selxavg3-sess log file /usr/local/freesurfer/dev/fsfast/bin/selxavg3-sess -s sess01 -analysis workmem.sm05.lh $Id: selxavg3-sess,v 1.67 2015/12/10 22:51:30 zkaufman Exp $ uid=8481(zkaufman) gid=8481(zkaufman) groups=8481(zkaufman),160(fsdev),1046(recon),1538(lcnweb),1590(fsbuild),1601(b40atlas) /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional Linux transfer 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Sun Mar 27 21:37:16 EDT 2016 preproc-sess -s sess01 -d /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional -a workmem.sm05.lh -nolog -------------------------------------------------------------- preproc-sess logfile is /dev/null -------------------------------------------------------------- $Id: preproc-sess,v 1.64 2015/12/10 22:51:30 zkaufman Exp $ zkaufman setenv FREESURFER_HOME /usr/local/freesurfer/dev setenv SUBJECTS_DIR /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects Linux transfer 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional /usr/local/freesurfer/dev/fsfast/bin/preproc-sess -s sess01 -d /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional -a workmem.sm05.lh -nolog Sun Mar 27 21:37:16 EDT 2016 instem f mc 1 f fmcpr stc 1 fmcpr fmcpr.up sm 0 mask 1 brain sess01 Template ----------------------------- mktemplate-sess -s sess01 -d /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional -fsd bold -nolog -update Session: /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01 ---------------- Sun Mar 27 21:37:16 EDT 2016 Detected input format at nii.gz /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional mri_convert /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/f.nii.gz /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/template.nii.gz --frame 0 mri_convert.bin /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/f.nii.gz /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/template.nii.gz --frame 0 $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/f.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) keeping frame 0 writing to /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/template.nii.gz... Run: 001 ---------------- Sun Mar 27 21:37:19 EDT 2016 /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional mri_convert /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/f.nii.gz /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/template.nii.gz --mid-frame mri_convert.bin /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/f.nii.gz /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/template.nii.gz --mid-frame $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/f.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) keeping frame 71 writing to /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/template.nii.gz... Run: 002 ---------------- Sun Mar 27 21:37:21 EDT 2016 /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional mri_convert /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/f.nii.gz /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/template.nii.gz --mid-frame mri_convert.bin /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/f.nii.gz /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/template.nii.gz --mid-frame $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/f.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) keeping frame 71 writing to /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/template.nii.gz... Run: 003 ---------------- Sun Mar 27 21:37:23 EDT 2016 /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional mri_convert /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/f.nii.gz /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/template.nii.gz --mid-frame mri_convert.bin /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/f.nii.gz /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/template.nii.gz --mid-frame $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/f.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) keeping frame 71 writing to /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/template.nii.gz... Run: 004 ---------------- Sun Mar 27 21:37:25 EDT 2016 /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional mri_convert /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/f.nii.gz /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/template.nii.gz --mid-frame mri_convert.bin /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/f.nii.gz /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/template.nii.gz --mid-frame $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/f.