.55886 -0.82239 10.93056; 0.00000 0.00000 0.00000 1.00000; Cleaning up
Started at Fri Sep 18 12:21:38 EDT 2020 Ended at Fri Sep 18 12:24:54 EDT 2020 BBR-Run-Time-Sec 196
bbregister Done To check results, run: tkregisterfv --mov sess01/rest/template.nii.gz --reg register.dof6.lta --surfs
On Sep 18, 2020, at 12:11 PM, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Can you send the bbregister log file?
On 9/18/2020 12:02 PM, Wenzhen Zhao wrote:
External Email - Use CautionDear Douglas,
tkregisterfv --mov sess01/rest/template.nii.gz --targ subject/mri/orig.mgz --reg register.lta
This is the command that I used to check registration. I also checked them by opening Freeview and manually open the template.nii.gz with registration file, then overlaid it with orig.mgz to see if they overlap.
Best, Wenzhen
On Sep 18, 2020, at 10:57 AM, Douglas Greve dgreve@mgh.harvard.edu wrote:
Can you send the commands you used to check the registration ?
On 9/16/20 2:24 PM, Wenzhen Zhao wrote:
External Email - Use CautionDear freesurfer developers,
I am working on preprocessing resting state fMRI and used the following command.
$ preproc-sess -s sess01 -fsd rest -stc siemens -surface fsaverage lhrh -surf-fwhm 5 -mni305-2mm -vol-fwhm 0 -per-session
When I tried to visualize f.nii.gz with registration file applied and overlaid with aparc+aseg.mgz from structural analysis, they do not overlap. It seems like the orientation is not the same, and the f.nii.gz with registration seems to be 90 degree rotated from apjarc+ aseg. mgz. (I wish I could attach a screenshot, but last time I tried, it says my email exceeded the capacity and sent to the moderator)
I also tried bbregister. I was suggested not to use —init-rr, so I tried all the other registration methods, but same problem occurs.
$bbregister --mov sess01/rest/001/template.nii.gz --t2 --s subject --lta register.dof6.lta
—init-rr does a good job when I checked visually by applying registration on f.nii.gz and checked if it overlaps with structural scan. But, I thought the registration file goes both ways, but when I checked structural scan (orig.mgz or aparc+aseg.mgz) with registration file and overlapped with functional scan (f.nii.gz), it does not overlap.
Is there a specific way that I have to apply a registration file to visualize the transformation in the opposite direction? If preprocess registration does not work, is there any other method that I can try to make them aligned?
Thank you for your time and help !
Best, Wenzhen
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