preproc-sess sess01 $Id: preproc-sess,v 1.64.2.1 2016/08/02 21:19:09 greve Exp $ Linux fsuser3-G5-5587 4.15.0-34-generic #37-Ubuntu SMP Mon Aug 27 15:21:48 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux Sun Sep 30 01:11:05 EDT 2018 /media/sda1/nmrclass/tutorial_data/fsfast-functional -s sess01 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run ProjectDir /media/sda1/nmrclass/tutorial_data/fsfast-functional sess01 Template ----------------------------- mktemplate-sess -s sess01 -d /media/sda1/nmrclass/tutorial_data/fsfast-functional -fsd bold -update Session: /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01 ---------------- Sun Sep 30 01:11:06 EDT 2018 Detected input format at nii.gz sess01 Update not needed Run: 001 ---------------- Sun Sep 30 01:11:07 EDT 2018 sess01 001 Update not needed Run: 002 ---------------- Sun Sep 30 01:11:07 EDT 2018 sess01 002 Update not needed Run: 003 ---------------- Sun Sep 30 01:11:07 EDT 2018 sess01 003 Update not needed Run: 004 ---------------- Sun Sep 30 01:11:07 EDT 2018 sess01 004 Update not needed Sun Sep 30 01:11:08 EDT 2018 mktemplate-sess completed sess01 Registration ----------------------------- register-sess -s sess01 -d /media/sda1/nmrclass/tutorial_data/fsfast-functional -fsd bold -delete-dat -dof 6 -bold -per-run -update -init-coreg -------------------------------------------------------------- register-sess logfile is /media/sda1/nmrclass/tutorial_data/fsfast-functional/log/register-sess.sess01.log -------------------------------------------------------------- Sun Sep 30 01:11:09 EDT 2018 setenv SUBJECTS_DIR /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects cd /media/sda1/nmrclass/tutorial_data/fsfast-functional /media/sda1/nmrclass/freesurfer/fsfast/bin/register-sess -s sess01 -d /media/sda1/nmrclass/tutorial_data/fsfast-functional -fsd bold -delete-dat -dof 6 -bold -per-run -update -init-coreg freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-tutorial-2beb96c Linux fsuser3-G5-5587 4.15.0-34-generic #37-Ubuntu SMP Mon Aug 27 15:21:48 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux Session: /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01 ---------------- Sun Sep 30 01:11:09 EDT 2018 -------------------------------------- /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01 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 tmp bold/tmp.bbregister.28089 Log file is bold/register.dof6.dat.log Sun Sep 30 01:11:10 EDT 2018 setenv SUBJECTS_DIR /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects cd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01 /media/sda1/nmrclass/freesurfer/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 1.75 2016/05/10 20:02:28 greve Exp $ Linux fsuser3-G5-5587 4.15.0-34-generic #37-Ubuntu SMP Mon Aug 27 15:21:48 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /media/sda1/nmrclass/freesurfer mri_convert bold/template.nii.gz bold/tmp.bbregister.28089/template.nii mri_convert.bin bold/template.nii.gz bold/tmp.bbregister.28089/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.28089/template.nii... mri_coreg --s fsf01anat --mov bold/tmp.bbregister.28089/template.nii --regdat bold/tmp.bbregister.28089/reg.init.dat --reg bold/tmp.bbregister.28089/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 $Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $ cwd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01 cmdline mri_coreg --s fsf01anat --mov bold/tmp.bbregister.28089/template.nii --regdat bold/tmp.bbregister.28089/reg.init.dat --reg bold/tmp.bbregister.28089/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass dof 6 nsep 1 cras0 1 ftol 0.000100 linmintol 0.010000 bf 1 bflim 30.000000 bfnsamp 30 SmoothRef 0 SatPct 99.990000 MovOOB 0 optschema 1 Reading in mov bold/tmp.bbregister.28089/template.nii Reading in ref /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/brainmask.mgz Reading in and applying refmask /media/sda1/nmrclass/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 -1.0213743763 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 -1.0505123 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6 Starting OpenPowel2(), sep = 4 InitialCost -1.0721068382 #@# 4 188 -6.02228 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0721068 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.072107 #@# 4 193 -6.64031 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0721399 #@# 4 195 -6.40256 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0721593 #@# 4 196 -6.41256 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0721594 #@# 4 200 -6.41256 -36.87573 49.23798 4.00000 0.00000 0.00000 -1.0744623 #@# 4 203 -6.41256 -39.98021 49.23798 4.00000 0.00000 0.00000 -1.0761819 #@# 4 205 -6.41256 -39.58806 49.23798 4.00000 0.00000 0.00000 -1.0762303 #@# 4 208 -6.41256 -39.54797 49.23798 4.00000 0.00000 0.00000 -1.0762312 #@# 4 216 -6.41256 -39.54797 49.33091 4.00000 0.00000 0.00000 -1.0762316 #@# 4 217 -6.41256 -39.54797 49.29183 4.00000 0.00000 0.00000 -1.0762324 #@# 4 218 -6.41256 -39.54797 49.28183 4.00000 0.00000 0.00000 -1.0762342 #@# 4 224 -6.41256 -39.54797 49.28183 3.38197 0.00000 0.00000 -1.0765897 #@# 4 226 -6.41256 -39.54797 49.28183 3.23161 0.00000 0.00000 -1.0765935 #@# 4 227 -6.41256 -39.54797 49.28183 3.26825 0.00000 0.00000 -1.0766006 #@# 4 229 -6.41256 -39.54797 49.28183 3.27825 0.00000 0.00000 -1.0766026 #@# 4 237 -6.41256 -39.54797 49.28183 3.27825 0.13233 0.00000 -1.0766056 #@# 4 238 -6.41256 -39.54797 49.28183 3.27825 0.14647 0.00000 -1.0766058 #@# 4 249 -6.41256 -39.54797 49.28183 3.27825 0.14647 -0.02220 -1.0766059 #@# 4 250 -6.41256 -39.54797 49.28183 3.27825 0.14647 -0.03220 -1.0766068 #@# 4 259 -6.44734 -39.93037 49.28574 3.21392 0.15952 -0.03507 -1.0766177 #@# 4 262 -6.44344 -39.88747 49.28530 3.22114 0.15806 -0.03475 -1.0766182 powell nthiter 1: fret = -1.076618 #@# 4 269 -6.50246 -39.88747 49.28530 3.22114 0.15806 -0.03475 -1.0766184 #@# 4 274 -6.51246 -39.88747 49.28530 3.22114 0.15806 -0.03475 -1.0766186 #@# 4 282 -6.51246 -39.88747 49.28530 3.22114 0.15806 -0.05276 -1.0766200 #@# 4 283 -6.51246 -39.88747 49.28530 3.22114 0.15806 -0.11094 -1.0766233 #@# 4 286 -6.51246 -39.88747 49.28530 3.22114 0.15806 -0.13128 -1.0766251 #@# 4 291 -6.51246 -39.88747 47.66726 3.22114 0.15806 -0.13128 -1.0766443 #@# 4 292 -6.51246 -39.88747 48.45848 3.22114 0.15806 -0.13128 -1.0768539 #@# 4 296 -6.51246 -39.88747 48.42080 3.22114 0.15806 -0.13128 -1.0768601 #@# 4 305 -6.51246 -39.88747 48.42080 2.60310 0.15806 -0.13128 -1.0771173 #@# 4 308 -6.51246 -39.88747 48.42080 2.58743 0.15806 -0.13128 -1.0771182 #@# 4 312 -6.51246 -39.88747 48.42080 2.57743 0.15806 -0.13128 -1.0771190 #@# 4 319 -6.51246 -39.88747 48.42080 2.57743 0.05744 -0.13128 -1.0771196 #@# 4 320 -6.51246 -39.88747 48.42080 2.57743 0.08731 -0.13128 -1.0771208 #@# 4 329 -6.54172 -40.20911 48.42409 2.52332 0.09829 -0.13370 -1.0771389 #@# 4 333 -6.67089 -40.87025 47.56635 1.76839 0.05011 -0.23520 -1.0774630 #@# 4 338 -6.75072 -41.27886 47.03624 1.30182 0.02033 -0.29793 -1.0775054 #@# 4 340 -6.73803 -41.21392 47.12048 1.37597 0.02506 -0.28796 -1.0775137 #@# 4 342 -6.72748 -41.15990 47.19057 1.43765 0.02900 -0.27966 -1.0775158 #@# 4 343 -6.72877 -41.16651 47.18199 1.43010 0.02852 -0.28068 -1.0775161 powell nthiter 2: fret = -1.077516 #@# 4 350 -6.34680 -41.16651 47.18199 1.43010 0.02852 -0.28068 -1.0776132 #@# 4 360 -6.34680 -41.16651 47.18199 1.43010 0.02852 -0.25966 -1.0776144 #@# 4 361 -6.34680 -41.16651 47.18199 1.43010 0.02852 -0.24966 -1.0776153 #@# 4 365 -6.34680 -41.16651 45.56396 1.43010 0.02852 -0.24966 -1.0777858 #@# 4 366 -6.34680 -41.16651 46.21438 1.43010 0.02852 -0.24966 -1.0779661 #@# 4 370 -6.34680 -41.16651 46.19966 1.43010 0.02852 -0.24966 -1.0779662 #@# 4 371 -6.34680 -41.16651 46.18966 1.43010 0.02852 -0.24966 -1.0779715 #@# 4 381 -6.30866 -40.74724 46.18537 1.50064 0.01420 -0.24651 -1.0780333 #@# 4 388 -6.30476 -40.70434 46.18493 1.50786 -0.60530 -0.24619 -1.0780683 #@# 4 390 -6.30476 -40.70434 46.18493 1.50786 -0.42711 -0.24619 -1.0780699 #@# 4 391 -6.30476 -40.70434 46.18493 1.50786 -0.48494 -0.24619 -1.0780715 #@# 4 392 -6.30476 -40.70434 46.18493 1.50786 -0.50062 -0.24619 -1.0780716 #@# 4 395 -6.43392 -41.36548 45.32719 0.75293 -0.54880 -0.34769 -1.0781331 #@# 4 399 -6.38459 -41.11295 45.65482 1.04128 -0.53039 -0.30892 -1.0781467 #@# 4 400 -6.39998 -41.19174 45.55259 0.95131 -0.53614 -0.32102 -1.0781513 #@# 4 401 -6.40127 -41.19835 45.54402 0.94376 -0.53662 -0.32203 -1.0781522 powell nthiter 3: fret = -1.078152 #@# 4 412 -6.31460 -41.19835 45.54402 0.94376 -0.53662 -0.32203 -1.0781558 #@# 4 416 -6.29760 -41.19835 45.54402 0.94376 -0.53662 -0.32203 -1.0781561 #@# 4 424 -6.29760 -41.19835 45.54402 0.94376 -0.53662 -0.21774 -1.0781724 #@# 4 425 -6.29760 -41.19835 45.54402 0.94376 -0.53662 -0.20151 -1.0781742 #@# 4 444 -6.26427 -40.83202 45.54027 1.00539 -0.54912 -0.19876 -1.0782316 #@# 4 445 -6.25673 -40.74915 45.53942 1.01933 -0.55195 -0.19814 -1.0782384 #@# 4 448 -6.25283 -40.70625 45.53899 1.02654 -0.55342 -0.19781 -1.0782415 #@# 4 456 -6.25283 -40.70625 45.53899 1.02654 -0.53133 -0.19781 -1.0782417 #@# 4 464 -6.30217 -40.95878 45.21136 0.73819 -0.54974 -0.23658 -1.0782661 #@# 4 465 -6.29075 -40.90031 45.28722 0.80495 -0.54548 -0.22761 -1.0782665 #@# 4 466 -6.29533 -40.92377 45.25677 0.77816 -0.54719 -0.23121 -1.0782671 #@# 4 467 -6.29662 -40.93039 45.24819 0.77061 -0.54767 -0.23222 -1.0782678 #@# 4 468 -6.29874 -40.94123 45.23412 0.75822 -0.54846 -0.23389 -1.0782683 #@# 4 470 -6.19621 -40.68411 44.92423 0.57269 -0.56030 -0.14574 -1.0782871 #@# 4 476 -6.23537 -40.78232 45.04260 0.64356 -0.55578 -0.17941 -1.0783006 #@# 4 479 -6.22964 -40.76796 45.02529 0.63319 -0.55644 -0.17449 -1.0783010 #@# 4 480 -6.23232 -40.77466 45.03337 0.63803 -0.55613 -0.17679 -1.0783017 Powell done niters total = 4 OptTimeSec 21.6 sec OptTimeMin 0.36 min nEvals 482 Final parameters -6.23231554 -40.77465820 45.03336716 0.63802844 -0.55612826 -0.17678551 Final cost -1.078301627543625 --------------------------------- mri_coreg utimesec 90.776619 mri_coreg stimesec 0.212038 mri_coreg ru_maxrss 424516 mri_coreg ru_ixrss 0 mri_coreg ru_idrss 0 mri_coreg ru_isrss 0 mri_coreg ru_minflt 125481 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 5479 mri_coreg ru_nivcsw 33 Final RefRAS-to-MovRAS 0.99995 -0.00309 -0.00971 -6.23232; 0.00319 0.99993 0.01113 -40.77466; 0.00967 -0.01117 0.99989 45.03337; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox 0.29089 -0.00282 0.00090 -5.31283; 0.00154 0.06908 -0.28258 59.63377; -0.00174 -0.19427 -0.04750 38.58438; 0.00000 0.00000 0.00000 1.00000; Final parameters -6.2323 -40.7747 45.0334 0.6380 -0.5561 -0.1768 nhits = 106089 out of 16777216, Percent Overlap: 40.5 mri_coreg RunTimeSec 91.0 sec To check run: tkregisterfv --mov bold/tmp.bbregister.28089/template.nii --targ /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/brainmask.mgz --reg bold/tmp.bbregister.28089/mri_coreg.lta --s fsf01anat --surfs mri_coreg done mri_segreg --mov bold/tmp.bbregister.28089/template.nii --init-reg bold/tmp.bbregister.28089/reg.init.dat --out-reg bold/tmp.bbregister.28089/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.113 2016/05/10 03:23:20 greve Exp $ setenv SUBJECTS_DIR /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects cd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01 mri_segreg --mov bold/tmp.bbregister.28089/template.nii --init-reg bold/tmp.bbregister.28089/reg.init.dat --out-reg bold/tmp.bbregister.28089/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass movvol bold/tmp.bbregister.28089/template.nii regfile bold/tmp.bbregister.28089/reg.init.dat subject fsf01anat dof 6 outregfile bold/tmp.bbregister.28089/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 1538735046 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99995 -0.00309 -0.00971 1.11697; 0.00870 -0.23751 0.97135 -37.92480; 0.00530 0.97138 0.23747 -1.72948; 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 1.058521 1 -25.0 -25.0 25.0 1.020712 2 -25.0 25.0 -25.0 1.073696 3 -25.0 25.0 25.0 1.034502 4 25.0 -25.0 -25.0 1.048734 5 25.0 -25.0 25.0 1.051877 6 25.0 25.0 -25.0 1.048711 7 25.0 25.0 25.0 1.063878 REL: 8 0.727494 8.400631 1.050079 rel = 0.692799 Initial costs ---------------- Number of surface hits 3062 WM Intensity 853.4886 +/- 215.6211 Ctx Intensity 864.4940 +/- 245.7752 Pct Contrast -0.3626 +/- 22.1801 Cost 0.7275 RelCost 0.6928 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 1.0658 1.0658 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 1.0562 1.0562 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 1.0177 1.0177 0.0 3 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 -4.0000 1.0036 1.0036 0.0 6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.9577 0.9577 0.0 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.9492 0.9492 0.0 18 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 -4.0000 0.9372 0.9372 0.0 19 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.0000 0.9328 0.9328 0.0 30 -4.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.9095 0.9095 0.0 33 -4.0000 -4.0000 0.0000 -4.0000 4.0000 -4.0000 0.8703 0.8703 0.0 34 -4.0000 -4.0000 0.0000 -4.0000 4.0000 0.0000 0.8685 0.8685 0.0 40 -4.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.8569 0.8569 0.0 273 0.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.8168 0.8168 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.7608 0.7608 0.0 282 0.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.7545 0.7545 0.0 283 0.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.5968 0.5968 0.0 Brute Force -------------------------- Min cost was 0.596809 Number of iterations 729 Search time 1.880000 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 = 0.596809 7 -0.252 -4.000 0.000 0.000 0.000 0.000 0.5964897096 12 -0.246 -4.000 0.000 0.000 0.000 0.000 0.5964892950 13 -0.248 -4.000 0.000 0.000 0.000 0.000 0.5964891536 16 -0.248 -3.000 0.000 0.000 0.000 0.000 0.5696416531 21 -0.248 -2.911 0.000 0.000 0.000 0.000 0.5691187415 23 -0.248 -2.879 0.000 0.000 0.000 0.000 0.5689988797 24 -0.248 -2.867 0.000 0.000 0.000 0.000 0.5689554082 25 -0.248 -2.838 0.000 0.000 0.000 0.000 0.5688959544 28 -0.248 -2.837 0.000 0.000 0.000 0.000 0.5688959290 36 -0.248 -2.837 0.069 0.000 0.000 0.000 0.5685862942 37 -0.248 -2.837 0.107 0.000 0.000 0.000 0.5685403072 38 -0.248 -2.837 0.106 0.000 0.000 0.000 0.5685393588 39 -0.248 -2.837 0.099 0.000 0.000 0.000 0.5685352999 45 -0.248 -2.837 0.099 -1.618 0.000 0.000 0.5637476362 46 -0.248 -2.837 0.099 -0.877 0.000 0.000 0.5493247597 52 -0.248 -2.837 0.099 -0.864 0.000 0.000 0.5493160291 53 -0.248 -2.837 0.099 -0.866 0.000 0.000 0.5493158088 54 -0.248 -2.837 0.099 -0.867 0.000 0.000 0.5493156361 62 -0.248 -2.837 0.099 -0.867 0.382 0.000 0.5442322567 73 -0.248 -2.837 0.099 -0.867 0.382 -0.287 0.5433864138 75 -0.248 -2.837 0.099 -0.867 0.382 -0.413 0.5428980567 77 -0.248 -2.837 0.099 -0.867 0.382 -0.365 0.5428077345 78 -0.248 -2.837 0.099 -0.867 0.382 -0.376 0.5428008869 79 -0.248 -2.837 0.099 -0.867 0.382 -0.375 0.5428006305 81 -0.248 -2.837 0.099 -0.867 0.382 -0.373 0.5428005899 powell nthiter 1: fret = 0.542801 91 -0.355 -2.837 0.099 -0.867 0.382 -0.373 0.5424442359 94 -0.485 -2.837 0.099 -0.867 0.382 -0.373 0.5424375309 95 -0.422 -2.837 0.099 -0.867 0.382 -0.373 0.5423809921 96 -0.423 -2.837 0.099 -0.867 0.382 -0.373 0.5423806648 97 -0.430 -2.837 0.099 -0.867 0.382 -0.373 0.5423770801 98 -0.451 -2.837 0.099 -0.867 0.382 -0.373 0.5423718415 100 -0.452 -2.837 0.099 -0.867 0.382 -0.373 0.5423717581 101 -0.453 -2.837 0.099 -0.867 0.382 -0.373 0.5423716717 111 -0.453 -2.854 0.099 -0.867 0.382 -0.373 0.5423712124 112 -0.453 -2.847 0.099 -0.867 0.382 -0.373 0.5423701204 113 -0.453 -2.846 0.099 -0.867 0.382 -0.373 0.5423699769 114 -0.453 -2.843 0.099 -0.867 0.382 -0.373 0.5423698253 115 -0.453 -2.844 0.099 -0.867 0.382 -0.373 0.5423697493 125 -0.453 -2.844 -0.005 -0.867 0.382 -0.373 0.5416957680 126 -0.453 -2.844 -0.004 -0.867 0.382 -0.373 0.5416940914 127 -0.453 -2.844 0.002 -0.867 0.382 -0.373 0.5416891427 130 -0.453 -2.844 0.003 -0.867 0.382 -0.373 0.5416886784 131 -0.453 -2.844 0.007 -0.867 0.382 -0.373 0.5416885119 133 -0.453 -2.844 0.006 -0.867 0.382 -0.373 0.5416882405 142 -0.453 -2.844 0.006 -0.816 0.382 -0.373 0.5414439474 145 -0.453 -2.844 0.006 -0.803 0.382 -0.373 0.5414292320 146 -0.453 -2.844 0.006 -0.801 0.382 -0.373 0.5414278804 148 -0.453 -2.844 0.006 -0.797 0.382 -0.373 0.5414257336 159 -0.453 -2.844 0.006 -0.797 0.331 -0.373 0.5412586725 161 -0.453 -2.844 0.006 -0.797 0.328 -0.373 0.5412582255 163 -0.453 -2.844 0.006 -0.797 0.329 -0.373 0.5412577706 171 -0.453 -2.844 0.006 -0.797 0.329 -0.353 0.5412371972 173 -0.453 -2.844 0.006 -0.797 0.329 -0.359 0.5412318440 174 -0.453 -2.844 0.006 -0.797 0.329 -0.358 0.5412313143 powell nthiter 2: fret = 0.541231 184 -0.439 -2.844 0.006 -0.797 0.329 -0.358 0.5412220509 185 -0.435 -2.844 0.006 -0.797 0.329 -0.358 0.5412179446 186 -0.409 -2.844 0.006 -0.797 0.329 -0.358 0.5412129798 187 -0.419 -2.844 0.006 -0.797 0.329 -0.358 0.5412066438 210 -0.419 -2.844 0.022 -0.797 0.329 -0.358 0.5411643725 211 -0.419 -2.844 0.024 -0.797 0.329 -0.358 0.5411638237 222 -0.419 -2.844 0.024 -0.789 0.329 -0.358 0.5411616859 245 -0.419 -2.844 0.024 -0.789 0.329 -0.364 0.5411569118 246 -0.419 -2.844 0.024 -0.789 0.329 -0.365 0.5411568266 powell nthiter 3: fret = 0.541157 257 -0.418 -2.844 0.024 -0.789 0.329 -0.365 0.5411564181 259 -0.415 -2.844 0.024 -0.789 0.329 -0.365 0.5411560878 272 -0.416 -2.837 0.024 -0.789 0.329 -0.365 0.5411558754 274 -0.416 -2.840 0.024 -0.789 0.329 -0.365 0.5411535669 276 -0.416 -2.841 0.024 -0.789 0.329 -0.365 0.5411533129 277 -0.416 -2.842 0.024 -0.789 0.329 -0.365 0.5411533004 286 -0.416 -2.842 0.027 -0.789 0.329 -0.365 0.5411531881 288 -0.416 -2.842 0.026 -0.789 0.329 -0.365 0.5411531156 297 -0.416 -2.842 0.026 -0.787 0.329 -0.365 0.5411528853 298 -0.416 -2.842 0.026 -0.786 0.329 -0.365 0.5411528547 311 -0.416 -2.842 0.026 -0.786 0.328 -0.365 0.5411526441 Powell done niters = 3 Computing relative cost 0 -25.0 -25.0 -25.0 1.030078 1 -25.0 -25.0 25.0 1.018910 2 -25.0 25.0 -25.0 1.070932 3 -25.0 25.0 25.0 1.039696 4 25.0 -25.0 -25.0 1.039458 5 25.0 -25.0 25.0 1.058910 6 25.0 25.0 -25.0 1.014520 7 25.0 25.0 25.0 1.032077 REL: 8 0.541153 8.304580 1.038073 rel = 0.521305 Number of iterations 3 Min cost was 0.541153 Number of FunctionCalls 322 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.837000 sec Parameters at optimum (transmm) -0.41643 -2.84237 0.02590 Parameters at optimum (rotdeg) -0.78626 0.32831 -0.36539 Final costs ---------------- Number of surface hits 3062 WM Intensity 817.5553 +/- 228.7225 Ctx Intensity 850.0679 +/- 262.9107 Pct Contrast 1.9518 +/- 22.9337 Cost 0.5412 RelCost 0.6928 Reg at min cost was 1.00000 0.00107 -0.00221 0.45158; 0.00239 -0.22417 0.97455 -40.79363; -0.00055 0.97455 0.22417 -1.18939; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/tmp.bbregister.28089/bbr.pass1.dat, type = 14 Original Reg 0.99995 -0.00309 -0.00971 1.11697; 0.00870 -0.23751 0.97135 -37.92480; 0.00530 0.97138 0.23747 -1.72948; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00005 -0.00415 -0.00750 0.66539; 0.00631 -0.01334 -0.00320 2.86883; 0.00585 -0.00317 0.01330 -0.54010; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 2.898395 Computing change in rh position Surface-RMS-Diff-mm 3.048050 0.665840 4.389890 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.28089/template.nii --init-reg bold/tmp.bbregister.28089/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.28089/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.113 2016/05/10 03:23:20 greve Exp $ setenv SUBJECTS_DIR /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects cd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01 mri_segreg --mov bold/tmp.bbregister.28089/template.nii --init-reg bold/tmp.bbregister.28089/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.28089/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass movvol bold/tmp.bbregister.28089/template.nii regfile bold/tmp.bbregister.28089/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 1538574736 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 1.00000 0.00107 -0.00221 0.45158; 0.00239 -0.22417 0.97455 -40.79363; -0.00055 0.97455 0.22417 -1.18939; 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 1.035272 1 -25.0 -25.0 25.0 1.052930 2 -25.0 25.0 -25.0 1.058225 3 -25.0 25.0 25.0 1.068828 4 25.0 -25.0 -25.0 1.040137 5 25.0 -25.0 25.0 1.042259 6 25.0 25.0 -25.0 1.024803 7 25.0 25.0 25.0 1.059264 REL: 8 0.565052 8.381718 1.047715 rel = 0.539319 Initial costs ---------------- Number of surface hits 304688 WM Intensity 822.2507 +/- 225.2877 Ctx Intensity 853.0911 +/- 260.6931 Pct Contrast 1.6172 +/- 23.2044 Cost 0.5651 RelCost 0.5393 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.5446 0.5446 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.5435 0.5435 0.0 2 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.5430 0.5430 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.5427 0.5427 0.0 5 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1000 0.5422 0.5422 0.0 32 -0.1000 -0.1000 0.0000 -0.1000 0.0000 0.1000 0.5420 0.5420 0.0 85 -0.1000 0.0000 -0.1000 -0.1000 0.0000 0.0000 0.5420 0.5420 0.0 94 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.0000 0.5418 0.5418 0.0 121 -0.1000 0.0000 0.0000 0.0000 0.0000 0.0000 0.5414 0.5414 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.5412 0.5412 0.0 Brute Force -------------------------- Min cost was 0.541153 Number of iterations 729 Search time 1.853000 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 = 0.565052 6 0.382 0.000 0.000 0.000 0.000 0.000 0.5645347124 7 0.218 0.000 0.000 0.000 0.000 0.000 0.5638515832 8 0.219 0.000 0.000 0.000 0.000 0.000 0.5638513115 9 0.224 0.000 0.000 0.000 0.000 0.000 0.5638509170 11 0.222 0.000 0.000 0.000 0.000 0.000 0.5638508397 18 0.222 0.382 0.000 0.000 0.000 0.000 0.5608939390 19 0.222 0.350 0.000 0.000 0.000 0.000 0.5608805752 20 0.222 0.357 0.000 0.000 0.000 0.000 0.5608794505 21 0.222 0.356 0.000 0.000 0.000 0.000 0.5608793552 22 0.222 0.355 0.000 0.000 0.000 0.000 0.5608793445 30 0.222 0.355 -0.051 0.000 0.000 0.000 0.5607925697 31 0.222 0.355 -0.061 0.000 0.000 0.000 0.5607920920 32 0.222 0.355 -0.057 0.000 0.000 0.000 0.5607916555 41 0.222 0.355 -0.058 -0.116 0.000 0.000 0.5605665329 42 0.222 0.355 -0.058 -0.105 0.000 0.000 0.5605631182 51 0.222 0.355 -0.058 -0.104 0.064 0.000 0.5604317583 53 0.222 0.355 -0.058 -0.104 0.066 0.000 0.5604316731 66 0.222 0.355 -0.058 -0.104 0.066 0.094 0.5603870544 67 0.222 0.355 -0.058 -0.104 0.066 0.072 0.5603787312 68 0.222 0.355 -0.058 -0.104 0.066 0.067 0.5603786588 69 0.222 0.355 -0.058 -0.104 0.066 0.069 0.5603785608 powell nthiter 1: fret = 0.560379 78 0.224 0.355 -0.058 -0.104 0.066 0.069 0.5603782569 82 0.225 0.355 -0.058 -0.104 0.066 0.069 0.5603782165 89 0.225 0.408 -0.058 -0.104 0.066 0.069 0.5603446809 90 0.225 0.396 -0.058 -0.104 0.066 0.069 0.5603423122 91 0.225 0.397 -0.058 -0.104 0.066 0.069 0.5603422872 102 0.225 0.398 -0.068 -0.104 0.066 0.069 0.5603409656 103 0.225 0.398 -0.065 -0.104 0.066 0.069 0.5603406585 114 0.225 0.398 -0.065 -0.103 0.066 0.069 0.5603406452 122 0.225 0.398 -0.065 -0.103 0.075 0.069 0.5603351827 123 0.225 0.398 -0.065 -0.103 0.081 0.069 0.5603338603 125 0.225 0.398 -0.065 -0.103 0.080 0.069 0.5603337348 135 0.225 0.398 -0.065 -0.103 0.080 0.065 0.5603333823 powell nthiter 2: fret = 0.560333 145 0.226 0.398 -0.065 -0.103 0.080 0.065 0.5603333672 154 0.226 0.399 -0.065 -0.103 0.080 0.065 0.5603333455 Powell done niters = 2 Computing relative cost 0 -25.0 -25.0 -25.0 1.035016 1 -25.0 -25.0 25.0 1.054814 2 -25.0 25.0 -25.0 1.061053 3 -25.0 25.0 25.0 1.072681 4 25.0 -25.0 -25.0 1.044652 5 25.0 -25.0 25.0 1.042142 6 25.0 25.0 -25.0 1.026722 7 25.0 25.0 25.0 1.061028 REL: 8 0.560333 8.398107 1.049763 rel = 0.533771 Number of iterations 2 Min cost was 0.560333 Number of FunctionCalls 200 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 19.524000 sec Parameters at optimum (transmm) 0.22606 0.40043 -0.06611 Parameters at optimum (rotdeg) -0.10269 0.07984 0.06491 Final costs ---------------- Number of surface hits 304688 WM Intensity 826.0221 +/- 221.3243 Ctx Intensity 857.8209 +/- 256.8013 Pct Contrast 1.7771 +/- 22.9017 Cost 0.5603 RelCost 0.5393 Reg at min cost was 0.99999 0.00268 -0.00300 0.72230; 0.00352 -0.22242 0.97494 -40.39473; -0.00195 0.97495 0.22243 -1.18301; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/register.dof6.dat, type = 14 Original Reg 1.00000 0.00107 -0.00221 0.45158; 0.00239 -0.22417 0.97455 -40.79363; -0.00055 0.97455 0.22417 -1.18939; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00001 -0.00161 0.00079 -0.27072; -0.00113 -0.00175 -0.00040 -0.39890; 0.00140 -0.00040 0.00174 -0.00637; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.430907 Computing change in rh position Surface-RMS-Diff-mm 0.462571 0.112167 0.705312 mri_segreg done MinCost: 0.560333 826.022111 857.820931 1.777085 tkregister2_cmdl --mov bold/template.nii.gz --reg bold/register.dof6.dat --noedit --ltaout bold/register.dof6.lta tkregister_tcl /media/sda1/nmrclass/freesurfer/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 1.132.2.1 2016/08/02 21:17:29 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- 0.99999 0.00268 -0.00300 0.72230; 0.00352 -0.22242 0.97494 -40.39473; -0.00195 0.97495 0.22243 -1.18301; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: loading target /media/sda1/nmrclass/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 0.00268 -0.00300 0.72230; 0.00352 -0.22242 0.97494 -40.39473; -0.00195 0.97495 0.22243 -1.18301; 0.00000 0.00000 0.00000 1.00000; Determinant -1 subject = fsf01anat RegMat --------------------------- 0.99999 0.00268 -0.00300 0.72230; 0.00352 -0.22242 0.97494 -40.39473; -0.00195 0.97495 0.22243 -1.18301; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Sun Sep 30 01:11:09 EDT 2018 Ended at Sun Sep 30 01:13:26 EDT 2018 BBR-Run-Time-Sec 136 bbregister Done To check results, run: tkregisterfv --mov bold/template.nii.gz --reg bold/register.dof6.lta --surfs Run: 001 ---------------- Sun Sep 30 01:13:26 EDT 2018 -------------------------------------- /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01 bbregister --s fsf01anat --init-coreg --6 --bold --mov bold/001/template.nii.gz --reg bold/001/register.dof6.dat --lta bold/001/register.dof6.lta --init-reg-out bold/001/init.register.dof6.dat tmp bold/001/tmp.bbregister.28189 Log file is bold/001/register.dof6.dat.log Sun Sep 30 01:13:26 EDT 2018 setenv SUBJECTS_DIR /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects cd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01 /media/sda1/nmrclass/freesurfer/bin/bbregister --s fsf01anat --init-coreg --6 --bold --mov bold/001/template.nii.gz --reg bold/001/register.dof6.dat --lta bold/001/register.dof6.lta --init-reg-out bold/001/init.register.dof6.dat $Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $ Linux fsuser3-G5-5587 4.15.0-34-generic #37-Ubuntu SMP Mon Aug 27 15:21:48 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /media/sda1/nmrclass/freesurfer mri_convert bold/001/template.nii.gz bold/001/tmp.bbregister.28189/template.nii mri_convert.bin bold/001/template.nii.gz bold/001/tmp.bbregister.28189/template.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from bold/001/template.nii.gz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.973976, -0.226651) k_ras = (-2.36491e-18, -0.226651, 0.973976) writing to bold/001/tmp.bbregister.28189/template.nii... mri_coreg --s fsf01anat --mov bold/001/tmp.bbregister.28189/template.nii --regdat bold/001/tmp.bbregister.28189/reg.init.dat --reg bold/001/tmp.bbregister.28189/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 $Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $ cwd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01 cmdline mri_coreg --s fsf01anat --mov bold/001/tmp.bbregister.28189/template.nii --regdat bold/001/tmp.bbregister.28189/reg.init.dat --reg bold/001/tmp.bbregister.28189/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass dof 6 nsep 1 cras0 1 ftol 0.000100 linmintol 0.010000 bf 1 bflim 30.000000 bfnsamp 30 SmoothRef 0 SatPct 99.990000 MovOOB 0 optschema 1 Reading in mov bold/001/tmp.bbregister.28189/template.nii Reading in ref /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/brainmask.mgz Reading in and applying refmask /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/aparc+aseg.mgz Setting cras translation parameters to align centers Creating random numbers for coordinate dithering Performing intensity dithering Initial parameters -6.0223 -45.2577 79.2380 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Separation list (1): 4 min = 4 DoSmoothing 1 DoCoordDither 1 DoIntensityDither 1 nitersmax 4 ftol 1.000e-04 linmintol 1.000e-02 SatPct 99.990000 Hist FWHM 7.000000 7.000000 nthreads 1 movsat = 1714.3334 mov gstd 0.9989 0.9989 0.0000 Smoothing mov refsat = 118.0000 ref gstd 1.8914 1.8914 1.8914 Smoothing ref COREGpreproc() done Testing if mov and target overlap Init cost -1.0212743062 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 -1.0504272 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6 Starting OpenPowel2(), sep = 4 InitialCost -1.0720103979 #@# 4 188 -6.02228 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0720104 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.072010 #@# 4 193 -6.64031 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0720539 #@# 4 195 -6.42229 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0720725 #@# 4 196 -6.41229 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0720727 #@# 4 197 -6.37305 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0720730 #@# 4 204 -6.37305 -36.87573 49.23798 4.00000 0.00000 0.00000 -1.0744518 #@# 4 207 -6.37305 -40.14326 49.23798 4.00000 0.00000 0.00000 -1.0762037 #@# 4 209 -6.37305 -39.56493 49.23798 4.00000 0.00000 0.00000 -1.0763277 #@# 4 219 -6.37305 -39.37363 49.23798 4.00000 0.00000 0.00000 -1.0763278 #@# 4 226 -6.37305 -39.37363 49.18098 4.00000 0.00000 0.00000 -1.0763319 #@# 4 228 -6.37305 -39.37363 49.16456 4.00000 0.00000 0.00000 -1.0763327 #@# 4 234 -6.37305 -39.37363 49.16456 3.38197 0.00000 0.00000 -1.0764936 #@# 4 236 -6.37305 -39.37363 49.16456 3.51166 0.00000 0.00000 -1.0765005 #@# 4 237 -6.37305 -39.37363 49.16456 3.48831 0.00000 0.00000 -1.0765010 #@# 4 238 -6.37305 -39.37363 49.16456 3.47831 0.00000 0.00000 -1.0765017 #@# 4 241 -6.37305 -39.37363 49.16456 3.45556 0.00000 0.00000 -1.0765027 #@# 4 248 -6.37305 -39.37363 49.16456 3.45556 0.38197 0.00000 -1.0765043 #@# 4 249 -6.37305 -39.37363 49.16456 3.45556 0.21001 0.00000 -1.0765108 #@# 4 251 -6.37305 -39.37363 49.16456 3.45556 0.22698 0.00000 -1.0765111 #@# 4 253 -6.37305 -39.37363 49.16456 3.45556 0.24959 0.00000 -1.0765116 #@# 4 254 -6.37305 -39.37363 49.16456 3.45556 0.26357 0.00000 -1.0765125 #@# 4 262 -6.37305 -39.37363 49.16456 3.45556 0.26357 -0.16009 -1.0765301 #@# 4 265 -6.37305 -39.37363 49.16456 3.45556 0.26357 -0.22691 -1.0765342 #@# 4 266 -6.37305 -39.37363 49.16456 3.45556 0.26357 -0.21691 -1.0765347 #@# 4 267 -6.37305 -39.37363 49.16456 3.45556 0.26357 -0.20691 -1.0765352 #@# 4 276 -6.41061 -39.81431 49.15670 3.39727 0.29179 -0.22906 -1.0765735 #@# 4 279 -6.41492 -39.86486 49.15580 3.39059 0.29503 -0.23160 -1.0765737 powell nthiter 1: fret = -1.076574 #@# 4 286 -6.35224 -39.86486 49.15580 3.39059 0.29503 -0.23160 -1.0765743 #@# 4 287 -6.37461 -39.86486 49.15580 3.39059 0.29503 -0.23160 -1.0765748 #@# 4 289 -6.39461 -39.86486 49.15580 3.39059 0.29503 -0.23160 -1.0765755 #@# 4 297 -6.39461 -39.86486 49.15580 3.39059 0.29503 -0.19974 -1.0765767 #@# 4 304 -6.39461 -39.86486 48.53776 3.39059 0.29503 -0.19974 -1.0767268 #@# 4 307 -6.39461 -39.86486 48.55776 3.39059 0.29503 -0.19974 -1.0767279 #@# 4 311 -6.39461 -39.86486 48.57049 3.39059 0.29503 -0.19974 -1.0767281 #@# 4 317 -6.39461 -39.86486 48.57049 2.77255 0.29503 -0.19974 -1.0767730 #@# 4 319 -6.39461 -39.86486 48.57049 3.02580 0.29503 -0.19974 -1.0768259 #@# 4 326 -6.39461 -39.86486 48.57049 3.02580 -0.32301 -0.19974 -1.0768292 #@# 4 328 -6.39461 -39.86486 48.57049 3.02580 -0.03212 -0.19974 -1.0768366 #@# 4 329 -6.39461 -39.86486 48.57049 3.02580 -0.04267 -0.19974 -1.0768398 #@# 4 331 -6.39461 -39.86486 48.57049 3.02580 -0.09008 -0.19974 -1.0768410 #@# 4 332 -6.39461 -39.86486 48.57049 3.02580 -0.06897 -0.19974 -1.0768416 #@# 4 344 -6.41617 -40.35610 47.97643 2.59604 -0.40151 -0.19258 -1.0770358 #@# 4 347 -6.45105 -41.15094 47.01521 1.90066 -0.93958 -0.18099 -1.0771307 #@# 4 348 -6.44582 -41.03174 47.15936 2.00495 -0.85888 -0.18272 -1.0771449 #@# 4 351 -6.44149 -40.93317 47.27857 2.09119 -0.79216 -0.18416 -1.0771509 #@# 4 353 -6.44207 -40.94633 47.26265 2.07967 -0.80107 -0.18397 -1.0771524 powell nthiter 2: fret = -1.077152 #@# 4 364 -6.53405 -40.94633 47.26265 2.07967 -0.80107 -0.18397 -1.0771614 #@# 4 386 -6.46466 -40.28503 47.27444 2.16714 -0.84342 -0.15073 -1.0772710 #@# 4 389 -6.44861 -40.09672 47.27780 2.19205 -0.85547 -0.14126 -1.0772750 #@# 4 390 -6.45533 -40.17553 47.27639 2.18163 -0.85043 -0.14522 -1.0772783 #@# 4 391 -6.45884 -40.21669 47.27566 2.17618 -0.84779 -0.14729 -1.0772790 #@# 4 402 -6.45884 -40.21669 47.27566 2.17618 0.15221 -0.14729 -1.0773213 #@# 4 406 -6.45884 -40.21669 47.27566 2.17618 -0.22976 -0.14729 -1.0773380 #@# 4 413 -6.48039 -40.70793 46.68159 1.74642 -0.56230 -0.14013 -1.0774356 #@# 4 418 -6.48104 -40.72263 46.66381 1.73356 -0.57225 -0.13991 -1.0774360 #@# 4 419 -6.48246 -40.75492 46.62476 1.70531 -0.59411 -0.13944 -1.0774391 #@# 4 423 -6.48191 -40.74259 46.63968 1.71610 -0.58576 -0.13962 -1.0774398 #@# 4 424 -6.48158 -40.73497 46.64890 1.72277 -0.58060 -0.13973 -1.0774415 powell nthiter 3: fret = -1.077441 #@# 4 433 -6.55972 -40.73497 46.64890 1.72277 -0.58060 -0.13973 -1.0774455 #@# 4 434 -6.54972 -40.73497 46.64890 1.72277 -0.58060 -0.13973 -1.0774457 #@# 4 442 -6.54972 -40.73497 46.64890 1.72277 -0.58060 -0.10190 -1.0774473 #@# 4 451 -6.51929 -40.37788 46.65527 1.77000 -0.60347 -0.08395 -1.0774992 #@# 4 452 -6.51074 -40.27760 46.65705 1.78326 -0.60989 -0.07891 -1.0775013 #@# 4 453 -6.51425 -40.31876 46.65632 1.77782 -0.60725 -0.08098 -1.0775017 #@# 4 460 -6.51425 -40.31876 46.65632 1.86043 -0.60725 -0.08098 -1.0775075 #@# 4 469 -6.51425 -40.31876 46.65632 1.86043 -0.22529 -0.08098 -1.0775394 #@# 4 475 -6.53581 -40.81000 46.06226 1.43066 -0.55783 -0.07381 -1.0775437 #@# 4 479 -6.52757 -40.62236 46.28917 1.59482 -0.43081 -0.07655 -1.0775645 #@# 4 480 -6.52523 -40.56889 46.35384 1.64161 -0.39461 -0.07733 -1.0775688 #@# 4 485 -6.56887 -40.40281 46.05879 1.56045 -0.20861 -0.01493 -1.0775833 Powell done niters total = 4 OptTimeSec 21.1 sec OptTimeMin 0.35 min nEvals 485 Final parameters -6.52522564 -40.56888580 46.35384369 1.64160538 -0.39460623 -0.07732873 Final cost -1.077568780125497 --------------------------------- mri_coreg utimesec 90.975061 mri_coreg stimesec 0.232079 mri_coreg ru_maxrss 424484 mri_coreg ru_ixrss 0 mri_coreg ru_idrss 0 mri_coreg ru_isrss 0 mri_coreg ru_minflt 125478 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 5479 mri_coreg ru_nivcsw 49 Final RefRAS-to-MovRAS 0.99998 -0.00135 -0.00689 -6.52523; 0.00155 0.99959 0.02865 -40.56889; 0.00685 -0.02866 0.99957 46.35384; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox 0.29090 -0.00200 0.00039 -5.27460; 0.00089 0.07402 -0.28133 59.01115; -0.00126 -0.19341 -0.05089 38.91278; 0.00000 0.00000 0.00000 1.00000; Final parameters -6.5252 -40.5689 46.3538 1.6416 -0.3946 -0.0773 nhits = 106039 out of 16777216, Percent Overlap: 40.5 mri_coreg RunTimeSec 91.3 sec To check run: tkregisterfv --mov bold/001/tmp.bbregister.28189/template.nii --targ /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/brainmask.mgz --reg bold/001/tmp.bbregister.28189/mri_coreg.lta --s fsf01anat --surfs mri_coreg done mri_segreg --mov bold/001/tmp.bbregister.28189/template.nii --init-reg bold/001/tmp.bbregister.28189/reg.init.dat --out-reg bold/001/tmp.bbregister.28189/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.113 2016/05/10 03:23:20 greve Exp $ setenv SUBJECTS_DIR /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects cd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01 mri_segreg --mov bold/001/tmp.bbregister.28189/template.nii --init-reg bold/001/tmp.bbregister.28189/reg.init.dat --out-reg bold/001/tmp.bbregister.28189/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass movvol bold/001/tmp.bbregister.28189/template.nii regfile bold/001/tmp.bbregister.28189/reg.init.dat subject fsf01anat dof 6 outregfile bold/001/tmp.bbregister.28189/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 1538313199 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99998 -0.00135 -0.00689 0.84339; 0.00632 -0.25447 0.96706 -37.60040; 0.00306 0.96708 0.25445 -2.02609; 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 1.052216 1 -25.0 -25.0 25.0 1.016991 2 -25.0 25.0 -25.0 1.071163 3 -25.0 25.0 25.0 1.036063 4 25.0 -25.0 -25.0 1.046794 5 25.0 -25.0 25.0 1.051092 6 25.0 25.0 -25.0 1.050856 7 25.0 25.0 25.0 1.050333 REL: 8 0.762722 8.375508 1.046939 rel = 0.728526 Initial costs ---------------- Number of surface hits 3062 WM Intensity 850.9482 +/- 212.1914 Ctx Intensity 854.6148 +/- 240.0966 Pct Contrast -1.0290 +/- 21.7752 Cost 0.7627 RelCost 0.7285 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 1.0578 1.0578 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 1.0555 1.0555 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 1.0204 1.0204 0.0 3 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 -4.0000 1.0104 1.0104 0.0 6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.9774 0.9774 0.0 8 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 4.0000 0.9475 0.9475 0.0 19 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.0000 0.9421 0.9421 0.0 30 -4.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.9015 0.9015 0.0 33 -4.0000 -4.0000 0.0000 -4.0000 4.0000 -4.0000 0.8905 0.8905 0.0 34 -4.0000 -4.0000 0.0000 -4.0000 4.0000 0.0000 0.8814 0.8814 0.0 273 0.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.8098 0.8098 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.7476 0.7476 0.0 283 0.