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) keeping frame 71 writing to /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/template.nii.gz... Sun Mar 27 21:37:27 EDT 2016 mktemplate-sess completed sess01 Registration ----------------------------- register-sess -s sess01 -d /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional -fsd bold -delete-dat -dof 6 -bold -per-run -nolog -update -init-coreg -------------------------------------------------------------- register-sess logfile is /dev/null -------------------------------------------------------------- Sun Mar 27 21:37:27 EDT 2016 setenv SUBJECTS_DIR /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects cd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional /usr/local/freesurfer/dev/fsfast/bin/register-sess -s sess01 -d /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional -fsd bold -delete-dat -dof 6 -bold -per-run -nolog -update -init-coreg freesurfer-Linux-centos6_x86_64-dev-20160325 Linux transfer 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Session: /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01 ---------------- Sun Mar 27 21:37:27 EDT 2016 -------------------------------------- /autofs/cluster/pubftp/data/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.6365 Log file is bold/register.dof6.dat.log Sun Mar 27 21:37:27 EDT 2016 setenv SUBJECTS_DIR /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects cd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01 /usr/local/freesurfer/dev/bin/bbregister --s fsf01anat --init-coreg --6 --bold --mov bold/template.nii.gz --reg bold/register.dof6.dat --lta bold/register.dof6.lta --init-reg-out bold/init.register.dof6.dat $Id: bbregister,v 1.74 2016/02/17 21:07:31 greve Exp $ Linux transfer 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer/dev mri_convert bold/template.nii.gz bold/tmp.bbregister.6365/template.nii mri_convert.bin bold/template.nii.gz bold/tmp.bbregister.6365/template.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from bold/template.nii.gz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.973976, -0.226651) k_ras = (-2.36491e-18, -0.226651, 0.973976) writing to bold/tmp.bbregister.6365/template.nii... mri_coreg --s fsf01anat --mov bold/tmp.bbregister.6365/template.nii --regdat bold/tmp.bbregister.6365/reg.init.dat --reg bold/tmp.bbregister.6365/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 freadFloat: fread failed $Id: mri_coreg.c,v 1.26 2016/01/20 23:42:39 greve Exp $ cwd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01 cmdline mri_coreg --s fsf01anat --mov bold/tmp.bbregister.6365/template.nii --regdat bold/tmp.bbregister.6365/reg.init.dat --reg bold/tmp.bbregister.6365/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 sysname Linux hostname transfer machine x86_64 user zkaufman dof 6 nsep 1 cras0 1 ftol 0.000100 linmintol 0.010000 bf 1 bflim 30.000000 bfnsamp 30 SmoothRef 0 SatPct 99.990000 MovOOB 0 Reading in mov bold/tmp.bbregister.6365/template.nii Reading in ref /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/brainmask.mgz freadFloat: fread failed Reading in and applying refmask /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/aparc+aseg.mgz Setting cras translation parameters to align centers Creating random numbers for coordinate dithering Performing intensity dithering Initial parameters -6.0223 -45.2577 79.2380 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Separation list (1): 4 min = 4 DoSmoothing 1 DoCoordDither 1 DoIntensityDither 1 nitersmax 4 ftol 1.000e-04 linmintol 1.000e-02 SatPct 99.990000 Hist FWHM 7.000000 7.000000 nthreads 1 movsat = 1823.3334 mov gstd 0.9989 0.9989 0.0000 Smoothing mov refsat = 118.0000 ref gstd 1.8914 1.8914 1.8914 Smoothing ref COREGpreproc() done Testing if mov and target overlap Init cost -1.0212885186 nhits = 106280 out of 16777216, Percent Overlap: 40.5 Initial RefRAS-to-MovRAS 1.00000 0.00000 0.00000 -6.02228; 0.00000 1.00000 0.00000 -45.25770; 0.00000 0.00000 1.00000 79.23798; 0.00000 0.00000 0.00000 1.00000; Initial RefVox-to-MovVox 0.29091 -0.00000 -0.00000 -5.59091; -0.00000 0.06593 -0.28334 59.21896; 0.00000 -0.19480 -0.04533 45.11600; 0.00000 0.00000 0.00000 1.00000; sep = 4 ----------------------------------- COREGoptBruteForce() 30 1 30 Turning on MovOOB for BruteForce Search #BF# sep= 4 iter=0 lim=30.0 delta=2.00 -6.02228 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0505087 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6 Starting OpenPowel2(), sep = 4 InitialCost -1.0720660686 #@# 4 188 -6.02228 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0720661 