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.5940 0.5940 0.0 Brute Force -------------------------- Min cost was 0.594029 Number of iterations 729 Search time 1.939000 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 = 0.594029 7 -0.198 -4.000 0.000 0.000 0.000 0.000 0.5933995501 9 -0.359 -4.000 0.000 0.000 0.000 0.000 0.5933806633 10 -0.280 -4.000 0.000 0.000 0.000 0.000 0.5930773580 11 -0.279 -4.000 0.000 0.000 0.000 0.000 0.5930763843 13 -0.274 -4.000 0.000 0.000 0.000 0.000 0.5930741639 14 -0.273 -4.000 0.000 0.000 0.000 0.000 0.5930741196 17 -0.273 -3.000 0.000 0.000 0.000 0.000 0.5842825087 21 -0.273 -3.382 0.000 0.000 0.000 0.000 0.5839232388 22 -0.273 -3.214 0.000 0.000 0.000 0.000 0.5830070078 24 -0.273 -3.249 0.000 0.000 0.000 0.000 0.5830016039 26 -0.273 -3.232 0.000 0.000 0.000 0.000 0.5829777400 28 -0.273 -3.229 0.000 0.000 0.000 0.000 0.5829775626 31 -0.273 -3.230 0.000 0.000 0.000 0.000 0.5829773975 39 -0.273 -3.231 0.069 0.000 0.000 0.000 0.5827597855 40 -0.273 -3.231 0.093 0.000 0.000 0.000 0.5827268296 42 -0.273 -3.231 0.104 0.000 0.000 0.000 0.5827217885 47 -0.273 -3.231 0.104 -1.618 0.000 0.000 0.5777617100 48 -0.273 -3.231 0.104 -0.911 0.000 0.000 0.5723692051 52 -0.273 -3.231 0.104 -0.775 0.000 0.000 0.5722592373 54 -0.273 -3.231 0.104 -0.694 0.000 0.000 0.5721407294 58 -0.273 -3.231 0.104 -0.691 0.000 0.000 0.5721404343 60 -0.273 -3.231 0.104 -0.689 0.000 0.000 0.5721403895 68 -0.273 -3.231 0.104 -0.689 0.382 0.000 0.5701685660 69 -0.273 -3.231 0.104 -0.689 0.351 0.000 0.5698072403 70 -0.273 -3.231 0.104 -0.689 0.245 0.000 0.5694104142 72 -0.273 -3.231 0.104 -0.689 0.225 0.000 0.5693811537 73 -0.273 -3.231 0.104 -0.689 0.216 0.000 0.5693627589 74 -0.273 -3.231 0.104 -0.689 0.191 0.000 0.5693393652 76 -0.273 -3.231 0.104 -0.689 0.197 0.000 0.5693380140 78 -0.273 -3.231 0.104 -0.689 0.198 0.000 0.5693374349 79 -0.273 -3.231 0.104 -0.689 0.200 0.000 0.5693367206 80 -0.273 -3.231 0.104 -0.689 0.202 0.000 0.5693362399 86 -0.273 -3.231 0.104 -0.689 0.202 -0.618 0.5691183265 93 -0.273 -3.231 0.104 -0.689 0.202 -0.605 0.5691150387 96 -0.273 -3.231 0.104 -0.689 0.202 -0.602 0.5691148883 97 -0.273 -3.231 0.104 -0.689 0.202 -0.603 0.5691148405 powell nthiter 1: fret = 0.569115 108 -0.348 -3.231 0.104 -0.689 0.202 -0.603 0.5686898251 109 -0.410 -3.231 0.104 -0.689 0.202 -0.603 0.5684471082 111 -0.399 -3.231 0.104 -0.689 0.202 -0.603 0.5684464557 112 -0.404 -3.231 0.104 -0.689 0.202 -0.603 0.5684435120 120 -0.404 -2.849 0.104 -0.689 0.202 -0.603 0.5676776329 121 -0.404 -2.972 0.104 -0.689 0.202 -0.603 0.5668424191 123 -0.404 -2.980 0.104 -0.689 0.202 -0.603 0.5668330488 124 -0.404 -2.984 0.104 -0.689 0.202 -0.603 0.5668322553 132 -0.404 -2.984 0.486 -0.689 0.202 -0.603 0.5647095933 133 -0.404 -2.984 0.462 -0.689 0.202 -0.603 0.5644883657 134 -0.404 -2.984 0.363 -0.689 0.202 -0.603 0.5644455591 136 -0.404 -2.984 0.409 -0.689 0.202 -0.603 0.5643252311 138 -0.404 -2.984 0.414 -0.689 0.202 -0.603 0.5643239156 140 -0.404 -2.984 0.416 -0.689 0.202 -0.603 0.5643238762 150 -0.404 -2.984 0.416 -0.785 0.202 -0.603 0.5637905686 152 -0.404 -2.984 0.416 -0.781 0.202 -0.603 0.5637891767 153 -0.404 -2.984 0.416 -0.779 0.202 -0.603 0.5637890645 154 -0.404 -2.984 0.416 -0.778 0.202 -0.603 0.5637890451 163 -0.404 -2.984 0.416 -0.778 0.178 -0.603 0.5637573180 165 -0.404 -2.984 0.416 -0.778 0.177 -0.603 0.5637572888 178 -0.404 -2.984 0.416 -0.778 0.177 -0.637 0.5637289342 179 -0.404 -2.984 0.416 -0.778 0.177 -0.624 0.5637033651 powell nthiter 2: fret = 0.563703 190 -0.383 -2.984 0.416 -0.778 0.177 -0.624 0.5636626501 191 -0.378 -2.984 0.416 -0.778 0.177 -0.624 0.5636607430 192 -0.377 -2.984 0.416 -0.778 0.177 -0.624 0.5636605613 194 -0.376 -2.984 0.416 -0.778 0.177 -0.624 0.5636605084 204 -0.376 -2.989 0.416 -0.778 0.177 -0.624 0.5636579345 205 -0.376 -2.988 0.416 -0.778 0.177 -0.624 0.5636578661 215 -0.376 -2.988 0.375 -0.778 0.177 -0.624 0.5635841705 216 -0.376 -2.988 0.382 -0.778 0.177 -0.624 0.5635717804 229 -0.376 -2.988 0.382 -0.796 0.177 -0.624 0.5635358245 230 -0.376 -2.988 0.382 -0.807 0.177 -0.624 0.5635325961 231 -0.376 -2.988 0.382 -0.804 0.177 -0.624 0.5635319949 234 -0.376 -2.988 0.382 -0.803 0.177 -0.624 0.5635318747 243 -0.376 -2.988 0.382 -0.803 0.167 -0.624 0.5635239379 245 -0.376 -2.988 0.382 -0.803 0.168 -0.624 0.5635237575 259 -0.376 -2.988 0.382 -0.803 0.168 -0.631 0.5635189399 powell nthiter 3: fret = 0.563519 271 -0.366 -2.988 0.382 -0.803 0.168 -0.631 0.5635166765 272 -0.370 -2.988 0.382 -0.803 0.168 -0.631 0.5635150394 273 -0.371 -2.988 0.382 -0.803 0.168 -0.631 0.5635149416 283 -0.371 -2.982 0.382 -0.803 0.168 -0.631 0.5635048515 284 -0.371 -2.978 0.382 -0.803 0.168 -0.631 0.5635018291 285 -0.371 -2.976 0.382 -0.803 0.168 -0.631 0.5635016801 295 -0.371 -2.976 0.367 -0.803 0.168 -0.631 0.5634978762 296 -0.371 -2.976 0.373 -0.803 0.168 -0.631 0.5634963192 297 -0.371 -2.976 0.372 -0.803 0.168 -0.631 0.5634961749 309 -0.371 -2.976 0.371 -0.817 0.168 -0.631 0.5634814666 310 -0.371 -2.976 0.371 -0.821 0.168 -0.631 0.5634801097 311 -0.371 -2.976 0.371 -0.823 0.168 -0.631 0.5634800597 321 -0.371 -2.976 0.371 -0.823 0.163 -0.631 0.5634795648 322 -0.371 -2.976 0.371 -0.823 0.164 -0.631 0.5634795421 335 -0.371 -2.976 0.371 -0.823 0.164 -0.638 0.5634705021 Powell done niters = 3 Computing relative cost 0 -25.0 -25.0 -25.0 1.057012 1 -25.0 -25.0 25.0 1.019236 2 -25.0 25.0 -25.0 1.047050 3 -25.0 25.0 25.0 1.036307 4 25.0 -25.0 -25.0 1.039100 5 25.0 -25.0 25.0 1.036142 6 25.0 25.0 -25.0 1.021026 7 25.0 25.0 25.0 1.018653 REL: 8 0.563471 8.274526 1.034316 rel = 0.544776 Number of iterations 3 Min cost was 0.563471 Number of FunctionCalls 338 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.915000 sec Parameters at optimum (transmm) -0.37095 -2.97586 0.37080 Parameters at optimum (rotdeg) -0.82271 0.16430 -0.63819 Final costs ---------------- Number of surface hits 3062 WM Intensity 815.1486 +/- 225.8000 Ctx Intensity 843.6750 +/- 256.7146 Pct Contrast 1.5216 +/- 21.5862 Cost 0.5635 RelCost 0.7285 Reg at min cost was 0.99999 -0.00125 0.00461 0.04904; -0.00478 -0.24056 0.97062 -40.60849; 0.00010 0.97063 0.24056 -1.11761; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/001/tmp.bbregister.28189/bbr.pass1.dat, type = 14 Original Reg 0.99998 -0.00135 -0.00689 0.84339; 0.00632 -0.25447 0.96706 -37.60040; 0.00306 0.96708 0.25445 -2.02609; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00001 -0.00010 -0.01150 0.79435; 0.01110 -0.01391 -0.00356 3.00809; 0.00296 -0.00355 0.01389 -0.90848; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 2.959653 Computing change in rh position Surface-RMS-Diff-mm 3.232120 0.705756 4.676483 WARNING: initial G-W contrast was negative, but expected positive. If the mov data has a T1 contrast, re-run with --T1 mri_segreg done mri_segreg --mov bold/001/tmp.bbregister.28189/template.nii --init-reg bold/001/tmp.bbregister.28189/bbr.pass1.dat --out-reg bold/001/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/001/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/001/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/001/tmp.bbregister.28189/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.113 2016/05/10 03:23:20 greve Exp $ setenv SUBJECTS_DIR /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects cd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01 mri_segreg --mov bold/001/tmp.bbregister.28189/template.nii --init-reg bold/001/tmp.bbregister.28189/bbr.pass1.dat --out-reg bold/001/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/001/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/001/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/001/tmp.bbregister.28189/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass movvol bold/001/tmp.bbregister.28189/template.nii regfile bold/001/tmp.bbregister.28189/bbr.pass1.dat subject fsf01anat dof 6 outregfile bold/001/register.dof6.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1538340604 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99999 -0.00125 0.00461 0.04904; -0.00478 -0.24056 0.97062 -40.60849; 0.00010 0.97063 0.24056 -1.11761; 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 1.043728 1 -25.0 -25.0 25.0 1.060022 2 -25.0 25.0 -25.0 1.060009 3 -25.0 25.0 25.0 1.068201 4 25.0 -25.0 -25.0 1.037344 5 25.0 -25.0 25.0 1.040077 6 25.0 25.0 -25.0 1.020283 7 25.0 25.0 25.0 1.051363 REL: 8 0.578609 8.381027 1.047628 rel = 0.552304 Initial costs ---------------- Number of surface hits 304688 WM Intensity 818.9929 +/- 222.6692 Ctx Intensity 846.8292 +/- 254.8342 Pct Contrast 1.4142 +/- 22.0324 Cost 0.5786 RelCost 0.5523 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.5672 0.5672 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.5654 0.5654 0.0 2 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.5643 0.5643 0.0 38 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.1000 0.5642 0.5642 0.0 83 -0.1000 0.0000 -0.1000 -0.1000 -0.1000 0.1000 0.5639 0.5639 0.0 164 -0.1000 0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.5630 0.5630 0.0 Brute Force -------------------------- Min cost was 0.563002 Number of iterations 729 Search time 1.926000 sec Parameters at best (transmm, rotdeg) -0.100 0.100 -0.100 -0.100 -0.100 0.100 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 -0.1 1 0.1 2 -0.1 3 -0.1 4 -0.1 5 0.1 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000000 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.577692 6 0.282 0.100 -0.100 -0.100 -0.100 0.100 0.5744414699 7 0.260 0.100 -0.100 -0.100 -0.100 0.100 0.5744246851 10 0.258 0.100 -0.100 -0.100 -0.100 0.100 0.5744246428 11 0.259 0.100 -0.100 -0.100 -0.100 0.100 0.5744246319 19 0.259 0.110 -0.100 -0.100 -0.100 0.100 0.5744218936 21 0.259 0.109 -0.100 -0.100 -0.100 0.100 0.5744218915 30 0.259 0.109 -0.304 -0.100 -0.100 0.100 0.5734597017 31 0.259 0.109 -0.298 -0.100 -0.100 0.100 0.5734574719 32 0.259 0.109 -0.293 -0.100 -0.100 0.100 0.5734566126 33 0.259 0.109 -0.292 -0.100 -0.100 0.100 0.5734565921 41 0.259 0.109 -0.292 -0.090 -0.100 0.100 0.5734554899 46 0.259 0.109 -0.292 -0.082 -0.100 0.100 0.5734553985 47 0.259 0.109 -0.292 -0.086 -0.100 0.100 0.5734549526 56 0.259 0.109 -0.292 -0.086 -0.066 0.100 0.5733888095 57 0.259 0.109 -0.292 -0.086 -0.052 0.100 0.5733806080 59 0.259 0.109 -0.292 -0.086 -0.051 0.100 0.5733805833 60 0.259 0.109 -0.292 -0.086 -0.050 0.100 0.5733805506 66 0.259 0.109 -0.292 -0.086 -0.050 0.482 0.5732534432 67 0.259 0.109 -0.292 -0.086 -0.050 0.305 0.5728712910 68 0.259 0.109 -0.292 -0.086 -0.050 0.304 0.5728708976 70 0.259 0.109 -0.292 -0.086 -0.050 0.297 0.5728703207 powell nthiter 1: fret = 0.572870 80 0.282 0.109 -0.292 -0.086 -0.050 0.299 0.5728622688 81 0.277 0.109 -0.292 -0.086 -0.050 0.299 0.5728616781 82 0.276 0.109 -0.292 -0.086 -0.050 0.299 0.5728616259 91 0.276 0.085 -0.292 -0.086 -0.050 0.299 0.5728573130 92 0.276 0.093 -0.292 -0.086 -0.050 0.299 0.5728571400 93 0.276 0.090 -0.292 -0.086 -0.050 0.299 0.5728570794 94 0.276 0.091 -0.292 -0.086 -0.050 0.299 0.5728570773 103 0.276 0.092 -0.293 -0.086 -0.050 0.299 0.5728570060 113 0.276 0.092 -0.294 -0.077 -0.050 0.299 0.5728514779 114 0.276 0.092 -0.294 -0.066 -0.050 0.299 0.5728480704 116 0.276 0.092 -0.294 -0.065 -0.050 0.299 0.5728480416 124 0.276 0.092 -0.294 -0.065 -0.045 0.299 0.5728473424 126 0.276 0.092 -0.294 -0.065 -0.043 0.299 0.5728473188 139 0.276 0.092 -0.294 -0.065 -0.043 0.311 0.5728472229 140 0.276 0.092 -0.294 -0.065 -0.043 0.305 0.5728468480 141 0.276 0.092 -0.294 -0.065 -0.043 0.304 0.5728467598 powell nthiter 2: fret = 0.572847 151 0.283 0.092 -0.294 -0.065 -0.043 0.304 0.5728464302 152 0.281 0.092 -0.294 -0.065 -0.043 0.304 0.5728463493 153 0.280 0.092 -0.294 -0.065 -0.043 0.304 0.5728463398 162 0.280 0.076 -0.294 -0.065 -0.043 0.304 0.5728418048 164 0.280 0.080 -0.294 -0.065 -0.043 0.304 0.5728412886 175 0.280 0.079 -0.289 -0.065 -0.043 0.304 0.5728409343 176 0.280 0.079 -0.290 -0.065 -0.043 0.304 0.5728408543 198 0.280 0.079 -0.291 -0.064 -0.042 0.304 0.5728408065 205 0.280 0.079 -0.291 -0.064 -0.042 0.314 0.5728389822 206 0.280 0.079 -0.291 -0.064 -0.042 0.317 0.5728388850 209 0.283 0.067 -0.289 -0.063 -0.041 0.327 0.5728381195 215 0.282 0.071 -0.290 -0.063 -0.042 0.323 0.5728371757 216 0.281 0.074 -0.290 -0.063 -0.042 0.321 0.5728371490 217 0.281 0.072 -0.290 -0.063 -0.042 0.322 0.5728371187 219 0.282 0.072 -0.290 -0.063 -0.042 0.322 0.5728371066 221 0.282 0.072 -0.290 -0.063 -0.042 0.322 0.5728370989 222 0.282 0.072 -0.290 -0.063 -0.042 0.322 0.5728370595 223 0.281 0.072 -0.290 -0.063 -0.042 0.322 0.5728370479 225 0.281 0.072 -0.290 -0.063 -0.042 0.322 0.5728370458 powell nthiter 3: fret = 0.572837 232 0.283 0.072 -0.290 -0.063 -0.042 0.322 0.5728367725 233 0.286 0.072 -0.290 -0.063 -0.042 0.322 0.5728367362 248 0.287 0.072 -0.290 -0.063 -0.042 0.329 0.5728363018 252 0.287 0.072 -0.290 -0.063 -0.042 0.330 0.5728361210 263 0.287 0.072 -0.291 -0.063 -0.042 0.330 0.5728361047 282 0.287 0.072 -0.291 -0.062 -0.040 0.330 0.5728357711 283 0.287 0.072 -0.291 -0.062 -0.036 0.330 0.5728355706 285 0.287 0.072 -0.291 -0.062 -0.038 0.330 0.5728354132 powell nthiter 4: fret = 0.572835 310 0.289 0.072 -0.291 -0.062 -0.038 0.330 0.5728353064 311 0.290 0.072 -0.291 -0.062 -0.038 0.330 0.5728352908 345 0.290 0.072 -0.291 -0.063 -0.038 0.330 0.5728352517 powell nthiter 5: fret = 0.572835 Powell done niters = 5 Computing relative cost 0 -25.0 -25.0 -25.0 1.041634 1 -25.0 -25.0 25.0 1.061344 2 -25.0 25.0 -25.0 1.059914 3 -25.0 25.0 25.0 1.066069 4 25.0 -25.0 -25.0 1.037260 5 25.0 -25.0 25.0 1.039706 6 25.0 25.0 -25.0 1.023215 7 25.0 25.0 25.0 1.055985 REL: 8 0.572835 8.385128 1.048141 rel = 0.546525 Number of iterations 5 Min cost was 0.572835 Number of FunctionCalls 437 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 33.858000 sec Parameters at optimum (transmm) 0.28860 0.07228 -0.29072 Parameters at optimum (rotdeg) -0.06406 -0.03784 0.32969 Final costs ---------------- Number of surface hits 304688 WM Intensity 819.6405 +/- 221.2256 Ctx Intensity 847.9361 +/- 253.3413 Pct Contrast 1.5002 +/- 21.9710 Cost 0.5728 RelCost 0.5523 Reg at min cost was 1.00000 -0.00051 -0.00113 0.57202; 0.00098 -0.23948 0.97090 -40.53648; 0.00076 0.97090 0.23948 -1.36290; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/001/register.dof6.dat, type = 14 Original Reg 0.99999 -0.00125 0.00461 0.04904; -0.00478 -0.24056 0.97062 -40.60849; 0.00010 0.97063 0.24056 -1.11761; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00001 -0.00074 0.00574 -0.52298; -0.00575 -0.00108 -0.00028 -0.07201; -0.00067 -0.00027 0.00108 0.24529; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.495809 Computing change in rh position Surface-RMS-Diff-mm 0.516507 0.098694 0.783207 mri_segreg done MinCost: 0.572835 819.640457 847.936082 1.500235 tkregister2_cmdl --mov bold/001/template.nii.gz --reg bold/001/register.dof6.dat --noedit --ltaout bold/001/register.dof6.lta tkregister_tcl /media/sda1/nmrclass/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume bold/001/template.nii.gz reg file bold/001/register.dof6.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- 1.00000 -0.00051 -0.00113 0.57202; 0.00098 -0.23948 0.97090 -40.53648; 0.00076 0.97090 0.23948 -1.36290; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: loading target /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/orig.mgz Ttarg: -------------------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading movable bold/001/template.nii.gz Tmov: -------------------- -3.43750 0.00000 0.00000 110.00000; 0.00000 0.00000 5.00000 -75.00000; 0.00000 -3.43750 0.00000 109.99999; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 1.00000 -0.00051 -0.00113 0.57202; 0.00098 -0.23948 0.97090 -40.53648; 0.00076 0.97090 0.23948 -1.36290; 0.00000 0.00000 0.00000 1.00000; Determinant -1 subject = fsf01anat RegMat --------------------------- 1.00000 -0.00051 -0.00113 0.57202; 0.00098 -0.23948 0.97090 -40.53648; 0.00076 0.97090 0.23948 -1.36290; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Sun Sep 30 01:13:26 EDT 2018 Ended at Sun Sep 30 01:15:57 EDT 2018 BBR-Run-Time-Sec 151 bbregister Done To check results, run: tkregisterfv --mov bold/001/template.nii.gz --reg bold/001/register.dof6.lta --surfs Run: 002 ---------------- Sun Sep 30 01:15:57 EDT 2018 -------------------------------------- /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01 bbregister --s fsf01anat --init-coreg --6 --bold --mov bold/002/template.nii.gz --reg bold/002/register.dof6.dat --lta bold/002/register.dof6.lta --init-reg-out bold/002/init.register.dof6.dat tmp bold/002/tmp.bbregister.28297 Log file is bold/002/register.dof6.dat.log Sun Sep 30 01:15:57 EDT 2018 setenv SUBJECTS_DIR /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects cd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01 /media/sda1/nmrclass/freesurfer/bin/bbregister --s fsf01anat --init-coreg --6 --bold --mov bold/002/template.nii.gz --reg bold/002/register.dof6.dat --lta bold/002/register.dof6.lta --init-reg-out bold/002/init.register.dof6.dat $Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $ Linux fsuser3-G5-5587 4.15.0-34-generic #37-Ubuntu SMP Mon Aug 27 15:21:48 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /media/sda1/nmrclass/freesurfer mri_convert bold/002/template.nii.gz bold/002/tmp.bbregister.28297/template.nii mri_convert.bin bold/002/template.nii.gz bold/002/tmp.bbregister.28297/template.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from bold/002/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/002/tmp.bbregister.28297/template.nii... mri_coreg --s fsf01anat --mov bold/002/tmp.bbregister.28297/template.nii --regdat bold/002/tmp.bbregister.28297/reg.init.dat --reg bold/002/tmp.bbregister.28297/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 $Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $ cwd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01 cmdline mri_coreg --s fsf01anat --mov bold/002/tmp.bbregister.28297/template.nii --regdat bold/002/tmp.bbregister.28297/reg.init.dat --reg bold/002/tmp.bbregister.28297/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass dof 6 nsep 1 cras0 1 ftol 0.000100 linmintol 0.010000 bf 1 bflim 30.000000 bfnsamp 30 SmoothRef 0 SatPct 99.990000 MovOOB 0 optschema 1 Reading in mov bold/002/tmp.bbregister.28297/template.nii Reading in ref /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/brainmask.mgz Reading in and applying refmask /media/sda1/nmrclass/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 = 1686.3334 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 -1.0209175279 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 -1.0503495 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6 Starting OpenPowel2(), sep = 4 InitialCost -1.0718444586 #@# 4 188 -6.02228 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0718445 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.071844 #@# 4 193 -6.64031 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0719624 #@# 4 195 -6.60756 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0719631 #@# 4 201 -6.61756 -36.87573 49.23798 4.00000 0.00000 0.00000 -1.0745862 #@# 4 204 -6.61756 -41.14009 49.23798 4.00000 0.00000 0.00000 -1.0760598 #@# 4 206 -6.61756 -39.72143 49.23798 4.00000 0.00000 0.00000 -1.0767061 #@# 4 207 -6.61756 -39.62170 49.23798 4.00000 0.00000 0.00000 -1.0767123 #@# 4 209 -6.61756 -39.63170 49.23798 4.00000 0.00000 0.00000 -1.0767125 #@# 4 211 -6.61756 -39.64170 49.23798 4.00000 0.00000 0.00000 -1.0767128 #@# 4 217 -6.61756 -39.64170 48.61994 4.00000 0.00000 0.00000 -1.0768503 #@# 4 219 -6.61756 -39.64170 48.63824 4.00000 0.00000 0.00000 -1.0768524 #@# 4 221 -6.61756 -39.64170 48.69941 4.00000 0.00000 0.00000 -1.0768546 #@# 4 230 -6.61756 -39.64170 48.69941 3.38197 0.00000 0.00000 -1.0768720 #@# 4 232 -6.61756 -39.64170 48.69941 3.67209 0.00000 0.00000 -1.0769360 #@# 4 233 -6.61756 -39.64170 48.69941 3.68209 0.00000 0.00000 -1.0769384 #@# 4 244 -6.61756 -39.64170 48.69941 3.68209 0.04531 0.00000 -1.0769385 #@# 4 246 -6.61756 -39.64170 48.69941 3.68209 0.05531 0.00000 -1.0769389 #@# 4 254 -6.61756 -39.64170 48.69941 3.68209 0.05531 -0.11340 -1.0769497 #@# 4 264 -6.64637 -39.85387 48.67334 3.66671 0.05799 -0.11889 -1.0769571 powell nthiter 1: fret = -1.076957 #@# 4 275 -6.62215 -39.85387 48.67334 3.66671 0.05799 -0.11889 -1.0769591 #@# 4 291 -6.60908 -39.85387 48.05531 3.66671 0.05799 -0.11889 -1.0770261 #@# 4 293 -6.60908 -39.85387 48.24796 3.66671 0.05799 -0.11889 -1.0770544 #@# 4 295 -6.60908 -39.85387 48.22765 3.66671 0.05799 -0.11889 -1.0770545 #@# 4 296 -6.60908 -39.85387 48.21764 3.66671 0.05799 -0.11889 -1.0770546 #@# 4 306 -6.60908 -39.85387 48.21764 3.35801 0.05799 -0.11889 -1.0771170 #@# 4 307 -6.60908 -39.85387 48.21764 3.36801 0.05799 -0.11889 -1.0771186 #@# 4 327 -6.62201 -39.94912 48.20594 3.36110 0.05919 -0.12135 -1.0771199 #@# 4 330 -6.62647 -40.25653 47.71247 3.04012 0.06307 -0.12931 -1.0772073 #@# 4 333 -6.63367 -40.75395 46.91403 2.52075 0.06935 -0.14217 -1.0772955 #@# 4 338 -6.63261 -40.68098 47.03115 2.59694 0.06843 -0.14029 -1.0773009 #@# 4 339 -6.63253 -40.67545 47.04004 2.60272 0.06836 -0.14014 -1.0773010 #@# 4 341 -6.63249 -40.67237 47.04498 2.60593 0.06832 -0.14006 -1.0773016 powell nthiter 2: fret = -1.077302 #@# 4 350 -6.61242 -40.66840 47.05136 2.61008 0.06827 -0.13996 -1.0773026 #@# 4 351 -6.59649 -40.66840 47.05136 2.61008 0.06827 -0.13996 -1.0773031 #@# 4 354 -6.58649 -40.66840 47.05136 2.61008 0.06827 -0.13996 -1.0773032 #@# 4 361 -6.58649 -40.66840 47.05136 2.61008 0.06827 -0.19519 -1.0773072 #@# 4 370 -6.51469 -40.13958 47.11632 2.64843 0.06160 -0.18151 -1.0773715 #@# 4 372 -6.48582 -39.92694 47.14244 2.66385 0.05891 -0.17601 -1.0773726 #@# 4 374 -6.49861 -40.02114 47.13087 2.65701 0.06010 -0.17845 -1.0773731 #@# 4 383 -6.49861 -40.02114 47.13087 2.59070 0.06010 -0.17845 -1.0773753 #@# 4 388 -6.49861 -40.02114 47.13087 2.58070 0.06010 -0.17845 -1.0773758 #@# 4 402 -6.50306 -40.32856 46.63741 2.25972 0.06398 -0.18640 -1.0774407 #@# 4 408 -6.50290 -40.31764 46.65494 2.27112 0.06384 -0.18611 -1.0774411 #@# 4 411 -6.50294 -40.32072 46.65000 2.26791 0.06388 -0.18619 -1.0774416 powell nthiter 3: fret = -1.077442 #@# 4 420 -6.56380 -40.32072 46.65000 2.26791 0.06388 -0.18619 -1.0774435 #@# 4 421 -6.55162 -40.32072 46.65000 2.26791 0.06388 -0.18619 -1.0774440 #@# 4 447 -6.55162 -40.32072 46.65000 2.23822 0.06388 -0.17619 -1.0774444 #@# 4 448 -6.55162 -40.32072 46.65000 2.22822 0.06388 -0.17619 -1.0774446 #@# 4 455 -6.55162 -40.32072 46.65000 2.22822 0.01455 -0.17619 -1.0774478 Powell done niters total = 3 OptTimeSec 18.3 sec OptTimeMin 0.30 min nEvals 471 Final parameters -6.55161905 -40.32071686 46.65000153 2.22822285 0.01454814 -0.17619428 Final cost -1.077447804602206 --------------------------------- mri_coreg utimesec 88.416249 mri_coreg stimesec 0.207991 mri_coreg ru_maxrss 424516 mri_coreg ru_ixrss 0 mri_coreg ru_idrss 0 mri_coreg ru_isrss 0 mri_coreg ru_minflt 125486 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 5409 mri_coreg ru_nivcsw 40 Final RefRAS-to-MovRAS 1.00000 -0.00308 0.00025 -6.55162; 0.00306 0.99924 0.03888 -40.32072; -0.00037 -0.03888 0.99924 46.65000; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox 0.29091 0.00007 0.00089 -5.50447; 0.00084 0.07690 -0.28056 58.59439; 0.00021 -0.19289 -0.05287 38.83891; 0.00000 0.00000 0.00000 1.00000; Final parameters -6.5516 -40.3207 46.6500 2.2282 0.0145 -0.1762 nhits = 105970 out of 16777216, Percent Overlap: 40.4 mri_coreg RunTimeSec 88.7 sec To check run: tkregisterfv --mov bold/002/tmp.bbregister.28297/template.nii --targ /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/brainmask.mgz --reg bold/002/tmp.bbregister.28297/mri_coreg.lta --s fsf01anat --surfs mri_coreg done mri_segreg --mov bold/002/tmp.bbregister.28297/template.nii --init-reg bold/002/tmp.bbregister.28297/reg.init.dat --out-reg bold/002/tmp.bbregister.28297/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.113 2016/05/10 03:23:20 greve Exp $ setenv SUBJECTS_DIR /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects cd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01 mri_segreg --mov bold/002/tmp.bbregister.28297/template.nii --init-reg bold/002/tmp.bbregister.28297/reg.init.dat --out-reg bold/002/tmp.bbregister.28297/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass movvol bold/002/tmp.bbregister.28297/template.nii regfile bold/002/tmp.bbregister.28297/reg.init.dat subject fsf01anat dof 6 outregfile bold/002/tmp.bbregister.28297/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 1538963353 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 1.00000 -0.00308 0.00025 0.49611; -0.00106 -0.26435 0.96443 -37.95303; 0.00290 0.96442 0.26435 -2.17968; 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 1.052476 1 -25.0 -25.0 25.0 1.016619 2 -25.0 25.0 -25.0 1.055042 3 -25.0 25.0 25.0 1.038191 4 25.0 -25.0 -25.0 1.034902 5 25.0 -25.0 25.0 1.055714 6 25.0 25.0 -25.0 1.056140 7 25.0 25.0 25.0 1.035190 REL: 8 0.735079 8.344274 1.043034 rel = 0.704751 Initial costs ---------------- Number of surface hits 3062 WM Intensity 846.7010 +/- 209.5847 Ctx Intensity 854.3215 +/- 236.5096 Pct Contrast -0.4630 +/- 21.0453 Cost 0.7351 RelCost 0.7048 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 1.0606 1.0606 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 1.0606 1.0606 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 1.0341 1.0341 0.0 3 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 -4.0000 1.0145 1.0145 0.0 4 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.0000 1.0059 1.0059 0.0 6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.9741 0.9741 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.9561 0.9561 0.0 8 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 4.0000 0.9514 0.9514 0.0 18 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 -4.0000 0.9479 0.9479 0.0 19 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.0000 0.9265 0.9265 0.0 30 -4.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.9109 0.9109 0.0 33 -4.0000 -4.0000 0.0000 -4.0000 4.0000 -4.0000 0.8918 0.8918 0.0 34 -4.0000 -4.0000 0.0000 -4.0000 4.0000 0.0000 0.8714 0.8714 0.0 273 0.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.8199 0.8199 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.7600 0.7600 0.0 282 0.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.7452 0.7452 0.0 283 0.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.5864 0.5864 0.0 Brute Force -------------------------- Min cost was 0.586449 Number of iterations 729 Search time 1.215000 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 = 0.586449 7 -0.162 -4.000 0.000 0.000 0.000 0.000 0.5862838477 8 -0.110 -4.000 0.000 0.000 0.000 0.000 0.5861440759 9 -0.096 -4.000 0.000 0.000 0.000 0.000 0.5861167233 11 -0.087 -4.000 0.000 0.000 0.000 0.000 0.5861129314 15 -0.087 -3.000 0.000 0.000 0.000 0.000 0.5725555134 21 -0.087 -2.958 0.000 0.000 0.000 0.000 0.5724563809 24 -0.087 -2.961 0.000 0.000 0.000 0.000 0.5724552756 26 -0.087 -2.960 0.000 0.000 0.000 0.000 0.5724552000 32 -0.087 -2.960 0.382 0.000 0.000 0.000 0.5715755590 34 -0.087 -2.960 0.361 0.000 0.000 0.000 0.5714888209 35 -0.087 -2.960 0.316 0.000 0.000 0.000 0.5713925966 37 -0.087 -2.960 0.311 0.000 0.000 0.000 0.5713907366 45 -0.087 -2.960 0.311 -0.618 0.000 0.000 0.5704955108 47 -0.087 -2.960 0.311 -0.369 0.000 0.000 0.5695526847 49 -0.087 -2.960 0.311 -0.393 0.000 0.000 0.5695216666 51 -0.087 -2.960 0.311 -0.426 0.000 0.000 0.5695172844 52 -0.087 -2.960 0.311 -0.413 0.000 0.000 0.5695139810 54 -0.087 -2.960 0.311 -0.406 0.000 0.000 0.5695132721 63 -0.087 -2.960 0.311 -0.406 0.382 0.000 0.5686072161 64 -0.087 -2.960 0.311 -0.406 0.259 0.000 0.5681564083 65 -0.087 -2.960 0.311 -0.406 0.242 0.000 0.5680993163 67 -0.087 -2.960 0.311 -0.406 0.219 0.000 0.5680762570 69 -0.087 -2.960 0.311 -0.406 0.218 0.000 0.5680762394 75 -0.087 -2.960 0.311 -0.406 0.218 -0.618 0.5623527429 77 -0.087 -2.960 0.311 -0.406 0.218 -0.523 0.5623182036 78 -0.087 -2.960 0.311 -0.406 0.218 -0.563 0.5620933605 80 -0.087 -2.960 0.311 -0.406 0.218 -0.564 0.5620932905 powell nthiter 1: fret = 0.562093 89 -0.189 -2.960 0.311 -0.406 0.218 -0.564 0.5620678152 90 -0.142 -2.960 0.311 -0.406 0.218 -0.564 0.5619162257 91 -0.140 -2.960 0.311 -0.406 0.218 -0.564 0.5619150115 92 -0.135 -2.960 0.311 -0.406 0.218 -0.564 0.5619136432 93 -0.136 -2.960 0.311 -0.406 0.218 -0.564 0.5619135917 101 -0.136 -2.920 0.311 -0.406 0.218 -0.564 0.5618165526 102 -0.136 -2.903 0.311 -0.406 0.218 -0.564 0.5618138527 103 -0.136 -2.910 0.311 -0.406 0.218 -0.564 0.5618131401 104 -0.136 -2.909 0.311 -0.406 0.218 -0.564 0.5618130741 112 -0.136 -2.909 0.127 -0.406 0.218 -0.564 0.5606698429 113 -0.136 -2.909 0.128 -0.406 0.218 -0.564 0.5606675921 116 -0.136 -2.909 0.132 -0.406 0.218 -0.564 0.5606636147 117 -0.136 -2.909 0.131 -0.406 0.218 -0.564 0.5606633199 118 -0.136 -2.909 0.130 -0.406 0.218 -0.564 0.5606630914 126 -0.136 -2.909 0.130 -0.417 0.218 -0.564 0.5605889152 128 -0.136 -2.909 0.130 -0.473 0.218 -0.564 0.5604193408 130 -0.136 -2.909 0.130 -0.463 0.218 -0.564 0.5604071499 143 -0.136 -2.909 0.130 -0.464 0.235 -0.564 0.5603474556 146 -0.136 -2.909 0.130 -0.464 0.236 -0.564 0.5603473957 156 -0.136 -2.909 0.130 -0.464 0.236 -0.572 0.5603435979 157 -0.136 -2.909 0.130 -0.464 0.236 -0.570 0.5603434547 158 -0.136 -2.909 0.130 -0.464 0.236 -0.569 0.5603433109 powell nthiter 2: fret = 0.560343 167 -0.219 -2.909 0.130 -0.464 0.236 -0.569 0.5603035449 168 -0.183 -2.909 0.130 -0.464 0.236 -0.569 0.5600884264 169 -0.179 -2.909 0.130 -0.464 0.236 -0.569 0.5600865855 170 -0.178 -2.909 0.130 -0.464 0.236 -0.569 0.5600864583 180 -0.178 -2.906 0.130 -0.464 0.236 -0.569 0.5600856863 191 -0.178 -2.906 0.148 -0.464 0.236 -0.569 0.5600497309 192 -0.178 -2.906 0.153 -0.464 0.236 -0.569 0.5600460794 205 -0.178 -2.906 0.152 -0.467 0.236 -0.569 0.5600452298 214 -0.178 -2.906 0.152 -0.467 0.247 -0.569 0.5599850846 216 -0.178 -2.906 0.152 -0.467 0.267 -0.569 0.5599790736 217 -0.178 -2.906 0.152 -0.467 0.258 -0.569 0.5599669859 219 -0.178 -2.906 0.152 -0.467 0.257 -0.569 0.5599669852 230 -0.178 -2.906 0.152 -0.467 0.257 -0.541 0.5598978874 231 -0.178 -2.906 0.152 -0.467 0.257 -0.544 0.5598968865 232 -0.178 -2.906 0.152 -0.467 0.257 -0.543 0.5598968045 234 -0.221 -2.903 0.174 -0.470 0.278 -0.516 0.5597984617 240 -0.205 -2.904 0.166 -0.469 0.270 -0.526 0.5597727083 242 -0.207 -2.904 0.167 -0.469 0.271 -0.525 0.5597715198 243 -0.208 -2.904 0.167 -0.469 0.271 -0.524 0.5597713759 249 -0.208 -2.904 0.167 -0.469 0.271 -0.524 0.5597712997 250 -0.208 -2.904 0.167 -0.469 0.271 -0.524 0.5597712302 powell nthiter 3: fret = 0.559771 259 -0.208 -2.904 0.167 -0.469 0.271 -0.528 0.5597709211 260 -0.208 -2.904 0.167 -0.469 0.271 -0.526 0.5597709080 270 -0.208 -2.901 0.167 -0.469 0.271 -0.526 0.5597693584 271 -0.208 -2.900 0.167 -0.469 0.271 -0.526 0.5597692693 282 -0.208 -2.900 0.162 -0.469 0.271 -0.526 0.5597605131 296 -0.208 -2.900 0.162 -0.473 0.271 -0.526 0.5597593949 307 -0.208 -2.900 0.162 -0.473 0.268 -0.526 0.5597577591 308 -0.208 -2.900 0.162 -0.473 0.269 -0.526 0.5597577218 316 -0.209 -2.900 0.163 -0.473 0.270 -0.526 0.5597576220 317 -0.209 -2.900 0.163 -0.473 0.269 -0.526 0.5597575522 318 -0.209 -2.900 0.163 -0.473 0.269 -0.526 0.5597574774 Powell done niters = 3 Computing relative cost 0 -25.0 -25.0 -25.0 1.060456 1 -25.0 -25.0 25.0 1.011417 2 -25.0 25.0 -25.0 1.045673 3 -25.0 25.0 25.0 1.051522 4 25.0 -25.0 -25.0 1.035864 5 25.0 -25.0 25.0 1.033476 6 25.0 25.0 -25.0 1.019210 7 25.0 25.0 25.0 1.021363 REL: 8 0.559757 8.278981 1.034873 rel = 0.540895 Number of iterations 3 Min cost was 0.559757 Number of FunctionCalls 321 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.669000 sec Parameters at optimum (transmm) -0.20864 -2.89987 0.16290 Parameters at optimum (rotdeg) -0.47263 0.26929 -0.52591 Final costs ---------------- Number of surface hits 3062 WM Intensity 812.2493 +/- 225.0165 Ctx Intensity 841.3749 +/- 254.3879 Pct Contrast 1.7084 +/- 21.2548 Cost 0.5598 RelCost 0.7048 Reg at min cost was 0.99995 -0.00089 0.01033 -0.06985; -0.01021 -0.25638 0.96652 -40.87247; -0.00179 0.96657 0.25638 -1.70595; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/002/tmp.bbregister.28297/bbr.pass1.dat, type = 14 Original Reg 1.00000 -0.00308 0.00025 0.49611; -0.00106 -0.26435 0.96443 -37.95303; 0.00290 0.96442 0.26435 -2.17968; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00005 -0.00219 -0.01008 0.56596; 0.00915 -0.00796 -0.00209 2.91943; 0.00469 -0.00215 0.00797 -0.47373; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 2.810470 Computing change in rh position Surface-RMS-Diff-mm 3.040622 0.458587 3.974780 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/002/tmp.bbregister.28297/template.nii --init-reg bold/002/tmp.bbregister.28297/bbr.pass1.dat --out-reg bold/002/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/002/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/002/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/002/tmp.bbregister.28297/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.113 2016/05/10 03:23:20 greve Exp $ setenv SUBJECTS_DIR /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects cd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01 mri_segreg --mov bold/002/tmp.bbregister.28297/template.nii --init-reg bold/002/tmp.bbregister.28297/bbr.pass1.dat --out-reg bold/002/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/002/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/002/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/002/tmp.bbregister.28297/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass movvol bold/002/tmp.bbregister.28297/template.nii regfile bold/002/tmp.bbregister.28297/bbr.pass1.dat subject fsf01anat dof 6 outregfile bold/002/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 1538567706 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99995 -0.00089 0.01033 -0.06985; -0.01021 -0.25638 0.96652 -40.87247; -0.00179 0.96657 0.25638 -1.70595; 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 1.047245 1 -25.0 -25.0 25.0 1.057645 2 -25.0 25.0 -25.0 1.054086 3 -25.0 25.0 25.0 1.067464 4 25.0 -25.0 -25.0 1.032214 5 25.0 -25.0 25.0 1.039836 6 25.0 25.0 -25.0 1.016451 7 25.0 25.0 25.0 1.049645 REL: 8 0.580647 8.364586 1.045573 rel = 0.555338 Initial costs ---------------- Number of surface hits 304688 WM Intensity 816.3693 +/- 221.7748 Ctx Intensity 844.3104 +/- 252.9194 Pct Contrast 1.4499 +/- 22.0522 Cost 0.5806 RelCost 0.5553 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.5640 0.5640 0.0 2 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.5635 0.5635 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.5629 0.5629 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.5626 0.5626 0.0 5 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1000 0.5619 0.5619 0.0 13 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.5615 0.5615 0.0 14 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.1000 0.5611 0.5611 0.0 23 -0.1000 -0.1000 -0.1000 0.1000 0.0000 0.1000 0.5608 0.5608 0.0 41 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.1000 0.5607 0.5607 0.0 50 -0.1000 -0.1000 0.0000 0.1000 0.0000 0.1000 0.5607 0.5607 0.0 53 -0.1000 -0.1000 0.0000 0.1000 0.1000 0.1000 0.5607 0.5607 0.0 71 -0.1000 -0.1000 0.1000 0.0000 0.1000 0.1000 0.5605 0.5605 0.0 94 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.0000 0.5604 0.5604 0.0 97 -0.1000 0.0000 -0.1000 0.0000 0.1000 0.0000 0.5602 0.5602 0.0 103 -0.1000 0.0000 -0.1000 0.1000 0.0000 0.0000 0.5601 0.5601 0.0 104 -0.1000 0.0000 -0.1000 0.1000 0.0000 0.1000 0.5598 0.5598 0.0 Brute Force -------------------------- Min cost was 0.559755 Number of iterations 729 Search time 1.415000 sec Parameters at best (transmm, rotdeg) -0.100 0.000 -0.100 0.100 0.000 0.100 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 -0.1 1 0 2 -0.1 3 0.1 4 0 5 0.1 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000000 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.581075 6 0.282 0.000 -0.100 0.100 0.000 0.100 0.5801378553 7 0.135 0.000 -0.100 0.100 0.000 0.100 0.5796389691 9 0.123 0.000 -0.100 0.100 0.000 0.100 0.5796380555 11 0.128 0.000 -0.100 0.100 0.000 0.100 0.5796371039 20 0.128 0.164 -0.100 0.100 0.000 0.100 0.5790397951 22 0.128 0.163 -0.100 0.100 0.000 0.100 0.5790397667 34 0.128 0.163 -0.147 0.100 0.000 0.100 0.5789636400 35 0.128 0.163 -0.155 0.100 0.000 0.100 0.5789635742 36 0.128 0.163 -0.151 0.100 0.000 0.100 0.5789632887 45 0.128 0.163 -0.151 -0.043 0.000 0.100 0.5786673600 46 0.128 0.163 -0.151 -0.029 0.000 0.100 0.5786570029 48 0.128 0.163 -0.151 -0.024 0.000 0.100 0.5786559448 50 0.128 0.163 -0.151 -0.025 0.000 0.100 0.5786559024 58 0.128 0.163 -0.151 -0.025 -0.178 0.100 0.5777163658 60 0.128 0.163 -0.151 -0.025 -0.154 0.100 0.5776925874 62 0.128 0.163 -0.151 -0.025 -0.153 0.100 0.5776922881 63 0.128 0.163 -0.151 -0.025 -0.148 0.100 0.5776919320 65 0.128 0.163 -0.151 -0.025 -0.150 0.100 0.5776918940 66 0.128 0.163 -0.151 -0.025 -0.151 0.100 0.5776917599 74 0.128 0.163 -0.151 -0.025 -0.151 0.179 0.5776353541 77 0.128 0.163 -0.151 -0.025 -0.151 0.188 0.5776340777 78 0.128 0.163 -0.151 -0.025 -0.151 0.189 0.5776338882 powell nthiter 1: fret = 0.577634 99 0.127 0.181 -0.151 -0.025 -0.151 0.189 0.5776260266 108 0.127 0.182 -0.148 -0.025 -0.151 0.189 0.5776259945 110 0.127 0.182 -0.149 -0.025 -0.151 0.189 0.5776259756 127 0.127 0.182 -0.149 -0.025 -0.144 0.189 0.5776259203 128 0.127 0.182 -0.149 -0.025 -0.147 0.189 0.5776255485 129 0.127 0.182 -0.149 -0.025 -0.146 0.189 0.5776254894 138 0.127 0.182 -0.149 -0.025 -0.146 0.191 0.5776254329 powell nthiter 2: fret = 0.577625 150 0.125 0.182 -0.149 -0.025 -0.146 0.191 0.5776253423 200 0.124 0.181 -0.150 -0.025 -0.146 0.190 0.5776253324 powell nthiter 3: fret = 0.577625 221 0.126 0.182 -0.150 -0.025 -0.146 0.190 0.5776253238 Powell done niters = 3 Computing relative cost 0 -25.0 -25.0 -25.0 1.045803 1 -25.0 -25.0 25.0 1.059393 2 -25.0 25.0 -25.0 1.054511 3 -25.0 25.0 25.0 1.065078 4 25.0 -25.0 -25.0 1.032353 5 25.0 -25.0 25.0 1.040253 6 25.0 25.0 -25.0 1.018498 7 25.0 25.0 25.0 1.052308 REL: 8 0.577625 8.368197 1.046025 rel = 0.55221 Number of iterations 3 Min cost was 0.577625 Number of FunctionCalls 262 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 21.669000 sec Parameters at optimum (transmm) 0.12557 0.18202 -0.15132 Parameters at optimum (rotdeg) -0.02505 -0.14621 0.19029 Final costs ---------------- Number of surface hits 304688 WM Intensity 818.0974 +/- 219.9203 Ctx Intensity 846.4794 +/- 250.9809 Pct Contrast 1.5453 +/- 21.8580 Cost 0.5776 RelCost 0.5553 Reg at min cost was 0.99998 -0.00250 0.00647 0.19578; -0.00689 -0.25597 0.96666 -40.69118; 0.00076 0.96668 0.25598 -1.83957; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/002/register.dof6.dat, type = 14 Original Reg 0.99995 -0.00089 0.01033 -0.06985; -0.01021 -0.25638 0.96652 -40.87247; -0.00179 0.96657 0.25638 -1.70595; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00003 0.00162 0.00386 -0.26563; -0.00332 -0.00041 -0.00014 -0.18129; -0.00256 -0.00011 0.00040 0.13362; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.325611 Computing change in rh position Surface-RMS-Diff-mm 0.349527 0.073975 0.536815 mri_segreg done MinCost: 0.577625 818.097379 846.479433 1.545259 tkregister2_cmdl --mov bold/002/template.nii.gz --reg bold/002/register.dof6.dat --noedit --ltaout bold/002/register.dof6.lta tkregister_tcl /media/sda1/nmrclass/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume bold/002/template.nii.gz reg file bold/002/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 -------- 0.99998 -0.00250 0.00647 0.19578; -0.00689 -0.25597 0.96666 -40.69118; 0.00076 0.96668 0.25598 -1.83957; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: loading target /media/sda1/nmrclass/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/002/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 -------- 0.99998 -0.00250 0.00647 0.19578; -0.00689 -0.25597 0.96666 -40.69118; 0.00076 0.96668 0.25598 -1.83957; 0.00000 0.00000 0.00000 1.00000; Determinant -1 subject = fsf01anat RegMat --------------------------- 0.99998 -0.00250 0.00647 0.19578; -0.00689 -0.25597 0.96666 -40.69118; 0.00076 0.96668 0.25598 -1.83957; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Sun Sep 30 01:15:57 EDT 2018 Ended at Sun Sep 30 01:18:07 EDT 2018 BBR-Run-Time-Sec 130 bbregister Done To check results, run: tkregisterfv --mov bold/002/template.nii.gz --reg bold/002/register.dof6.lta --surfs Run: 003 ---------------- Sun Sep 30 01:18:07 EDT 2018 -------------------------------------- /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01 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 tmp bold/003/tmp.bbregister.28396 Log file is bold/003/register.dof6.dat.log Sun Sep 30 01:18:07 EDT 2018 setenv SUBJECTS_DIR /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects cd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01 /media/sda1/nmrclass/freesurfer/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 1.75 2016/05/10 20:02:28 greve Exp $ Linux fsuser3-G5-5587 4.15.0-34-generic #37-Ubuntu SMP Mon Aug 27 15:21:48 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /media/sda1/nmrclass/freesurfer mri_convert bold/003/template.nii.gz bold/003/tmp.bbregister.28396/template.nii mri_convert.bin bold/003/template.nii.gz bold/003/tmp.bbregister.28396/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.28396/template.nii... mri_coreg --s fsf01anat --mov bold/003/tmp.bbregister.28396/template.nii --regdat bold/003/tmp.bbregister.28396/reg.init.dat --reg bold/003/tmp.bbregister.28396/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 $Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $ cwd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01 cmdline mri_coreg --s fsf01anat --mov bold/003/tmp.bbregister.28396/template.nii --regdat bold/003/tmp.bbregister.28396/reg.init.dat --reg bold/003/tmp.bbregister.28396/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass dof 6 nsep 1 cras0 1 ftol 0.000100 linmintol 0.010000 bf 1 bflim 30.000000 bfnsamp 30 SmoothRef 0 SatPct 99.990000 MovOOB 0 optschema 1 Reading in mov bold/003/tmp.bbregister.28396/template.nii Reading in ref /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/brainmask.mgz Reading in and applying refmask /media/sda1/nmrclass/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 -1.0203739481 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 -1.0499676 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6 Starting OpenPowel2(), sep = 4 InitialCost -1.0710361004 #@# 4 188 -6.02228 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0710361 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.071036 #@# 4 191 -7.64031 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0714359 #@# 4 192 -7.24285 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0715013 #@# 4 196 -7.16198 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0715045 #@# 4 201 -7.15198 -36.87573 49.23798 4.00000 0.00000 0.00000 -1.0740182 #@# 4 204 -7.15198 -40.09756 49.23798 4.00000 0.00000 0.00000 -1.0760325 #@# 4 206 -7.15198 -39.65488 49.23798 4.00000 0.00000 0.00000 -1.0760782 #@# 4 207 -7.15198 -39.68793 49.23798 4.00000 0.00000 0.00000 -1.0760798 #@# 4 208 -7.15198 -39.73872 49.23798 4.00000 0.00000 0.00000 -1.0760820 #@# 4 215 -7.15198 -39.73872 47.61994 4.00000 0.00000 0.00000 -1.0762073 #@# 4 216 -7.15198 -39.73872 48.31561 4.00000 0.00000 0.00000 -1.0763485 #@# 4 229 -7.15198 -39.73872 48.31561 3.38197 0.00000 0.00000 -1.0764537 #@# 4 231 -7.15198 -39.73872 48.31561 3.59170 0.00000 0.00000 -1.0764949 #@# 4 233 -7.15198 -39.73872 48.31561 3.54260 0.00000 0.00000 -1.0764967 #@# 4 237 -7.15198 -39.73872 48.31561 3.53260 0.00000 0.00000 -1.0764968 #@# 4 244 -7.15198 -39.73872 48.31561 3.53260 -0.21804 0.00000 -1.0765020 #@# 4 250 -7.15198 -39.73872 48.31561 3.53260 -0.22804 0.00000 -1.0765023 #@# 4 255 -7.15198 -39.73872 48.31561 3.53260 -0.22804 -0.61803 -1.0766971 #@# 4 257 -7.15198 -39.73872 48.31561 3.53260 -0.22804 -0.47589 -1.0767196 #@# 4 259 -7.15198 -39.73872 48.31561 3.53260 -0.22804 -0.50991 -1.0767221 #@# 4 262 -7.15198 -39.73872 48.31561 3.53260 -0.22804 -0.49991 -1.0767229 powell nthiter 1: fret = -1.076723 #@# 4 271 -7.01741 -39.73872 48.31561 3.53260 -0.22804 -0.49991 -1.0767343 #@# 4 272 -7.02741 -39.73872 48.31561 3.53260 -0.22804 -0.49991 -1.0767353 #@# 4 273 -7.05533 -39.73872 48.31561 3.53260 -0.22804 -0.49991 -1.0767354 #@# 4 283 -7.04533 -39.90714 48.31561 3.53260 -0.22804 -0.49991 -1.0767496 #@# 4 284 -7.04533 -39.92172 48.31561 3.53260 -0.22804 -0.49991 -1.0767498 #@# 4 290 -7.04533 -39.92172 47.69758 3.53260 -0.22804 -0.49991 -1.0768741 #@# 4 292 -7.04533 -39.92172 47.71188 3.53260 -0.22804 -0.49991 -1.0768752 #@# 4 295 -7.04533 -39.92172 47.72188 3.53260 -0.22804 -0.49991 -1.0768756 #@# 4 303 -7.04533 -39.92172 47.72188 3.29551 -0.22804 -0.49991 -1.0769212 #@# 4 305 -7.04533 -39.92172 47.72188 3.33143 -0.22804 -0.49991 -1.0769229 #@# 4 307 -7.04533 -39.92172 47.72188 3.34143 -0.22804 -0.49991 -1.0769235 #@# 4 316 -7.04533 -39.92172 47.72188 3.34143 -0.39797 -0.49991 -1.0769315 #@# 4 317 -7.04533 -39.92172 47.72188 3.34143 -0.42034 -0.49991 -1.0769317 #@# 4 319 -7.04533 -39.92172 47.72188 3.34143 -0.41034 -0.49991 -1.0769322 #@# 4 326 -7.04533 -39.92172 47.72188 3.34143 -0.41034 -0.57261 -1.0769359 #@# 4 327 -7.04533 -39.92172 47.72188 3.34143 -0.41034 -0.56092 -1.0769366 #@# 4 330 -6.93868 -40.10472 47.12814 3.15026 -0.59263 -0.60028 -1.0770614 #@# 4 335 -6.87277 -40.21783 46.76120 3.03211 -0.70530 -0.63130 -1.0770668 #@# 4 338 -6.85721 -40.24453 46.67457 3.00421 -0.73189 -0.63863 -1.0770688 #@# 4 340 -6.86303 -40.23454 46.70698 3.01465 -0.72194 -0.63589 -1.0770699 #@# 4 341 -6.86197 -40.23637 46.70104 3.01274 -0.72377 -0.63639 -1.0770717 powell nthiter 2: fret = -1.077072 #@# 4 359 -6.86036 -40.07433 46.69209 3.00985 -0.72651 -0.63715 -1.0770750 #@# 4 362 -6.86036 -40.15836 46.69209 3.00985 -0.72651 -0.63715 -1.0770758 #@# 4 363 -6.86036 -40.18921 46.69209 3.00985 -0.72651 -0.63715 -1.0770763 #@# 4 372 -6.86036 -40.18921 46.69209 3.00985 -0.72651 -0.70671 -1.0770774 #@# 4 373 -6.86036 -40.18921 46.69209 3.00985 -0.72651 -0.67840 -1.0770789 #@# 4 380 -6.86036 -40.18921 46.69209 2.39182 -0.72651 -0.67840 -1.0770946 #@# 4 382 -6.86036 -40.18921 46.69209 2.68330 -0.72651 -0.67840 -1.0771564 #@# 4 385 -6.86036 -40.18921 46.69209 2.66896 -0.72651 -0.67840 -1.0771579 #@# 4 392 -6.86036 -40.18921 46.69209 2.66896 -0.34455 -0.67840 -1.0771731 #@# 4 397 -6.86036 -40.18921 46.69209 2.66896 -0.37244 -0.67840 -1.0771741 #@# 4 399 -6.86036 -40.18921 46.69209 2.66896 -0.36244 -0.67840 -1.0771748 #@# 4 405 -6.81962 -40.25911 46.46530 2.59594 -0.43207 -0.69757 -1.0771890 #@# 4 406 -6.81349 -40.26963 46.43116 2.58495 -0.44255 -0.70045 -1.0771892 #@# 4 409 -6.80477 -40.28460 46.38261 2.56931 -0.45746 -0.70456 -1.0771968 powell nthiter 3: fret = -1.077197 #@# 4 420 -6.79242 -40.28460 46.38261 2.56931 -0.45746 -0.70456 -1.0771970 #@# 4 431 -6.79242 -40.27460 46.38261 2.56931 -0.45746 -0.70456 -1.0771972 #@# 4 439 -6.79242 -40.27460 46.38261 2.56931 -0.45746 -0.76277 -1.0771991 #@# 4 443 -6.79242 -40.27460 46.38261 2.56931 -0.45746 -0.79396 -1.0771992 #@# 4 452 -6.79242 -40.27460 46.38261 2.40883 -0.45746 -0.79396 -1.0772178 #@# 4 473 -6.78081 -40.29453 46.31795 2.38801 -0.47731 -0.79943 -1.0772204 #@# 4 475 -6.78283 -40.29106 46.32921 2.39163 -0.47385 -0.79848 -1.0772210 #@# 4 477 -6.78423 -40.28865 46.33700 2.39414 -0.47146 -0.79782 -1.0772221 Powell done niters total = 3 OptTimeSec 24.1 sec OptTimeMin 0.40 min nEvals 478 Final parameters -6.78423309 -40.28865433 46.33700180 2.39414263 -0.47146299 -0.79781985 Final cost -1.077222058294229 --------------------------------- mri_coreg utimesec 97.138904 mri_coreg stimesec 0.220070 mri_coreg ru_maxrss 424536 mri_coreg ru_ixrss 0 mri_coreg ru_idrss 0 mri_coreg ru_isrss 0 mri_coreg ru_minflt 125482 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 5453 mri_coreg ru_nivcsw 124 Final RefRAS-to-MovRAS 0.99987 -0.01392 -0.00823 -6.78423; 0.01426 0.99903 0.04177 -40.28865; 0.00764 -0.04188 0.99909 46.33700; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox 0.29087 -0.00239 0.00405 -5.40445; 0.00454 0.07771 -0.28030 58.00127; -0.00084 -0.19273 -0.05344 38.94445; 0.00000 0.00000 0.00000 1.00000; Final parameters -6.7842 -40.2887 46.3370 2.3941 -0.4715 -0.7978 nhits = 105949 out of 16777216, Percent Overlap: 40.4 mri_coreg RunTimeSec 97.4 sec To check run: tkregisterfv --mov bold/003/tmp.bbregister.28396/template.nii --targ /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/brainmask.mgz --reg bold/003/tmp.bbregister.28396/mri_coreg.lta --s fsf01anat --surfs mri_coreg done mri_segreg --mov bold/003/tmp.bbregister.28396/template.nii --init-reg bold/003/tmp.bbregister.28396/reg.init.dat --out-reg bold/003/tmp.bbregister.28396/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.113 2016/05/10 03:23:20 greve Exp $ setenv SUBJECTS_DIR /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects cd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01 mri_segreg --mov bold/003/tmp.bbregister.28396/template.nii --init-reg bold/003/tmp.bbregister.28396/reg.init.dat --out-reg bold/003/tmp.bbregister.28396/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass movvol bold/003/tmp.bbregister.28396/template.nii regfile bold/003/tmp.bbregister.28396/reg.init.dat subject fsf01anat dof 6 outregfile bold/003/tmp.bbregister.28396/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 1538738908 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99987 -0.01392 -0.00823 -0.13446; 0.00421 -0.26722 0.96363 -38.36523; 0.01562 0.96353 0.26713 -2.23862; 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 1.059994 1 -25.0 -25.0 25.0 1.022821 2 -25.0 25.0 -25.0 1.072420 3 -25.0 25.0 25.0 1.027855 4 25.0 -25.0 -25.0 1.041630 5 25.0 -25.0 25.0 1.045588 6 25.0 25.0 -25.0 1.056984 7 25.0 25.0 25.0 1.039236 REL: 8 0.716286 8.366528 1.045816 rel = 0.684906 Initial costs ---------------- Number of surface hits 3062 WM Intensity 844.6587 +/- 208.1985 Ctx Intensity 852.0551 +/- 235.4653 Pct Contrast -0.5487 +/- 20.6876 Cost 0.7163 RelCost 0.6849 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 1.0676 1.0676 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 1.0653 1.0653 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 1.0307 1.0307 0.0 3 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 -4.0000 1.0141 1.0141 0.0 4 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.0000 1.0068 1.0068 0.0 6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.9721 0.9721 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.9452 0.9452 0.0 18 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 -4.0000 0.9373 0.9373 0.0 19 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.0000 0.9349 0.9349 0.0 30 -4.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.9112 0.9112 0.0 33 -4.0000 -4.0000 0.0000 -4.0000 4.0000 -4.0000 0.8806 0.8806 0.0 34 -4.0000 -4.0000 0.0000 -4.0000 4.0000 0.0000 0.8736 0.8736 0.0 273 0.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.8138 0.8138 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.7479 0.7479 0.0 282 0.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.7207 0.7207 0.0 283 0.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.5924 0.5924 0.0 Brute Force -------------------------- Min cost was 0.592385 Number of iterations 729 Search time 1.755000 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 = 0.592385 7 -0.112 -4.000 0.000 0.000 0.000 0.000 0.5919498103 8 -0.107 -4.000 0.000 0.000 0.000 0.000 0.5919494783 16 -0.107 -3.000 0.000 0.000 0.000 0.000 0.5712621841 21 -0.107 -2.955 0.000 0.000 0.000 0.000 0.5707273814 22 -0.107 -2.736 0.000 0.000 0.000 0.000 0.5705725033 23 -0.107 -2.838 0.000 0.000 0.000 0.000 0.5700880567 32 -0.107 -2.838 0.095 0.000 0.000 0.000 0.5692908664 34 -0.107 -2.838 0.103 0.000 0.000 0.000 0.5692902242 35 -0.107 -2.838 0.100 0.000 0.000 0.000 0.5692898647 42 -0.107 -2.838 0.100 -0.618 0.000 0.000 0.5686173043 47 -0.107 -2.838 0.100 -0.674 0.000 0.000 0.5683618102 49 -0.107 -2.838 0.100 -0.671 0.000 0.000 0.5683602197 50 -0.107 -2.838 0.100 -0.667 0.000 0.000 0.5683578505 53 -0.107 -2.838 0.100 -0.666 0.000 0.000 0.5683574577 55 -0.107 -2.838 0.100 -0.665 0.000 0.000 0.5683573433 63 -0.107 -2.838 0.100 -0.665 0.085 0.000 0.5680061511 65 -0.107 -2.838 0.100 -0.665 0.066 0.000 0.5679713664 67 -0.107 -2.838 0.100 -0.665 0.067 0.000 0.5679712604 75 -0.107 -2.838 0.100 -0.665 0.067 -0.227 0.5677078522 76 -0.107 -2.838 0.100 -0.665 0.067 -0.167 0.5675662366 77 -0.107 -2.838 0.100 -0.665 0.067 -0.141 0.5674868057 78 -0.107 -2.838 0.100 -0.665 0.067 -0.087 0.5674678287 79 -0.107 -2.838 0.100 -0.665 0.067 -0.108 0.5674345186 powell nthiter 1: fret = 0.567434 91 -0.009 -2.838 0.100 -0.665 0.067 -0.108 0.5670731120 92 -0.013 -2.838 0.100 -0.665 0.067 -0.108 0.5670554000 93 -0.037 -2.838 0.100 -0.665 0.067 -0.108 0.5669678659 95 -0.046 -2.838 0.100 -0.665 0.067 -0.108 0.5669570606 96 -0.047 -2.838 0.100 -0.665 0.067 -0.108 0.5669567539 97 -0.048 -2.838 0.100 -0.665 0.067 -0.108 0.5669567370 108 -0.048 -2.803 0.100 -0.665 0.067 -0.108 0.5669200421 109 -0.048 -2.809 0.100 -0.665 0.067 -0.108 0.5669170442 110 -0.048 -2.810 0.100 -0.665 0.067 -0.108 0.5669166718 120 -0.048 -2.810 0.010 -0.665 0.067 -0.108 0.5667203583 124 -0.048 -2.810 -0.013 -0.665 0.067 -0.108 0.5666992180 128 -0.048 -2.810 -0.014 -0.665 0.067 -0.108 0.5666985928 140 -0.048 -2.810 -0.014 -0.677 0.067 -0.108 0.5666983220 141 -0.048 -2.810 -0.014 -0.671 0.067 -0.108 0.5666982570 143 -0.048 -2.810 -0.014 -0.674 0.067 -0.108 0.5666980908 152 -0.048 -2.810 -0.014 -0.674 0.151 -0.108 0.5663382509 154 -0.048 -2.810 -0.014 -0.674 0.137 -0.108 0.5662709356 156 -0.048 -2.810 -0.014 -0.674 0.133 -0.108 0.5662685228 157 -0.048 -2.810 -0.014 -0.674 0.134 -0.108 0.5662683179 166 -0.048 -2.810 -0.014 -0.674 0.134 -0.186 0.5662116093 167 -0.048 -2.810 -0.014 -0.674 0.134 -0.185 0.5662107322 168 -0.048 -2.810 -0.014 -0.674 0.134 -0.165 0.5661902119 170 -0.048 -2.810 -0.014 -0.674 0.134 -0.160 0.5661895990 171 -0.048 -2.810 -0.014 -0.674 0.134 -0.161 0.5661895723 powell nthiter 2: fret = 0.566190 181 -0.002 -2.810 -0.014 -0.674 0.134 -0.162 0.5661641241 182 -0.018 -2.810 -0.014 -0.674 0.134 -0.162 0.5661191853 183 -0.022 -2.810 -0.014 -0.674 0.134 -0.162 0.5661170014 184 -0.023 -2.810 -0.014 -0.674 0.134 -0.162 0.5661168502 185 -0.024 -2.810 -0.014 -0.674 0.134 -0.162 0.5661168203 199 -0.024 -2.812 -0.014 -0.674 0.134 -0.162 0.5661168031 209 -0.024 -2.812 -0.007 -0.674 0.134 -0.162 0.5661137472 210 -0.024 -2.812 -0.008 -0.674 0.134 -0.162 0.5661132399 211 -0.024 -2.812 -0.009 -0.674 0.134 -0.162 0.5661129969 212 -0.024 -2.812 -0.011 -0.674 0.134 -0.162 0.5661126922 222 -0.024 -2.812 -0.011 -0.713 0.134 -0.162 0.5660900824 223 -0.024 -2.812 -0.011 -0.700 0.134 -0.162 0.5660826147 224 -0.024 -2.812 -0.011 -0.699 0.134 -0.162 0.5660822934 226 -0.024 -2.812 -0.011 -0.697 0.134 -0.162 0.5660818300 228 -0.024 -2.812 -0.011 -0.695 0.134 -0.162 0.5660816466 238 -0.024 -2.812 -0.011 -0.695 0.139 -0.162 0.5660655532 240 -0.024 -2.812 -0.011 -0.695 0.141 -0.162 0.5660648334 242 -0.024 -2.812 -0.011 -0.695 0.140 -0.162 0.5660640557 262 -0.015 -2.813 -0.010 -0.704 0.142 -0.162 0.5660533302 264 -0.014 -2.813 -0.010 -0.705 0.143 -0.162 0.5660530803 266 -0.014 -2.813 -0.010 -0.705 0.143 -0.162 0.5660529158 267 -0.012 -2.813 -0.009 -0.707 0.143 -0.162 0.5660527492 268 -0.012 -2.813 -0.009 -0.707 0.143 -0.162 0.5660527461 269 -0.012 -2.813 -0.009 -0.707 0.143 -0.162 0.5660526897 271 -0.011 -2.813 -0.009 -0.707 0.144 -0.162 0.5660526583 powell nthiter 3: fret = 0.566053 284 -0.012 -2.813 -0.009 -0.707 0.143 -0.168 0.5660465214 285 -0.012 -2.813 -0.009 -0.707 0.143 -0.179 0.5660418154 295 -0.012 -2.796 -0.009 -0.707 0.143 -0.179 0.5660225987 296 -0.012 -2.779 -0.009 -0.707 0.143 -0.179 0.5660042652 298 -0.012 -2.774 -0.009 -0.707 0.143 -0.179 0.5660026206 299 -0.012 -2.772 -0.009 -0.707 0.143 -0.179 0.5660020993 310 -0.012 -2.772 -0.019 -0.707 0.143 -0.179 0.5659999023 311 -0.012 -2.772 -0.017 -0.707 0.143 -0.179 0.5659972585 322 -0.012 -2.772 -0.017 -0.749 0.143 -0.179 0.5659419787 325 -0.012 -2.772 -0.017 -0.755 0.143 -0.179 0.5659402740 326 -0.012 -2.772 -0.017 -0.756 0.143 -0.179 0.5659401653 338 -0.012 -2.772 -0.017 -0.757 0.148 -0.179 0.5659367779 340 -0.012 -2.772 -0.017 -0.757 0.147 -0.179 0.5659362456 341 -0.012 -2.772 -0.017 -0.757 0.146 -0.179 0.5659361465 349 -0.007 -2.772 -0.017 -0.761 0.147 -0.179 0.5659312221 351 -0.008 -2.772 -0.017 -0.760 0.147 -0.179 0.5659308024 353 -0.008 -2.772 -0.017 -0.760 0.147 -0.179 0.5659307662 powell nthiter 4: fret = 0.565931 369 -0.008 -2.772 -0.017 -0.760 0.147 -0.170 0.5659248495 370 -0.008 -2.772 -0.017 -0.760 0.147 -0.169 0.5659245366 372 -0.008 -2.772 -0.017 -0.760 0.147 -0.167 0.5659244551 373 -0.008 -2.772 -0.017 -0.760 0.147 -0.166 0.5659243219 381 -0.008 -2.748 -0.017 -0.760 0.147 -0.166 0.5658922803 382 -0.008 -2.741 -0.017 -0.760 0.147 -0.166 0.5658917125 383 -0.008 -2.743 -0.017 -0.760 0.147 -0.166 0.5658915909 384 -0.008 -2.742 -0.017 -0.760 0.147 -0.166 0.5658915699 391 -0.008 -2.742 -0.023 -0.760 0.147 -0.166 0.5658764926 393 -0.008 -2.742 -0.037 -0.760 0.147 -0.166 0.5658654829 394 -0.008 -2.742 -0.035 -0.760 0.147 -0.166 0.5658646666 406 -0.008 -2.742 -0.035 -0.755 0.147 -0.166 0.5658575711 408 -0.008 -2.742 -0.035 -0.751 0.147 -0.166 0.5658561838 419 -0.008 -2.742 -0.035 -0.751 0.158 -0.166 0.5658447662 420 -0.008 -2.742 -0.035 -0.751 0.157 -0.166 0.5658436706 421 -0.008 -2.742 -0.035 -0.751 0.155 -0.166 0.5658427897 422 -0.008 -2.742 -0.035 -0.751 0.152 -0.166 0.5658421187 424 -0.008 -2.742 -0.035 -0.751 0.153 -0.166 0.5658420755 432 -0.005 -2.742 -0.035 -0.754 0.154 -0.166 0.5658400088 powell nthiter 5: fret = 0.565840 448 -0.005 -2.742 -0.035 -0.754 0.154 -0.164 0.5658379560 449 -0.005 -2.742 -0.035 -0.754 0.154 -0.160 0.5658374444 450 -0.005 -2.742 -0.035 -0.754 0.154 -0.161 0.5658369662 460 -0.005 -2.738 -0.035 -0.754 0.154 -0.161 0.5658364065 461 -0.005 -2.739 -0.035 -0.754 0.154 -0.161 0.5658362987 462 -0.005 -2.740 -0.035 -0.754 0.154 -0.161 0.5658362540 463 -0.005 -2.741 -0.035 -0.754 0.154 -0.161 0.5658362006 470 -0.005 -2.741 -0.029 -0.754 0.154 -0.161 0.5658325964 472 -0.005 -2.741 -0.031 -0.754 0.154 -0.161 0.5658317192 503 -0.005 -2.741 -0.031 -0.753 0.154 -0.161 0.5658316336 506 -0.006 -2.741 -0.031 -0.753 0.153 -0.161 0.5658316122 508 -0.006 -2.741 -0.031 -0.753 0.153 -0.161 0.5658315662 509 -0.006 -2.741 -0.031 -0.753 0.153 -0.161 0.5658314160 Powell done niters = 5 Computing relative cost 0 -25.0 -25.0 -25.0 1.050907 1 -25.0 -25.0 25.0 1.010683 2 -25.0 25.0 -25.0 1.031256 3 -25.0 25.0 25.0 1.037009 4 25.0 -25.0 -25.0 1.025698 5 25.0 -25.0 25.0 1.041193 6 25.0 25.0 -25.0 1.006945 7 25.0 25.0 25.0 1.041166 REL: 8 0.565831 8.244856 1.030607 rel = 0.549027 Number of iterations 5 Min cost was 0.565831 Number of FunctionCalls 510 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 1.353000 sec Parameters at optimum (transmm) -0.00560 -2.74080 -0.03080 Parameters at optimum (rotdeg) -0.75319 0.15347 -0.16142 Final costs ---------------- Number of surface hits 3062 WM Intensity 812.1043 +/- 221.9214 Ctx Intensity 840.3369 +/- 250.4278 Pct Contrast 1.6179 +/- 20.7464 Cost 0.5658 RelCost 0.6849 Reg at min cost was 0.99992 -0.01205 -0.00482 -0.25286; 0.00160 -0.25450 0.96707 -41.13160; 0.01288 0.96700 0.25446 -1.76455; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/003/tmp.bbregister.28396/bbr.pass1.dat, type = 14 Original Reg 0.99987 -0.01392 -0.00823 -0.13446; 0.00421 -0.26722 0.96363 -38.36523; 0.01562 0.96353 0.26713 -2.23862; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00005 -0.00187 -0.00341 0.11840; 0.00261 -0.01272 -0.00345 2.76637; 0.00273 -0.00346 0.01267 -0.47408; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 2.804869 Computing change in rh position Surface-RMS-Diff-mm 2.863935 0.596876 4.044450 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.28396/template.nii --init-reg bold/003/tmp.bbregister.28396/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.28396/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.113 2016/05/10 03:23:20 greve Exp $ setenv SUBJECTS_DIR /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects cd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01 mri_segreg --mov bold/003/tmp.bbregister.28396/template.nii --init-reg bold/003/tmp.bbregister.28396/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.28396/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass movvol bold/003/tmp.bbregister.28396/template.nii regfile bold/003/tmp.bbregister.28396/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 1538871494 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99992 -0.01205 -0.00482 -0.25286; 0.00160 -0.25450 0.96707 -41.13160; 0.01288 0.96700 0.25446 -1.76455; 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 1.037826 1 -25.0 -25.0 25.0 1.056778 2 -25.0 25.0 -25.0 1.051309 3 -25.0 25.0 25.0 1.064235 4 25.0 -25.0 -25.0 1.025181 5 25.0 -25.0 25.0 1.035811 6 25.0 25.0 -25.0 1.014423 7 25.0 25.0 25.0 1.057193 REL: 8 0.586883 8.342756 1.042844 rel = 0.562771 Initial costs ---------------- Number of surface hits 304688 WM Intensity 816.0936 +/- 217.8685 Ctx Intensity 842.9800 +/- 248.9276 Pct Contrast 1.3139 +/- 21.7167 Cost 0.5869 RelCost 0.5628 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.5687 0.5687 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.5686 0.5686 0.0 9 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 -0.1000 0.5673 0.5673 0.0 10 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.0000 0.5673 0.5673 0.0 18 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 -0.1000 0.5670 0.5670 0.0 19 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 0.0000 0.5668 0.5668 0.0 45 -0.1000 -0.1000 0.0000 0.1000 -0.1000 -0.1000 0.5667 0.5667 0.0 46 -0.1000 -0.1000 0.0000 0.1000 -0.1000 0.0000 0.5666 0.5666 0.0 282 0.0000 -0.1000 0.0000 0.0000 0.0000 -0.1000 0.5665 0.5665 0.0 283 0.0000 -0.1000 0.0000 0.0000 0.0000 0.0000 0.5662 0.5662 0.0 292 0.0000 -0.1000 0.0000 0.1000 0.0000 0.0000 0.5662 0.5662 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.5658 0.5658 0.0 Brute Force -------------------------- Min cost was 0.565831 Number of iterations 729 Search time 1.805000 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 = 0.586883 7 0.150 0.000 0.000 0.000 0.000 0.000 0.5863518954 8 0.149 0.000 0.000 0.000 0.000 0.000 0.5863516942 9 0.146 0.000 0.000 0.000 0.000 0.000 0.5863513688 11 0.145 0.000 0.000 0.000 0.000 0.000 0.5863513432 20 0.145 0.161 0.000 0.000 0.000 0.000 0.5858449411 21 0.145 0.162 0.000 0.000 0.000 0.000 0.5858444898 22 0.145 0.172 0.000 0.000 0.000 0.000 0.5858434934 24 0.145 0.169 0.000 0.000 0.000 0.000 0.5858432973 25 0.145 0.168 0.000 0.000 0.000 0.000 0.5858432800 34 0.145 0.168 -0.042 0.000 0.000 0.000 0.5857784015 35 0.145 0.168 -0.054 0.000 0.000 0.000 0.5857763489 36 0.145 0.168 -0.052 0.000 0.000 0.000 0.5857760299 44 0.145 0.168 -0.051 0.382 0.000 0.000 0.5852557653 45 0.145 0.168 -0.051 0.232 0.000 0.000 0.5848056234 46 0.145 0.168 -0.051 0.227 0.000 0.000 0.5848055741 47 0.145 0.168 -0.051 0.230 0.000 0.000 0.5848054446 48 0.145 0.168 -0.051 0.231 0.000 0.000 0.5848053792 55 0.145 0.168 -0.051 0.231 -0.234 0.000 0.5831600451 57 0.145 0.168 -0.051 0.231 -0.228 0.000 0.5831593376 60 0.145 0.168 -0.051 0.231 -0.230 0.000 0.5831593170 66 0.145 0.168 -0.051 0.231 -0.230 -0.618 0.5823491756 68 0.145 0.168 -0.051 0.231 -0.230 -0.367 0.5815587180 69 0.145 0.168 -0.051 0.231 -0.230 -0.363 0.5815576978 70 0.145 0.168 -0.051 0.231 -0.230 -0.354 0.5815562613 73 0.145 0.168 -0.051 0.231 -0.230 -0.352 0.5815562343 74 0.145 0.168 -0.051 0.231 -0.230 -0.351 0.5815560992 powell nthiter 1: fret = 0.581556 83 0.073 0.168 -0.051 0.231 -0.230 -0.351 0.5814673636 84 0.085 0.168 -0.051 0.231 -0.230 -0.351 0.5814616396 85 0.088 0.168 -0.051 0.231 -0.230 -0.351 0.5814613415 86 0.089 0.168 -0.051 0.231 -0.230 -0.351 0.5814612989 95 0.090 0.107 -0.051 0.231 -0.230 -0.351 0.5813532467 96 0.090 0.093 -0.051 0.231 -0.230 -0.351 0.5813517528 97 0.090 0.097 -0.051 0.231 -0.230 -0.351 0.5813512123 108 0.090 0.096 -0.039 0.231 -0.230 -0.351 0.5813485681 110 0.090 0.096 -0.041 0.231 -0.230 -0.351 0.5813484556 120 0.090 0.096 -0.040 0.243 -0.230 -0.351 0.5813453647 121 0.090 0.096 -0.040 0.242 -0.230 -0.351 0.5813452947 129 0.090 0.096 -0.040 0.242 -0.291 -0.351 0.5813216866 130 0.090 0.096 -0.040 0.242 -0.266 -0.351 0.5813016984 131 0.090 0.096 -0.040 0.242 -0.265 -0.351 0.5813014436 133 0.090 0.096 -0.040 0.242 -0.264 -0.351 0.5813013943 142 0.090 0.096 -0.040 0.242 -0.264 -0.363 0.5812986308 143 0.090 0.096 -0.040 0.242 -0.264 -0.364 0.5812985277 powell nthiter 2: fret = 0.581299 154 0.084 0.096 -0.040 0.242 -0.264 -0.364 0.5812970375 155 0.083 0.096 -0.040 0.242 -0.264 -0.364 0.5812969824 156 0.082 0.096 -0.040 0.242 -0.264 -0.364 0.5812969629 176 0.082 0.095 -0.045 0.242 -0.264 -0.364 0.5812962218 186 0.082 0.095 -0.046 0.240 -0.264 -0.364 0.5812959208 188 0.082 0.095 -0.046 0.241 -0.264 -0.364 0.5812959109 196 0.082 0.095 -0.046 0.241 -0.268 -0.364 0.5812950682 198 0.082 0.095 -0.046 0.241 -0.270 -0.364 0.5812948515 powell nthiter 3: fret = 0.581295 221 0.081 0.095 -0.046 0.241 -0.270 -0.364 0.5812948356 229 0.081 0.099 -0.046 0.241 -0.270 -0.364 0.5812946423 230 0.081 0.098 -0.046 0.241 -0.270 -0.364 0.5812946127 239 0.081 0.098 -0.047 0.241 -0.270 -0.364 0.5812945545 240 0.081 0.098 -0.048 0.241 -0.270 -0.364 0.5812945394 250 0.081 0.098 -0.048 0.238 -0.270 -0.364 0.5812943078 251 0.081 0.098 -0.048 0.237 -0.270 -0.364 0.5812942760 powell nthiter 4: fret = 0.581294 292 0.082 0.101 -0.048 0.236 -0.270 -0.364 0.5812940500 313 0.082 0.102 -0.049 0.235 -0.270 -0.364 0.5812940289 314 0.082 0.102 -0.049 0.234 -0.270 -0.364 0.5812940109 powell nthiter 5: fret = 0.581294 346 0.081 0.102 -0.049 0.234 -0.270 -0.364 0.5812939865 Powell done niters = 5 Computing relative cost 0 -25.0 -25.0 -25.0 1.037452 1 -25.0 -25.0 25.0 1.055120 2 -25.0 25.0 -25.0 1.052500 3 -25.0 25.0 25.0 1.065054 4 25.0 -25.0 -25.0 1.027753 5 25.0 -25.0 25.0 1.034331 6 25.0 25.0 -25.0 1.012954 7 25.0 25.0 25.0 1.054794 REL: 8 0.581294 8.339958 1.042495 rel = 0.557599 Number of iterations 5 Min cost was 0.581294 Number of FunctionCalls 396 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 38.113000 sec Parameters at optimum (transmm) 0.08113 0.10290 -0.04817 Parameters at optimum (rotdeg) 0.23367 -0.27020 -0.36353 Final costs ---------------- Number of surface hits 304688 WM Intensity 816.8157 +/- 217.8065 Ctx Intensity 844.2287 +/- 248.8138 Pct Contrast 1.4037 +/- 21.6878 Cost 0.5813 RelCost 0.5628 Reg at min cost was 0.99983 -0.01825 0.00009 -0.42354; -0.00480 -0.25833 0.96604 -41.01879; 0.01760 0.96588 0.25838 -1.98162; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/003/register.dof6.dat, type = 14 Original Reg 0.99992 -0.01205 -0.00482 -0.25286; 0.00160 -0.25450 0.96707 -41.13160; 0.01288 0.96700 0.25446 -1.76455; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00008 0.00619 -0.00491 0.17067; 0.00640 0.00383 0.00103 -0.11282; -0.00472 0.00111 -0.00392 0.21708; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.495557 Computing change in rh position Surface-RMS-Diff-mm 0.426626 0.174500 0.845800 mri_segreg done MinCost: 0.581294 816.815693 844.228663 1.403695 tkregister2_cmdl --mov bold/003/template.nii.gz --reg bold/003/register.dof6.dat --noedit --ltaout bold/003/register.dof6.lta tkregister_tcl /media/sda1/nmrclass/freesurfer/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 1.132.2.1 2016/08/02 21:17:29 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- 0.99983 -0.01825 0.00009 -0.42354; -0.00480 -0.25833 0.96604 -41.01879; 0.01760 0.96588 0.25838 -1.98162; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: loading target /media/sda1/nmrclass/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 -------- 0.99983 -0.01825 0.00009 -0.42354; -0.00480 -0.25833 0.96604 -41.01879; 0.01760 0.96588 0.25838 -1.98162; 0.00000 0.00000 0.00000 1.00000; Determinant -1 subject = fsf01anat RegMat --------------------------- 0.99983 -0.01825 0.00009 -0.42354; -0.00480 -0.25833 0.96604 -41.01879; 0.01760 0.96588 0.25838 -1.98162; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Sun Sep 30 01:18:07 EDT 2018 Ended at Sun Sep 30 01:20:48 EDT 2018 BBR-Run-Time-Sec 161 bbregister Done To check results, run: tkregisterfv --mov bold/003/template.nii.gz --reg bold/003/register.dof6.lta --surfs Run: 004 ---------------- Sun Sep 30 01:20:48 EDT 2018 -------------------------------------- /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01 bbregister --s fsf01anat --init-coreg --6 --bold --mov bold/004/template.nii.gz --reg bold/004/register.dof6.dat --lta bold/004/register.dof6.lta --init-reg-out bold/004/init.register.dof6.dat tmp bold/004/tmp.bbregister.28503 Log file is bold/004/register.dof6.dat.log Sun Sep 30 01:20:49 EDT 2018 setenv SUBJECTS_DIR /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects cd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01 /media/sda1/nmrclass/freesurfer/bin/bbregister --s fsf01anat --init-coreg --6 --bold --mov bold/004/template.nii.gz --reg bold/004/register.dof6.dat --lta bold/004/register.dof6.lta --init-reg-out bold/004/init.register.dof6.dat $Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $ Linux fsuser3-G5-5587 4.15.0-34-generic #37-Ubuntu SMP Mon Aug 27 15:21:48 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /media/sda1/nmrclass/freesurfer mri_convert bold/004/template.nii.gz bold/004/tmp.bbregister.28503/template.nii mri_convert.bin bold/004/template.nii.gz bold/004/tmp.bbregister.28503/template.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from bold/004/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/004/tmp.bbregister.28503/template.nii... mri_coreg --s fsf01anat --mov bold/004/tmp.bbregister.28503/template.nii --regdat bold/004/tmp.bbregister.28503/reg.init.dat --reg bold/004/tmp.bbregister.28503/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 $Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $ cwd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01 cmdline mri_coreg --s fsf01anat --mov bold/004/tmp.bbregister.28503/template.nii --regdat bold/004/tmp.bbregister.28503/reg.init.dat --reg bold/004/tmp.bbregister.28503/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass dof 6 nsep 1 cras0 1 ftol 0.000100 linmintol 0.010000 bf 1 bflim 30.000000 bfnsamp 30 SmoothRef 0 SatPct 99.990000 MovOOB 0 optschema 1 Reading in mov bold/004/tmp.bbregister.28503/template.nii Reading in ref /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/brainmask.mgz Reading in and applying refmask /media/sda1/nmrclass/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 = 1723.6666 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 -1.0204177155 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 -8.02228 -35.25770 49.23798 4.00000 -2.00000 0.00000 -1.0499900 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6 Starting OpenPowel2(), sep = 4 InitialCost -1.0709418058 #@# 4 188 -8.02228 -35.25770 49.23798 4.00000 -2.00000 0.00000 -1.0709418 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.070942 #@# 4 194 -7.64031 -35.25770 49.23798 4.00000 -2.00000 0.00000 -1.0709554 #@# 4 195 -7.78570 -35.25770 49.23798 4.00000 -2.00000 0.00000 -1.0709684 #@# 4 196 -7.79761 -35.25770 49.23798 4.00000 -2.00000 0.00000 -1.0709686 #@# 4 197 -7.81433 -35.25770 49.23798 4.00000 -2.00000 0.00000 -1.0709690 #@# 4 203 -7.81433 -36.87573 49.23798 4.00000 -2.00000 0.00000 -1.0733082 #@# 4 206 -7.81433 -39.84036 49.23798 4.00000 -2.00000 0.00000 -1.0753930 #@# 4 212 -7.81433 -39.82741 47.61994 4.00000 -2.00000 0.00000 -1.0759039 #@# 4 213 -7.81433 -39.82741 47.89967 4.00000 -2.00000 0.00000 -1.0759630 #@# 4 218 -7.81433 -39.82741 47.93245 4.00000 -2.00000 0.00000 -1.0759639 #@# 4 219 -7.81433 -39.82741 47.94245 4.00000 -2.00000 0.00000 -1.0759643 #@# 4 227 -7.81433 -39.82741 47.94245 3.38197 -2.00000 0.00000 -1.0760576 #@# 4 229 -7.81433 -39.82741 47.94245 3.58383 -2.00000 0.00000 -1.0760773 #@# 4 230 -7.81433 -39.82741 47.94245 3.56486 -2.00000 0.00000 -1.0760788 #@# 4 231 -7.81433 -39.82741 47.94245 3.53459 -2.00000 0.00000 -1.0760794 #@# 4 232 -7.81433 -39.82741 47.94245 3.54459 -2.00000 0.00000 -1.0760802 #@# 4 235 -7.81433 -39.82741 47.94245 3.54459 -1.00000 0.00000 -1.0761870 #@# 4 248 -7.81433 -39.82741 47.94245 3.54459 -1.00000 -0.61803 -1.0761943 #@# 4 250 -7.81433 -39.82741 47.94245 3.54459 -1.00000 -0.31663 -1.0762736 #@# 4 252 -7.81433 -39.82741 47.94245 3.54459 -1.00000 -0.34040 -1.0762745 powell nthiter 1: fret = -1.076275 #@# 4 262 -7.43237 -39.82741 47.94245 3.54459 -1.00000 -0.33040 -1.0763267 #@# 4 263 -7.50552 -39.82741 47.94245 3.54459 -1.00000 -0.33040 -1.0763276 #@# 4 264 -7.48084 -39.82741 47.94245 3.54459 -1.00000 -0.33040 -1.0763279 #@# 4 273 -7.47084 -39.98575 47.94245 3.54459 -1.00000 -0.33040 -1.0763378 #@# 4 274 -7.47084 -40.00915 47.94245 3.54459 -1.00000 -0.33040 -1.0763379 #@# 4 276 -7.47084 -39.99915 47.94245 3.54459 -1.00000 -0.33040 -1.0763386 #@# 4 281 -7.47084 -39.99915 47.32441 3.54459 -1.00000 -0.33040 -1.0763654 #@# 4 283 -7.47084 -39.99915 47.57781 3.54459 -1.00000 -0.33040 -1.0763932 #@# 4 286 -7.47084 -39.99915 47.55356 3.54459 -1.00000 -0.33040 -1.0763937 #@# 4 293 -7.47084 -39.99915 47.55356 2.92655 -1.00000 -0.33040 -1.0764090 #@# 4 295 -7.47084 -39.99915 47.55356 3.21444 -1.00000 -0.33040 -1.0764902 #@# 4 298 -7.47084 -39.99915 47.55356 3.20198 -1.00000 -0.33040 -1.0764906 #@# 4 299 -7.47084 -39.99915 47.55356 3.19198 -1.00000 -0.33040 -1.0764909 #@# 4 305 -7.47084 -39.99915 47.55356 3.19198 -0.61803 -0.33040 -1.0765015 #@# 4 306 -7.47084 -39.99915 47.55356 3.19198 -0.70313 -0.33040 -1.0765079 #@# 4 309 -7.47084 -39.99915 47.55356 3.19198 -0.67063 -0.33040 -1.0765084 #@# 4 318 -7.47084 -39.99915 47.55356 3.19198 -0.67063 -0.55333 -1.0765487 #@# 4 319 -7.47084 -39.99915 47.55356 3.19198 -0.67063 -0.54333 -1.0765494 #@# 4 321 -7.47084 -39.99915 47.55356 3.19198 -0.67063 -0.53333 -1.0765501 #@# 4 322 -7.12734 -40.17089 47.16468 2.83936 -0.34125 -0.73626 -1.0767455 #@# 4 325 -6.57155 -40.44877 46.53545 2.26882 0.19169 -1.06461 -1.0769247 #@# 4 329 -6.45302 -40.50803 46.40127 2.14715 0.30534 -1.13463 -1.0769382 #@# 4 331 -6.46225 -40.50342 46.41172 2.15662 0.29649 -1.12918 -1.0769393 powell nthiter 2: fret = -1.076939 #@# 4 342 -6.60315 -40.50342 46.41172 2.15662 0.29649 -1.12918 -1.0769477 #@# 4 343 -6.57963 -40.50342 46.41172 2.15662 0.29649 -1.12918 -1.0769485 #@# 4 344 -6.56941 -40.50342 46.41172 2.15662 0.29649 -1.12918 -1.0769489 #@# 4 346 -6.55533 -40.50342 46.41172 2.15662 0.29649 -1.12918 -1.0769490 #@# 4 355 -6.55533 -40.55133 46.41172 2.15662 0.29649 -1.12918 -1.0769508 #@# 4 375 -6.55533 -40.55133 46.41172 2.15662 0.29649 -1.25670 -1.0769607 #@# 4 376 -6.55533 -40.55133 46.41172 2.15662 0.29649 -1.23804 -1.0769622 #@# 4 379 -6.55533 -40.55133 46.41172 2.15662 0.29649 -1.20923 -1.0769624 #@# 4 385 -6.55533 -40.55133 46.41172 2.15662 -0.32154 -1.20923 -1.0770530 #@# 4 392 -6.21183 -40.72308 46.02283 1.80401 0.00783 -1.41216 -1.0770625 #@# 4 396 -6.34304 -40.65748 46.17137 1.93870 -0.11798 -1.33464 -1.0770723 #@# 4 399 -6.37095 -40.64352 46.20298 1.96735 -0.14475 -1.31815 -1.0770744 powell nthiter 3: fret = -1.077074 #@# 4 409 -6.43767 -40.64137 46.20784 1.97177 -0.14887 -1.31561 -1.0770788 #@# 4 411 -6.42767 -40.64137 46.20784 1.97177 -0.14887 -1.31561 -1.0770789 #@# 4 421 -6.42767 -40.65137 46.20784 1.97177 -0.14887 -1.31561 -1.0770792 #@# 4 422 -6.42767 -40.66137 46.20784 1.97177 -0.14887 -1.31561 -1.0770798 #@# 4 431 -6.42767 -40.66137 45.97576 1.97177 -0.14887 -1.31561 -1.0770938 #@# 4 432 -6.42767 -40.66137 46.00433 1.97177 -0.14887 -1.31561 -1.0770944 #@# 4 434 -6.42767 -40.66137 46.02610 1.97177 -0.14887 -1.31561 -1.0770947 #@# 4 436 -6.42767 -40.66137 46.05262 1.97177 -0.14887 -1.31561 -1.0770956 #@# 4 438 -6.42767 -40.66137 46.04249 1.97177 -0.14887 -1.31561 -1.0770978 #@# 4 445 -6.42767 -40.66137 46.04249 1.97177 -0.14887 -1.33769 -1.0770981 #@# 4 447 -6.42767 -40.66137 46.04249 1.97177 -0.14887 -1.32769 -1.0770983 #@# 4 454 -6.42767 -40.66137 46.04249 1.97177 -0.38970 -1.32769 -1.0771011 #@# 4 455 -6.42767 -40.66137 46.04249 1.97177 -0.32393 -1.32769 -1.0771031 #@# 4 457 -6.42767 -40.66137 46.04249 1.97177 -0.31393 -1.32769 -1.0771034 #@# 4 458 -6.42767 -40.66137 46.04249 1.97177 -0.30393 -1.32769 -1.0771039 Powell done niters total = 3 OptTimeSec 17.9 sec OptTimeMin 0.30 min nEvals 470 Final parameters -6.42767096 -40.66136932 46.04249191 1.97176516 -0.30392572 -1.32768750 Final cost -1.077103847066786 --------------------------------- mri_coreg utimesec 84.275916 mri_coreg stimesec 0.287972 mri_coreg ru_maxrss 424556 mri_coreg ru_ixrss 0 mri_coreg ru_idrss 0 mri_coreg ru_isrss 0 mri_coreg ru_minflt 125483 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 5449 mri_coreg ru_nivcsw 311 Final RefRAS-to-MovRAS 0.99972 -0.02317 -0.00530 -6.42767; 0.02334 0.99914 0.03441 -40.66137; 0.00450 -0.03452 0.99939 46.04249; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox 0.29083 -0.00154 0.00674 -5.76718; 0.00691 0.07564 -0.28082 58.03795; 0.00018 -0.19312 -0.05202 38.70510; 0.00000 0.00000 0.00000 1.00000; Final parameters -6.4277 -40.6614 46.0425 1.9718 -0.3039 -1.3277 nhits = 105999 out of 16777216, Percent Overlap: 40.4 mri_coreg RunTimeSec 84.7 sec To check run: tkregisterfv --mov bold/004/tmp.bbregister.28503/template.nii --targ /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/brainmask.mgz --reg bold/004/tmp.bbregister.28503/mri_coreg.lta --s fsf01anat --surfs mri_coreg done mri_segreg --mov bold/004/tmp.bbregister.28503/template.nii --init-reg bold/004/tmp.bbregister.28503/reg.init.dat --out-reg bold/004/tmp.bbregister.28503/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.113 2016/05/10 03:23:20 greve Exp $ setenv SUBJECTS_DIR /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects cd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01 mri_segreg --mov bold/004/tmp.bbregister.28503/template.nii --init-reg bold/004/tmp.bbregister.28503/reg.init.dat --out-reg bold/004/tmp.bbregister.28503/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass movvol bold/004/tmp.bbregister.28503/template.nii regfile bold/004/tmp.bbregister.28503/reg.init.dat subject fsf01anat dof 6 outregfile bold/004/tmp.bbregister.28503/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 1538346987 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99972 -0.02317 -0.00530 -0.42599; -0.00090 -0.26008 0.96559 -38.24387; 0.02375 0.96531 0.26003 -2.26926; 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 1.055351 1 -25.0 -25.0 25.0 1.019757 2 -25.0 25.0 -25.0 1.071212 3 -25.0 25.0 25.0 1.018278 4 25.0 -25.0 -25.0 1.049193 5 25.0 -25.0 25.0 1.045652 6 25.0 25.0 -25.0 1.066338 7 25.0 25.0 25.0 1.039477 REL: 8 0.752149 8.365258 1.045657 rel = 0.719307 Initial costs ---------------- Number of surface hits 3062 WM Intensity 851.0628 +/- 209.8219 Ctx Intensity 855.1873 +/- 236.7353 Pct Contrast -1.0315 +/- 21.2926 Cost 0.7521 RelCost 0.7193 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 1.0489 1.0489 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 1.0171 1.0171 0.0 3 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 -4.0000 1.0069 1.0069 0.0 5 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 4.0000 1.0022 1.0022 0.0 6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.9744 0.9744 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.9461 0.9461 0.0 10 -4.0000 -4.0000 -4.0000 0.0000 -4.0000 0.0000 0.9435 0.9435 0.0 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.9424 0.9424 0.0 18 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 -4.0000 0.9323 0.9323 0.0 19 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.0000 0.9319 0.9319 0.0 30 -4.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.9087 0.9087 0.0 33 -4.0000 -4.0000 0.0000 -4.0000 4.0000 -4.0000 0.8799 0.8799 0.0 34 -4.0000 -4.0000 0.0000 -4.0000 4.0000 0.0000 0.8746 0.8746 0.0 40 -4.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.8682 0.8682 0.0 273 0.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.8160 0.8160 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.7385 0.7385 0.0 283 0.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.5830 0.5830 0.0 Brute Force -------------------------- Min cost was 0.582998 Number of iterations 729 Search time 1.380000 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 = 0.582998 8 -0.026 -4.000 0.000 0.000 0.000 0.000 0.5829665118 9 -0.027 -4.000 0.000 0.000 0.000 0.000 0.5829663399 10 -0.028 -4.000 0.000 0.000 0.000 0.000 0.5829661887 14 -0.029 -3.000 0.000 0.000 0.000 0.000 0.5816083464 18 -0.029 -3.382 0.000 0.000 0.000 0.000 0.5810588769 19 -0.029 -3.229 0.000 0.000 0.000 0.000 0.5804502948 23 -0.029 -3.231 0.000 0.000 0.000 0.000 0.5804498849 32 -0.029 -3.231 0.382 0.000 0.000 0.000 0.5786012769 34 -0.029 -3.231 0.412 0.000 0.000 0.000 0.5785860482 36 -0.029 -3.231 0.406 0.000 0.000 0.000 0.5785847755 42 -0.029 -3.231 0.406 -1.618 0.000 0.000 0.5742722009 43 -0.029 -3.231 0.406 -0.900 0.000 0.000 0.5628521692 47 -0.029 -3.231 0.406 -0.971 0.000 0.000 0.5622774719 48 -0.029 -3.231 0.406 -1.009 0.000 0.000 0.5621711988 49 -0.029 -3.231 0.406 -1.018 0.000 0.000 0.5621574652 51 -0.029 -3.231 0.406 -1.040 0.000 0.000 0.5621562384 52 -0.029 -3.231 0.406 -1.030 0.000 0.000 0.5621514585 54 -0.029 -3.231 0.406 -1.031 0.000 0.000 0.5621514496 65 -0.029 -3.231 0.406 -1.031 -0.014 0.000 0.5620992885 67 -0.029 -3.231 0.406 -1.031 -0.015 0.000 0.5620987510 68 -0.029 -3.231 0.406 -1.031 -0.016 0.000 0.5620978956 69 -0.029 -3.231 0.406 -1.031 -0.019 0.000 0.5620977606 71 -0.029 -3.231 0.406 -1.031 -0.018 0.000 0.5620974048 72 -0.029 -3.231 0.406 -1.031 -0.017 0.000 0.5620973036 79 -0.029 -3.231 0.406 -1.031 -0.017 -0.168 0.5611688169 80 -0.029 -3.231 0.406 -1.031 -0.017 -0.187 0.5609779931 82 -0.029 -3.231 0.406 -1.031 -0.017 -0.235 0.5609051581 83 -0.029 -3.231 0.406 -1.031 -0.017 -0.218 0.5608668342 84 -0.029 -3.231 0.406 -1.031 -0.017 -0.217 0.5608663851 85 -0.029 -3.231 0.406 -1.031 -0.017 -0.215 0.5608661997 88 -0.029 -3.231 0.406 -1.031 -0.017 -0.216 0.5608655814 powell nthiter 1: fret = 0.560866 99 -0.025 -3.231 0.406 -1.031 -0.017 -0.216 0.5608633582 102 -0.021 -3.231 0.406 -1.031 -0.017 -0.216 0.5608622819 118 -0.020 -3.224 0.406 -1.031 -0.017 -0.216 0.5608566837 119 -0.020 -3.225 0.406 -1.031 -0.017 -0.216 0.5608563575 127 -0.020 -3.225 0.191 -1.031 -0.017 -0.216 0.5594621432 128 -0.020 -3.225 0.212 -1.031 -0.017 -0.216 0.5592822648 129 -0.020 -3.225 0.258 -1.031 -0.017 -0.216 0.5590882384 130 -0.020 -3.225 0.265 -1.031 -0.017 -0.216 0.5590824832 131 -0.020 -3.225 0.267 -1.031 -0.017 -0.216 0.5590819026 132 -0.020 -3.225 0.268 -1.031 -0.017 -0.216 0.5590817975 141 -0.020 -3.225 0.268 -1.014 -0.017 -0.216 0.5590505866 143 -0.020 -3.225 0.268 -1.011 -0.017 -0.216 0.5590495590 144 -0.020 -3.225 0.268 -1.010 -0.017 -0.216 0.5590495519 152 -0.020 -3.225 0.268 -1.010 -0.036 -0.216 0.5590426229 153 -0.020 -3.225 0.268 -1.010 -0.031 -0.216 0.5590385067 154 -0.020 -3.225 0.268 -1.010 -0.029 -0.216 0.5590381887 165 -0.020 -3.225 0.268 -1.010 -0.029 -0.263 0.5588485042 166 -0.020 -3.225 0.268 -1.010 -0.029 -0.260 0.5588422640 167 -0.020 -3.225 0.268 -1.010 -0.029 -0.255 0.5588383767 177 -0.020 -3.225 0.262 -1.009 -0.029 -0.256 0.5588271666 178 -0.019 -3.225 0.258 -1.009 -0.030 -0.258 0.5588226653 181 -0.019 -3.225 0.256 -1.008 -0.030 -0.258 0.5588217567 182 -0.019 -3.225 0.256 -1.008 -0.030 -0.258 0.5588216226 185 -0.019 -3.225 0.256 -1.008 -0.030 -0.258 0.5588215963 powell nthiter 2: fret = 0.558822 194 0.051 -3.225 0.256 -1.008 -0.030 -0.258 0.5586201249 196 0.043 -3.225 0.256 -1.008 -0.030 -0.258 0.5586173438 198 0.044 -3.225 0.256 -1.008 -0.030 -0.258 0.5586172756 207 0.045 -3.054 0.256 -1.008 -0.030 -0.258 0.5581739226 209 0.045 -2.973 0.256 -1.008 -0.030 -0.258 0.5580620192 211 0.045 -2.997 0.256 -1.008 -0.030 -0.258 0.5580510803 213 0.045 -2.989 0.256 -1.008 -0.030 -0.258 0.5580403138 222 0.045 -2.989 0.256 -1.008 -0.030 -0.129 0.5569858253 223 0.045 -2.989 0.256 -1.008 -0.030 -0.098 0.5569405513 225 0.045 -2.989 0.256 -1.008 -0.030 -0.105 0.5569343249 227 0.045 -2.989 0.256 -1.008 -0.030 -0.107 0.5569339736 236 0.045 -2.989 0.256 -1.013 -0.030 -0.107 0.5569270533 237 0.045 -2.989 0.256 -1.021 -0.030 -0.107 0.5569252229 239 0.045 -2.989 0.256 -1.018 -0.030 -0.107 0.5569248410 240 0.045 -2.989 0.256 -1.019 -0.030 -0.107 0.5569248313 248 0.045 -2.989 0.256 -1.019 -0.048 -0.107 0.5568739459 250 0.045 -2.989 0.256 -1.019 -0.057 -0.107 0.5568676120 251 0.045 -2.989 0.256 -1.019 -0.058 -0.107 0.5568676111 260 0.049 -2.987 0.203 -1.011 -0.063 -0.122 0.5566279934 261 0.049 -2.987 0.202 -1.011 -0.063 -0.122 0.5566277635 264 0.049 -2.986 0.202 -1.011 -0.063 -0.122 0.5566277255 powell nthiter 3: fret = 0.556628 277 0.072 -2.986 0.202 -1.011 -0.063 -0.122 0.5565531658 279 0.086 -2.986 0.202 -1.011 -0.063 -0.122 0.5565467074 280 0.082 -2.986 0.202 -1.011 -0.063 -0.122 0.5565453315 291 0.081 -2.988 0.202 -1.011 -0.063 -0.122 0.5565447483 292 0.081 -2.992 0.202 -1.011 -0.063 -0.122 0.5565443549 293 0.081 -2.991 0.202 -1.011 -0.063 -0.122 0.5565441833 302 0.081 -2.990 0.202 -1.011 -0.063 -0.088 0.5565127126 303 0.081 -2.990 0.202 -1.011 -0.063 -0.095 0.5565106892 313 0.081 -2.990 0.202 -1.021 -0.063 -0.095 0.5564927220 314 0.081 -2.990 0.202 -1.028 -0.063 -0.095 0.5564893367 315 0.081 -2.990 0.202 -1.027 -0.063 -0.095 0.5564892350 316 0.081 -2.990 0.202 -1.026 -0.063 -0.095 0.5564891640 329 0.081 -2.990 0.202 -1.026 -0.062 -0.095 0.5564891438 337 0.082 -2.989 0.192 -1.025 -0.063 -0.098 0.5564697916 338 0.082 -2.989 0.189 -1.024 -0.063 -0.098 0.5564687618 339 0.082 -2.989 0.190 -1.024 -0.063 -0.098 0.5564687113 powell nthiter 4: fret = 0.556469 357 0.074 -2.989 0.190 -1.024 -0.063 -0.098 0.5564642454 358 0.073 -2.989 0.190 -1.024 -0.063 -0.098 0.5564641008 376 0.073 -2.989 0.190 -1.024 -0.063 -0.093 0.5564637208 377 0.073 -2.989 0.190 -1.024 -0.063 -0.094 0.5564636989 378 0.073 -2.989 0.190 -1.024 -0.063 -0.095 0.5564635826 387 0.073 -2.989 0.190 -1.026 -0.063 -0.095 0.5564616012 388 0.073 -2.989 0.190 -1.035 -0.063 -0.095 0.5564540527 391 0.073 -2.989 0.190 -1.036 -0.063 -0.095 0.5564539547 401 0.073 -2.989 0.190 -1.037 -0.076 -0.095 0.5564449143 402 0.073 -2.989 0.190 -1.037 -0.073 -0.095 0.5564440854 403 0.073 -2.989 0.190 -1.037 -0.074 -0.095 0.5564440657 410 0.074 -2.989 0.186 -1.036 -0.074 -0.096 0.5564366827 411 0.074 -2.989 0.181 -1.035 -0.075 -0.098 0.5564343743 412 0.074 -2.989 0.182 -1.035 -0.074 -0.098 0.5564342695 Powell done niters = 4 Computing relative cost 0 -25.0 -25.0 -25.0 1.038363 1 -25.0 -25.0 25.0 1.012295 2 -25.0 25.0 -25.0 1.038288 3 -25.0 25.0 25.0 1.018793 4 25.0 -25.0 -25.0 1.035020 5 25.0 -25.0 25.0 1.027677 6 25.0 25.0 -25.0 1.022640 7 25.0 25.0 25.0 1.036930 REL: 8 0.556434 8.230007 1.028751 rel = 0.540883 Number of iterations 4 Min cost was 0.556434 Number of FunctionCalls 418 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.891000 sec Parameters at optimum (transmm) 0.07382 -2.98888 0.18241 Parameters at optimum (rotdeg) -1.03542 -0.07446 -0.09758 Final costs ---------------- Number of surface hits 3062 WM Intensity 814.2915 +/- 222.9866 Ctx Intensity 843.4465 +/- 252.6395 Pct Contrast 1.6656 +/- 21.0956 Cost 0.5564 RelCost 0.7193 Reg at min cost was 0.99968 -0.02484 -0.00397 -0.41532; -0.00218 -0.24255 0.97014 -41.26674; 0.02506 0.96982 0.24253 -1.39595; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/004/tmp.bbregister.28503/bbr.pass1.dat, type = 14 Original Reg 0.99972 -0.02317 -0.00530 -0.42599; -0.00090 -0.26008 0.96559 -38.24387; 0.02375 0.96531 0.26003 -2.26926; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00003 0.00167 -0.00134 -0.01068; 0.00127 -0.01753 -0.00455 3.02287; -0.00131 -0.00451 0.01750 -0.87331; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 3.149030 Computing change in rh position Surface-RMS-Diff-mm 3.179530 0.809840 4.777493 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/004/tmp.bbregister.28503/template.nii --init-reg bold/004/tmp.bbregister.28503/bbr.pass1.dat --out-reg bold/004/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/004/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/004/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/004/tmp.bbregister.28503/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.113 2016/05/10 03:23:20 greve Exp $ setenv SUBJECTS_DIR /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects cd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01 mri_segreg --mov bold/004/tmp.bbregister.28503/template.nii --init-reg bold/004/tmp.bbregister.28503/bbr.pass1.dat --out-reg bold/004/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/004/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/004/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/004/tmp.bbregister.28503/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass movvol bold/004/tmp.bbregister.28503/template.nii regfile bold/004/tmp.bbregister.28503/bbr.pass1.dat subject fsf01anat dof 6 outregfile bold/004/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 1539082840 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99968 -0.02484 -0.00397 -0.41532; -0.00218 -0.24255 0.97014 -41.26674; 0.02506 0.96982 0.24253 -1.39595; 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 1.035594 1 -25.0 -25.0 25.0 1.046918 2 -25.0 25.0 -25.0 1.054372 3 -25.0 25.0 25.0 1.061165 4 25.0 -25.0 -25.0 1.037523 5 25.0 -25.0 25.0 1.029247 6 25.0 25.0 -25.0 1.018700 7 25.0 25.0 25.0 1.051653 REL: 8 0.579214 8.335173 1.041897 rel = 0.555923 Initial costs ---------------- Number of surface hits 304688 WM Intensity 817.7986 +/- 218.4486 Ctx Intensity 846.7195 +/- 250.3919 Pct Contrast 1.5185 +/- 21.6969 Cost 0.5792 RelCost 0.5559 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.5597 0.5597 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.5587 0.5587 0.0 2 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.5582 0.5582 0.0 5 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1000 0.5580 0.5580 0.0 31 -0.1000 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.5580 0.5580 0.0 40 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.0000 0.5578 0.5578 0.0 41 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.1000 0.5576 0.5576 0.0 86 -0.1000 0.0000 -0.1000 -0.1000 0.0000 0.1000 0.5574 0.5574 0.0 95 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.1000 0.5573 0.5573 0.0 119 -0.1000 0.0000 0.0000 0.0000 -0.1000 0.1000 0.5572 0.5572 0.0 121 -0.1000 0.0000 0.0000 0.0000 0.0000 0.0000 0.5570 0.5570 0.0 122 -0.1000 0.0000 0.0000 0.0000 0.0000 0.1000 0.5566 0.5566 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.5564 0.5564 0.0 Brute Force -------------------------- Min cost was 0.556434 Number of iterations 729 Search time 1.247000 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 = 0.579214 7 -0.193 0.000 0.000 0.000 0.000 0.000 0.5785394596 8 -0.180 0.000 0.000 0.000 0.000 0.000 0.5785387001 9 -0.185 0.000 0.000 0.000 0.000 0.000 0.5785378815 18 -0.186 0.173 0.000 0.000 0.000 0.000 0.5778941692 19 -0.186 0.172 0.000 0.000 0.000 0.000 0.5778931169 20 -0.186 0.154 0.000 0.000 0.000 0.000 0.5778803324 23 -0.186 0.150 0.000 0.000 0.000 0.000 0.5778795570 30 -0.186 0.150 -0.618 0.000 0.000 0.000 0.5777482920 32 -0.186 0.150 -0.313 0.000 0.000 0.000 0.5755448010 40 -0.186 0.150 -0.313 0.382 0.000 0.000 0.5744852138 41 -0.186 0.150 -0.313 0.263 0.000 0.000 0.5740733648 43 -0.186 0.150 -0.313 0.260 0.000 0.000 0.5740731013 53 -0.186 0.150 -0.313 0.261 0.021 0.000 0.5740669090 54 -0.186 0.150 -0.313 0.261 0.016 0.000 0.5740656978 55 -0.186 0.150 -0.313 0.261 0.015 0.000 0.5740656582 63 -0.186 0.150 -0.313 0.261 0.015 0.008 0.5740642167 64 -0.186 0.150 -0.313 0.261 0.015 0.012 0.5740641659 65 -0.186 0.150 -0.313 0.261 0.015 0.010 0.5740640469 66 -0.186 0.150 -0.313 0.261 0.015 0.011 0.5740640179 powell nthiter 1: fret = 0.574064 75 -0.187 0.150 -0.313 0.261 0.015 0.011 0.5740638824 76 -0.188 0.150 -0.313 0.261 0.015 0.011 0.5740638551 85 -0.188 0.179 -0.313 0.261 0.015 0.011 0.5740280208 86 -0.188 0.191 -0.313 0.261 0.015 0.011 0.5740272301 87 -0.188 0.186 -0.313 0.261 0.015 0.011 0.5740266745 96 -0.188 0.187 -0.333 0.261 0.015 0.011 0.5740154528 98 -0.188 0.187 -0.332 0.261 0.015 0.011 0.5740154062 108 -0.188 0.187 -0.332 0.259 0.015 0.011 0.5740148414 109 -0.188 0.187 -0.332 0.256 0.015 0.011 0.5740147631 111 -0.188 0.187 -0.332 0.257 0.015 0.011 0.5740146702 119 -0.188 0.187 -0.332 0.257 0.016 0.011 0.5740144660 128 -0.188 0.187 -0.332 0.257 0.016 0.030 0.5740125793 130 -0.188 0.187 -0.332 0.257 0.016 0.023 0.5740120468 131 -0.188 0.187 -0.332 0.257 0.016 0.024 0.5740118644 powell nthiter 2: fret = 0.574012 150 -0.186 0.193 -0.332 0.257 0.016 0.024 0.5740117660 152 -0.186 0.190 -0.332 0.257 0.016 0.024 0.5740115897 161 -0.186 0.190 -0.334 0.257 0.016 0.024 0.5740112573 162 -0.186 0.190 -0.335 0.257 0.016 0.024 0.5740112480 182 -0.186 0.190 -0.335 0.258 0.015 0.024 0.5740111742 powell nthiter 3: fret = 0.574011 202 -0.187 0.190 -0.335 0.258 0.015 0.024 0.5740111691 221 -0.187 0.190 -0.334 0.258 0.015 0.024 0.5740111675 231 -0.187 0.190 -0.334 0.257 0.015 0.024 0.5740111384 Powell done niters = 3 Computing relative cost 0 -25.0 -25.0 -25.0 1.037216 1 -25.0 -25.0 25.0 1.049973 2 -25.0 25.0 -25.0 1.054634 3 -25.0 25.0 25.0 1.064042 4 25.0 -25.0 -25.0 1.036346 5 25.0 -25.0 25.0 1.028757 6 25.0 25.0 -25.0 1.017873 7 25.0 25.0 25.0 1.049921 REL: 8 0.574011 8.338762 1.042345 rel = 0.550692 Number of iterations 3 Min cost was 0.574011 Number of FunctionCalls 252 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 17.999000 sec Parameters at optimum (transmm) -0.18748 0.19035 -0.33419 Parameters at optimum (rotdeg) 0.25700 0.01547 0.02432 Final costs ---------------- Number of surface hits 304688 WM Intensity 819.4644 +/- 217.7484 Ctx Intensity 848.3369 +/- 249.6806 Pct Contrast 1.5360 +/- 21.7967 Cost 0.5740 RelCost 0.5559 Reg at min cost was 0.99969 -0.02448 -0.00431 -0.58571; -0.00187 -0.24691 0.96904 -41.06988; 0.02478 0.96873 0.24688 -1.91512; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/004/register.dof6.dat, type = 14 Original Reg 0.99968 -0.02484 -0.00397 -0.41532; -0.00218 -0.24255 0.97014 -41.26674; 0.02506 0.96982 0.24253 -1.39595; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00001 -0.00037 0.00034 0.17039; -0.00031 0.00436 0.00110 -0.19686; 0.00028 0.00109 -0.00435 0.51916; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.513493 Computing change in rh position Surface-RMS-Diff-mm 0.526881 0.123444 0.817693 mri_segreg done MinCost: 0.574011 819.464353 848.336910 1.535989 tkregister2_cmdl --mov bold/004/template.nii.gz --reg bold/004/register.dof6.dat --noedit --ltaout bold/004/register.dof6.lta tkregister_tcl /media/sda1/nmrclass/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume bold/004/template.nii.gz reg file bold/004/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 -------- 0.99969 -0.02448 -0.00431 -0.58571; -0.00187 -0.24691 0.96904 -41.06988; 0.02478 0.96873 0.24688 -1.91512; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: loading target /media/sda1/nmrclass/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/004/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 -------- 0.99969 -0.02448 -0.00431 -0.58571; -0.00187 -0.24691 0.96904 -41.06988; 0.02478 0.96873 0.24688 -1.91512; 0.00000 0.00000 0.00000 1.00000; Determinant -1 subject = fsf01anat RegMat --------------------------- 0.99969 -0.02448 -0.00431 -0.58571; -0.00187 -0.24691 0.96904 -41.06988; 0.02478 0.96873 0.24688 -1.91512; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Sun Sep 30 01:20:49 EDT 2018 Ended at Sun Sep 30 01:22:50 EDT 2018 BBR-Run-Time-Sec 121 bbregister Done To check results, run: tkregisterfv --mov bold/004/template.nii.gz --reg bold/004/register.dof6.lta --surfs Sun Sep 30 01:22:50 EDT 2018 register-sess completed sess01 Mask ------------------------ mkbrainmask-sess -maskstem brain -fsd bold -s sess01 -d /media/sda1/nmrclass/tutorial_data/fsfast-functional -per-run -update ------------------------------------------------ /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01 Sun Sep 30 01:22:50 EDT 2018 mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -reg /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/register.dof6.lta -ndil 1 -nerode 0 Sun Sep 30 01:22:51 EDT 2018 setenv SUBJECTS_DIR /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects cd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold /media/sda1/nmrclass/freesurfer/fsfast/bin/mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -reg /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/register.dof6.lta -ndil 1 -nerode 0 freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-tutorial-2beb96c $Id: mkbrainmask,v 1.17 2015/12/10 22:51:30 zkaufman Exp $ Linux fsuser3-G5-5587 4.15.0-34-generic #37-Ubuntu SMP Mon Aug 27 15:21:48 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux mri_vol2vol --mov template.nii.gz --reg /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/register.dof6.lta --inv --interp nearest --o masks/brain.nii.gz --targ /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/aparc+aseg.mgz regio_read_register: loading lta Matrix from regfile: 0.99999 0.00268 -0.00300 0.72231; 0.00352 -0.22242 0.97494 -40.39471; -0.00195 0.97495 0.22243 -1.18300; 0.00000 0.00000 0.00000 1.00000; movvol template.nii.gz targvol /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/aparc+aseg.mgz outvol masks/brain.nii.gz regfile /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/register.dof6.lta invert 1 tal 0 talres 2 regheader 0 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1538873989 Invert! Inverting registration Final tkRAS-to-tkRAS Matrix is: 0.99999 0.00352 -0.00195 -0.58232; 0.00268 -0.22242 0.97495 -7.83319; -0.00300 0.97494 0.22243 39.64790; -0.00000 -0.00000 -0.00000 1.00000; Vox2Vox Matrix is: 3.43747 -0.00669 -0.01761 19.06136; -0.01032 0.76460 -4.87472 137.33600; -0.00921 -3.35138 -1.11210 244.38734; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_binarize --i masks/brain.nii.gz --o masks/brain.nii.gz --min 0.5 $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold cmdline mri_binarize.bin --i masks/brain.nii.gz --o masks/brain.nii.gz --min 0.5 sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass input masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 24188 values in range Counting number of voxels in first frame Found 24188 voxels in final mask Count: 24188 1429076.079605 122880 19.684245 mri_binarize done Diliating 1 mri_binarize --i masks/brain.nii.gz --min 0.5 --dilate 1 --o masks/brain.nii.gz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold cmdline mri_binarize.bin --i masks/brain.nii.gz --min 0.5 --dilate 1 --o masks/brain.nii.gz sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass input masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 24188 values in range Dilating 1 voxels in 3d Counting number of voxels in first frame Found 35032 voxels in final mask Count: 35032 2069761.585114 122880 28.509115 mri_binarize done Started at Sun Sep 30 01:22:51 EDT 2018 Ended at Sun Sep 30 01:22:52 EDT 2018 Mkbrainmask-Run-Time-Sec 1 mkbrainmask Done mri_binarize --i masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o masks/brain.e3.nii.gz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold cmdline mri_binarize.bin --i masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o masks/brain.e3.nii.gz sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass input masks/brain.nii.gz frame 0 nErode3d 3 nErode2d 0 output masks/brain.e3.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 34360 values in range Eroding 3 voxels in 3d Counting number of voxels in first frame Found 13946 voxels in final mask Count: 13946 823957.954613 122880 11.349284 mri_binarize done mkbrainmask -i 001/template.nii.gz -o 001/masks/brain.nii.gz -reg /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/001/register.dof6.lta -ndil 1 -nerode 0 Sun Sep 30 01:22:53 EDT 2018 setenv SUBJECTS_DIR /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects cd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold /media/sda1/nmrclass/freesurfer/fsfast/bin/mkbrainmask -i 001/template.nii.gz -o 001/masks/brain.nii.gz -reg /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/001/register.dof6.lta -ndil 1 -nerode 0 freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-tutorial-2beb96c $Id: mkbrainmask,v 1.17 2015/12/10 22:51:30 zkaufman Exp $ Linux fsuser3-G5-5587 4.15.0-34-generic #37-Ubuntu SMP Mon Aug 27 15:21:48 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux mri_vol2vol --mov 001/template.nii.gz --reg /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/001/register.dof6.lta --inv --interp nearest --o 001/masks/brain.nii.gz --targ /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/aparc+aseg.mgz regio_read_register: loading lta Matrix from regfile: 1.00000 -0.00051 -0.00113 0.57201; 0.00098 -0.23948 0.97090 -40.53648; 0.00076 0.97090 0.23948 -1.36292; 0.00000 0.00000 0.00000 1.00000; movvol 001/template.nii.gz targvol /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/aparc+aseg.mgz outvol 001/masks/brain.nii.gz regfile /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/001/register.dof6.lta invert 1 tal 0 talres 2 regheader 0 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1538978735 Invert! Inverting registration Final tkRAS-to-tkRAS Matrix is: 1.00000 0.00098 0.00076 -0.53141; -0.00051 -0.23948 0.97090 -8.38411; -0.00113 0.97090 0.23948 39.68396; -0.00000 -0.00000 -0.00000 1.00000; Vox2Vox Matrix is: 3.43750 0.00263 -0.00488 18.52054; -0.00389 0.82321 -4.85451 134.91533; 0.00175 -3.33747 -1.19740 244.32001; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_binarize --i 001/masks/brain.nii.gz --o 001/masks/brain.nii.gz --min 0.5 $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold cmdline mri_binarize.bin --i 001/masks/brain.nii.gz --o 001/masks/brain.nii.gz --min 0.5 sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass input 001/masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output 001/masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 24282 values in range Counting number of voxels in first frame Found 24282 voxels in final mask Count: 24282 1434629.790184 122880 19.760742 mri_binarize done Diliating 1 mri_binarize --i 001/masks/brain.nii.gz --min 0.5 --dilate 1 --o 001/masks/brain.nii.gz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold cmdline mri_binarize.bin --i 001/masks/brain.nii.gz --min 0.5 --dilate 1 --o 001/masks/brain.nii.gz sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass input 001/masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output 001/masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 24282 values in range Dilating 1 voxels in 3d Counting number of voxels in first frame Found 35036 voxels in final mask Count: 35036 2069997.913223 122880 28.512370 mri_binarize done Started at Sun Sep 30 01:22:53 EDT 2018 Ended at Sun Sep 30 01:22:54 EDT 2018 Mkbrainmask-Run-Time-Sec 1 mkbrainmask Done mri_binarize --i 001/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 001/masks/brain.e3.nii.gz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold cmdline mri_binarize.bin --i 001/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 001/masks/brain.e3.nii.gz sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass input 001/masks/brain.nii.gz frame 0 nErode3d 3 nErode2d 0 output 001/masks/brain.e3.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 34360 values in range Eroding 3 voxels in 3d Counting number of voxels in first frame Found 13936 voxels in final mask Count: 13936 823367.134338 122880 11.341146 mri_binarize done mkbrainmask -i 002/template.nii.gz -o 002/masks/brain.nii.gz -reg /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/002/register.dof6.lta -ndil 1 -nerode 0 Sun Sep 30 01:22:55 EDT 2018 setenv SUBJECTS_DIR /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects cd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold /media/sda1/nmrclass/freesurfer/fsfast/bin/mkbrainmask -i 002/template.nii.gz -o 002/masks/brain.nii.gz -reg /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/002/register.dof6.lta -ndil 1 -nerode 0 freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-tutorial-2beb96c $Id: mkbrainmask,v 1.17 2015/12/10 22:51:30 zkaufman Exp $ Linux fsuser3-G5-5587 4.15.0-34-generic #37-Ubuntu SMP Mon Aug 27 15:21:48 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux mri_vol2vol --mov 002/template.nii.gz --reg /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/002/register.dof6.lta --inv --interp nearest --o 002/masks/brain.nii.gz --targ /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/aparc+aseg.mgz regio_read_register: loading lta Matrix from regfile: 0.99998 -0.00250 0.00647 0.19577; -0.00689 -0.25597 0.96666 -40.69115; 0.00076 0.96668 0.25598 -1.83958; 0.00000 0.00000 0.00000 1.00000; movvol 002/template.nii.gz targvol /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/aparc+aseg.mgz outvol 002/masks/brain.nii.gz regfile /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/002/register.dof6.lta invert 1 tal 0 talres 2 regheader 0 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1538829089 Invert! Inverting registration Final tkRAS-to-tkRAS Matrix is: 0.99998 -0.00689 0.00076 -0.47481; -0.00250 -0.25597 0.96668 -8.63701; 0.00647 0.96666 0.25598 39.80412; -0.00000 -0.00000 -0.00000 1.00000; Vox2Vox Matrix is: 3.43742 0.00262 0.03446 17.87655; 0.02223 0.87994 -4.83330 131.82587; 0.00860 -3.32297 -1.27986 244.62051; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_binarize --i 002/masks/brain.nii.gz --o 002/masks/brain.nii.gz --min 0.5 $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold cmdline mri_binarize.bin --i 002/masks/brain.nii.gz --o 002/masks/brain.nii.gz --min 0.5 sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass input 002/masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output 002/masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 24283 values in range Counting number of voxels in first frame Found 24283 voxels in final mask Count: 24283 1434688.872211 122880 19.761556 mri_binarize done Diliating 1 mri_binarize --i 002/masks/brain.nii.gz --min 0.5 --dilate 1 --o 002/masks/brain.nii.gz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold cmdline mri_binarize.bin --i 002/masks/brain.nii.gz --min 0.5 --dilate 1 --o 002/masks/brain.nii.gz sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass input 002/masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output 002/masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 24283 values in range Dilating 1 voxels in 3d Counting number of voxels in first frame Found 35048 voxels in final mask Count: 35048 2070706.897552 122880 28.522135 mri_binarize done Started at Sun Sep 30 01:22:55 EDT 2018 Ended at Sun Sep 30 01:22:56 EDT 2018 Mkbrainmask-Run-Time-Sec 1 mkbrainmask Done mri_binarize --i 002/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 002/masks/brain.e3.nii.gz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold cmdline mri_binarize.bin --i 002/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 002/masks/brain.e3.nii.gz sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass input 002/masks/brain.nii.gz frame 0 nErode3d 3 nErode2d 0 output 002/masks/brain.e3.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 34376 values in range Eroding 3 voxels in 3d Counting number of voxels in first frame Found 13880 voxels in final mask Count: 13880 820058.540802 122880 11.295573 mri_binarize done mkbrainmask -i 003/template.nii.gz -o 003/masks/brain.nii.gz -reg /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/003/register.dof6.lta -ndil 1 -nerode 0 Sun Sep 30 01:22:57 EDT 2018 setenv SUBJECTS_DIR /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects cd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold /media/sda1/nmrclass/freesurfer/fsfast/bin/mkbrainmask -i 003/template.nii.gz -o 003/masks/brain.nii.gz -reg /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/003/register.dof6.lta -ndil 1 -nerode 0 freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-tutorial-2beb96c $Id: mkbrainmask,v 1.17 2015/12/10 22:51:30 zkaufman Exp $ Linux fsuser3-G5-5587 4.15.0-34-generic #37-Ubuntu SMP Mon Aug 27 15:21:48 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux mri_vol2vol --mov 003/template.nii.gz --reg /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/003/register.dof6.lta --inv --interp nearest --o 003/masks/brain.nii.gz --targ /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/aparc+aseg.mgz regio_read_register: loading lta Matrix from regfile: 0.99983 -0.01825 0.00009 -0.42357; -0.00480 -0.25833 0.96604 -41.01878; 0.01760 0.96588 0.25838 -1.98164; 0.00000 0.00000 0.00000 1.00000; movvol 003/template.nii.gz targvol /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/aparc+aseg.mgz outvol 003/masks/brain.nii.gz regfile /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/003/register.dof6.lta invert 1 tal 0 talres 2 regheader 0 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1538757203 Invert! Inverting registration Final tkRAS-to-tkRAS Matrix is: 0.99983 -0.00480 0.01760 0.26151; -0.01825 -0.25833 0.96588 -8.69022; 0.00009 0.96604 0.25838 40.13798; -0.00000 -0.00000 -0.00000 1.00000; Vox2Vox Matrix is: 3.43693 0.06051 0.02400 15.46057; 0.00030 0.88817 -4.83022 131.88400; 0.06272 -3.32022 -1.29167 242.92496; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_binarize --i 003/masks/brain.nii.gz --o 003/masks/brain.nii.gz --min 0.5 $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold cmdline mri_binarize.bin --i 003/masks/brain.nii.gz --o 003/masks/brain.nii.gz --min 0.5 sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass input 003/masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output 003/masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 24347 values in range Counting number of voxels in first frame Found 24347 voxels in final mask Count: 24347 1438470.121967 122880 19.813639 mri_binarize done Diliating 1 mri_binarize --i 003/masks/brain.nii.gz --min 0.5 --dilate 1 --o 003/masks/brain.nii.gz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold cmdline mri_binarize.bin --i 003/masks/brain.nii.gz --min 0.5 --dilate 1 --o 003/masks/brain.nii.gz sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass input 003/masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output 003/masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 24347 values in range Dilating 1 voxels in 3d Counting number of voxels in first frame Found 35050 voxels in final mask Count: 35050 2070825.061607 122880 28.523763 mri_binarize done Started at Sun Sep 30 01:22:57 EDT 2018 Ended at Sun Sep 30 01:22:58 EDT 2018 Mkbrainmask-Run-Time-Sec 1 mkbrainmask Done mri_binarize --i 003/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 003/masks/brain.e3.nii.gz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold cmdline mri_binarize.bin --i 003/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 003/masks/brain.e3.nii.gz sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass input 003/masks/brain.nii.gz frame 0 nErode3d 3 nErode2d 0 output 003/masks/brain.e3.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 34362 values in range Eroding 3 voxels in 3d Counting number of voxels in first frame Found 13952 voxels in final mask Count: 13952 824312.446777 122880 11.354167 mri_binarize done mkbrainmask -i 004/template.nii.gz -o 004/masks/brain.nii.gz -reg /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/004/register.dof6.lta -ndil 1 -nerode 0 Sun Sep 30 01:22:59 EDT 2018 setenv SUBJECTS_DIR /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects cd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold /media/sda1/nmrclass/freesurfer/fsfast/bin/mkbrainmask -i 004/template.nii.gz -o 004/masks/brain.nii.gz -reg /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/004/register.dof6.lta -ndil 1 -nerode 0 freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-tutorial-2beb96c $Id: mkbrainmask,v 1.17 2015/12/10 22:51:30 zkaufman Exp $ Linux fsuser3-G5-5587 4.15.0-34-generic #37-Ubuntu SMP Mon Aug 27 15:21:48 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux mri_vol2vol --mov 004/template.nii.gz --reg /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/004/register.dof6.lta --inv --interp nearest --o 004/masks/brain.nii.gz --targ /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/aparc+aseg.mgz regio_read_register: loading lta Matrix from regfile: 0.99969 -0.02448 -0.00431 -0.58571; -0.00187 -0.24691 0.96904 -41.06988; 0.02478 0.96873 0.24688 -1.91511; 0.00000 0.00000 0.00000 1.00000; movvol 004/template.nii.gz targvol /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/aparc+aseg.mgz outvol 004/masks/brain.nii.gz regfile /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/004/register.dof6.lta invert 1 tal 0 talres 2 regheader 0 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1538590017 Invert! Inverting registration Final tkRAS-to-tkRAS Matrix is: 0.99969 -0.00187 0.02478 0.55637; -0.02448 -0.24691 0.96873 -8.29958; -0.00431 0.96904 0.24688 40.26850; -0.00000 -0.00000 -0.00000 1.00000; Vox2Vox Matrix is: 3.43644 0.08520 0.00933 14.61147; -0.01482 0.84864 -4.84518 133.72714; 0.08414 -3.33001 -1.23454 242.08621; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_binarize --i 004/masks/brain.nii.gz --o 004/masks/brain.nii.gz --min 0.5 $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold cmdline mri_binarize.bin --i 004/masks/brain.nii.gz --o 004/masks/brain.nii.gz --min 0.5 sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass input 004/masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output 004/masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 24267 values in range Counting number of voxels in first frame Found 24267 voxels in final mask Count: 24267 1433743.559772 122880 19.748535 mri_binarize done Diliating 1 mri_binarize --i 004/masks/brain.nii.gz --min 0.5 --dilate 1 --o 004/masks/brain.nii.gz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold cmdline mri_binarize.bin --i 004/masks/brain.nii.gz --min 0.5 --dilate 1 --o 004/masks/brain.nii.gz sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass input 004/masks/brain.nii.gz frame 0 nErode3d 0 nErode2d 0 output 004/masks/brain.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 24267 values in range Dilating 1 voxels in 3d Counting number of voxels in first frame Found 34978 voxels in final mask Count: 34978 2066571.155632 122880 28.465169 mri_binarize done Started at Sun Sep 30 01:22:59 EDT 2018 Ended at Sun Sep 30 01:23:00 EDT 2018 Mkbrainmask-Run-Time-Sec 1 mkbrainmask Done mri_binarize --i 004/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 004/masks/brain.e3.nii.gz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold cmdline mri_binarize.bin --i 004/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 004/masks/brain.e3.nii.gz sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass input 004/masks/brain.nii.gz frame 0 nErode3d 3 nErode2d 0 output 004/masks/brain.e3.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 34288 values in range Eroding 3 voxels in 3d Counting number of voxels in first frame Found 13871 voxels in final mask Count: 13871 819526.802555 122880 11.288249 mri_binarize done meanval --i 001/f.nii.gz --m 001/masks/brain.e3.nii.gz --o 001/global.meanval.dat --avgwf 001/global.waveform.dat Sun Sep 30 01:23:00 EDT 2018 setenv SUBJECTS_DIR /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects cd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold /media/sda1/nmrclass/freesurfer/bin/meanval --i 001/f.nii.gz --m 001/masks/brain.e3.nii.gz --o 001/global.meanval.dat --avgwf 001/global.waveform.dat freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-tutorial-2beb96c Linux fsuser3-G5-5587 4.15.0-34-generic #37-Ubuntu SMP Mon Aug 27 15:21:48 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux mri_segstats --seg 001/masks/brain.e3.nii.gz --id 1 --sum /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/001/tmpdir.meanval.29232/blah.29232 --in 001/f.nii.gz --sfavg 001/global.meanval.dat --avgwf 001/global.waveform.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --seg 001/masks/brain.e3.nii.gz --id 1 --sum /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/001/tmpdir.meanval.29232/blah.29232 --in 001/f.nii.gz --sfavg 001/global.meanval.dat --avgwf 001/global.waveform.dat sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass UseRobust 0 Loading 001/masks/brain.e3.nii.gz Loading 001/f.nii.gz Voxel Volume is 59.082 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to 001/global.meanval.dat 0 866.272 Writing to 001/global.waveform.dat mri_segstats done meanval --i 002/f.nii.gz --m 002/masks/brain.e3.nii.gz --o 002/global.meanval.dat --avgwf 002/global.waveform.dat Sun Sep 30 01:23:02 EDT 2018 setenv SUBJECTS_DIR /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects cd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold /media/sda1/nmrclass/freesurfer/bin/meanval --i 002/f.nii.gz --m 002/masks/brain.e3.nii.gz --o 002/global.meanval.dat --avgwf 002/global.waveform.dat freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-tutorial-2beb96c Linux fsuser3-G5-5587 4.15.0-34-generic #37-Ubuntu SMP Mon Aug 27 15:21:48 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux mri_segstats --seg 002/masks/brain.e3.nii.gz --id 1 --sum /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/002/tmpdir.meanval.29275/blah.29275 --in 002/f.nii.gz --sfavg 002/global.meanval.dat --avgwf 002/global.waveform.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --seg 002/masks/brain.e3.nii.gz --id 1 --sum /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/002/tmpdir.meanval.29275/blah.29275 --in 002/f.nii.gz --sfavg 002/global.meanval.dat --avgwf 002/global.waveform.dat sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass UseRobust 0 Loading 002/masks/brain.e3.nii.gz Loading 002/f.nii.gz Voxel Volume is 59.082 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to 002/global.meanval.dat 0 863.584 Writing to 002/global.waveform.dat mri_segstats done meanval --i 003/f.nii.gz --m 003/masks/brain.e3.nii.gz --o 003/global.meanval.dat --avgwf 003/global.waveform.dat Sun Sep 30 01:23:03 EDT 2018 setenv SUBJECTS_DIR /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects cd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold /media/sda1/nmrclass/freesurfer/bin/meanval --i 003/f.nii.gz --m 003/masks/brain.e3.nii.gz --o 003/global.meanval.dat --avgwf 003/global.waveform.dat freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-tutorial-2beb96c Linux fsuser3-G5-5587 4.15.0-34-generic #37-Ubuntu SMP Mon Aug 27 15:21:48 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux mri_segstats --seg 003/masks/brain.e3.nii.gz --id 1 --sum /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/003/tmpdir.meanval.29317/blah.29317 --in 003/f.nii.gz --sfavg 003/global.meanval.dat --avgwf 003/global.waveform.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --seg 003/masks/brain.e3.nii.gz --id 1 --sum /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/003/tmpdir.meanval.29317/blah.29317 --in 003/f.nii.gz --sfavg 003/global.meanval.dat --avgwf 003/global.waveform.dat sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass UseRobust 0 Loading 003/masks/brain.e3.nii.gz Loading 003/f.nii.gz Voxel Volume is 59.082 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to 003/global.meanval.dat 0 863.342 Writing to 003/global.waveform.dat mri_segstats done meanval --i 004/f.nii.gz --m 004/masks/brain.e3.nii.gz --o 004/global.meanval.dat --avgwf 004/global.waveform.dat Sun Sep 30 01:23:05 EDT 2018 setenv SUBJECTS_DIR /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects cd /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold /media/sda1/nmrclass/freesurfer/bin/meanval --i 004/f.nii.gz --m 004/masks/brain.e3.nii.gz --o 004/global.meanval.dat --avgwf 004/global.waveform.dat freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-tutorial-2beb96c Linux fsuser3-G5-5587 4.15.0-34-generic #37-Ubuntu SMP Mon Aug 27 15:21:48 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux mri_segstats --seg 004/masks/brain.e3.nii.gz --id 1 --sum /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/004/tmpdir.meanval.29359/blah.29359 --in 004/f.nii.gz --sfavg 004/global.meanval.dat --avgwf 004/global.waveform.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --seg 004/masks/brain.e3.nii.gz --id 1 --sum /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/004/tmpdir.meanval.29359/blah.29359 --in 004/f.nii.gz --sfavg 004/global.meanval.dat --avgwf 004/global.waveform.dat sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass UseRobust 0 Loading 004/masks/brain.e3.nii.gz Loading 004/f.nii.gz Voxel Volume is 59.082 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to 004/global.meanval.dat 0 864.522 Writing to 004/global.waveform.dat mri_segstats done Sun Sep 30 01:23:06 EDT 2018 mkbrainmask-sess done sess01 MC ----------------------------- mc-sess -fstem f -fmcstem fmcpr -s sess01 -d /media/sda1/nmrclass/tutorial_data/fsfast-functional -fsd bold -per-run -update Logfile is /media/sda1/nmrclass/tutorial_data/fsfast-functional/log/mc-sess01-bold.log ------------------------------------------- /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01 RunList: 001 002 003 004 sess01 001 Update not needed sess01 002 Update not needed sess01 003 Update not needed sess01 004 Update not needed Sun Sep 30 01:23:08 EDT 2018 mc-sess completed SUCCESSFULLY sess01 STC ----------------------------- stc-sess -i fmcpr -o fmcpr.up -ngroups 1 -so up -s sess01 -d /media/sda1/nmrclass/tutorial_data/fsfast-functional -fsd bold -update Sun Sep 30 01:23:08 EDT 2018 /media/sda1/nmrclass/tutorial_data/fsfast-functional /media/sda1/nmrclass/freesurfer/fsfast/bin/stc-sess -i fmcpr -o fmcpr.up -ngroups 1 -so up -s sess01 -d /media/sda1/nmrclass/tutorial_data/fsfast-functional -fsd bold -update $Id: stc-sess,v 1.13 2015/12/10 22:51:31 zkaufman Exp $ fsuser3-G5-5587 sess01 ----------------- Sun Sep 30 01:23:09 EDT 2018 --------------------------------------------- /media/sda1/nmrclass/tutorial_data/fsfast-functional stc.fsl --i /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/001/fmcpr.nii.gz --o /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/001/fmcpr.up.nii.gz --ngroups 1 --up Sun Sep 30 01:23:09 EDT 2018 /media/sda1/nmrclass/tutorial_data/fsfast-functional /media/sda1/nmrclass/freesurfer/fsfast/bin/stc.fsl --i /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/001/fmcpr.nii.gz --o /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/001/fmcpr.up.nii.gz --ngroups 1 --up $Id: stc.fsl,v 1.11 2015/12/10 22:51:31 zkaufman Exp $ fsuser3-G5-5587 /media/sda1/nmrclass/tutorial_data/fsfast-functional mri_info --nslices --o /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/001/tmp.29512/nslices.dat /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/001/fmcpr.nii.gz nslices = 30 slicedelay --nslices 30 --up --o /media/sda1/nmrclass/tutorial_data/fsfast-functional/sess01/bold/001/tmp.29512/sdf.txt --ngroups 1 slicedelay: Command not found.