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.072066 #@# 4 193 -6.64031 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0720886 #@# 4 195 -6.38299 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0721114 #@# 4 197 -6.30410 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0721116 #@# 4 199 -6.33944 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0721121 #@# 4 204 -6.34944 -36.87573 49.23798 4.00000 0.00000 0.00000 -1.0743937 #@# 4 207 -6.34944 -40.01580 49.23798 4.00000 0.00000 0.00000 -1.0761501 #@# 4 209 -6.34944 -39.59603 49.23798 4.00000 0.00000 0.00000 -1.0762134 #@# 4 231 -6.34944 -39.59603 49.23798 3.38197 0.00000 0.00000 -1.0765741 #@# 4 233 -6.34944 -39.59603 49.23798 3.21876 0.00000 0.00000 -1.0765885 #@# 4 234 -6.34944 -39.59603 49.23798 3.22876 0.00000 0.00000 -1.0765890 #@# 4 235 -6.34944 -39.59603 49.23798 3.25060 0.00000 0.00000 -1.0765903 #@# 4 238 -6.34944 -39.59603 49.23798 3.24060 0.00000 0.00000 -1.0765922 #@# 4 244 -6.34944 -39.59603 49.23798 3.24060 0.38197 0.00000 -1.0765955 #@# 4 245 -6.34944 -39.59603 49.23798 3.24060 0.23124 0.00000 -1.0765957 #@# 4 246 -6.34944 -39.59603 49.23798 3.24060 0.29701 0.00000 -1.0765992 #@# 4 248 -6.34944 -39.59603 49.23798 3.24060 0.28701 0.00000 -1.0765996 #@# 4 250 -6.34944 -39.59603 49.23798 3.24060 0.27701 0.00000 -1.0766003 #@# 4 257 -6.34944 -39.59603 49.23798 3.24060 0.27701 -0.11474 -1.0766048 #@# 4 258 -6.34944 -39.59603 49.23798 3.24060 0.27701 -0.07780 -1.0766064 #@# 4 260 -6.34944 -39.59603 49.23798 3.24060 0.27701 -0.08780 -1.0766071 #@# 4 269 -6.37729 -39.96533 49.23798 3.17596 0.30059 -0.09528 -1.0766178 powell nthiter 1: fret = -1.076618 #@# 4 283 -6.38729 -39.96533 49.23798 3.17596 0.30059 -0.09528 -1.0766183 #@# 4 298 -6.38729 -39.96533 47.61994 3.17596 0.30059 -0.09528 -1.0766504 #@# 4 299 -6.38729 -39.96533 48.39967 3.17596 0.30059 -0.09528 -1.0768719 #@# 4 303 -6.38729 -39.96533 48.38255 3.17596 0.30059 -0.09528 -1.0768723 #@# 4 304 -6.38729 -39.96533 48.36356 3.17596 0.30059 -0.09528 -1.0768774 #@# 4 307 -6.38729 -39.96533 48.34749 3.17596 0.30059 -0.09528 -1.0768780 #@# 4 308 -6.38729 -39.96533 48.33749 3.17596 0.30059 -0.09528 -1.0768782 #@# 4 313 -6.38729 -39.96533 48.33749 2.55793 0.30059 -0.09528 -1.0771557 #@# 4 316 -6.38729 -39.96533 48.33749 2.53099 0.30059 -0.09528 -1.0771587 #@# 4 327 -6.38729 -39.96533 48.33749 2.53099 0.13331 -0.09528 -1.0771602 #@# 4 328 -6.38729 -39.96533 48.33749 2.53099 0.17348 -0.09528 -1.0771612 #@# 4 329 -6.38729 -39.96533 48.33749 2.53099 0.19911 -0.09528 -1.0771617 #@# 4 332 -6.38729 -39.96533 48.33749 2.53099 0.18911 -0.09528 -1.0771620 #@# 4 339 -6.40911 -40.25465 48.33749 2.48034 0.20758 -0.10113 -1.0771667 #@# 4 340 -6.40108 -40.14819 48.33749 2.49898 0.20078 -0.09898 -1.0771717 #@# 4 341 -6.39781 -40.10480 48.33749 2.50657 0.19801 -0.09810 -1.0771728 #@# 4 343 -6.44618 -40.61357 47.43700 1.77254 0.11902 -0.10840 -1.0776173 #@# 4 346 -6.52444 -41.43678 45.97999 0.58486 -0.00880 -0.12506 -1.0779318 #@# 4 354 -6.52554 -41.44830 45.95959 0.56824 -0.01059 -0.12529 -1.0779326 #@# 4 355 -6.52602 -41.45339 45.95059 0.56090 -0.01138 -0.12539 -1.0779327 powell nthiter 2: fret = -1.077933 #@# 4 381 -6.51602 -41.45339 45.33255 0.56090 -0.01138 -0.12539 -1.0781561 #@# 4 384 -6.51602 -41.45339 45.29290 0.56090 -0.01138 -0.12539 -1.0781580 #@# 4 385 -6.51602 -41.45339 45.28108 0.56090 -0.01138 -0.12539 -1.0781593 #@# 4 394 -6.46746 -40.80951 45.28108 0.67360 -0.05249 -0.11236 -1.0783229 #@# 4 395 -6.46302 -40.75062 45.28108 0.68391 -0.05625 -0.11117 -1.0783257 #@# 4 396 -6.45898 -40.69698 45.28108 0.69330 -0.05967 -0.11008 -1.0783294 #@# 4 400 -6.45570 -40.65359 45.28108 0.70090 -0.06244 -0.10921 -1.0783297 #@# 4 405 -6.45570 -40.65359 45.28108 0.70090 -0.68048 -0.10921 -1.0783579 #@# 4 407 -6.45570 -40.65359 45.28108 0.70090 -0.49850 -0.10921 -1.0783703 #@# 4 417 -6.47418 -40.84793 44.93712 0.42052 -0.52868 -0.11314 -1.0784123 #@# 4 418 -6.48349 -40.94590 44.76371 0.27916 -0.54389 -0.11512 -1.0784197 #@# 4 421 -6.48229 -40.93325 44.78611 0.29742 -0.54193 -0.11487 -1.0784198 powell nthiter 3: fret = -1.078420 #@# 4 439 -6.49229 -40.93325 44.78611 0.29742 -0.54193 -0.03213 -1.0784249 #@# 4 440 -6.49229 -40.93325 44.78611 0.29742 -0.54193 -0.04305 -1.0784262 #@# 4 441 -6.49229 -40.93325 44.78611 0.29742 -0.54193 -0.06127 -1.0784266 #@# 4 459 -6.48520 -40.83922 44.78611 0.31388 -0.54793 -0.05937 -1.0784274 #@# 4 479 -6.48980 -40.88761 44.70045 0.24406 -0.55544 -0.06035 -1.0784291 #@# 4 481 -6.48818 -40.87054 44.73068 0.26870 -0.55279 -0.06001 -1.0784304 Powell done niters total = 3 OptTimeSec 24.2 sec OptTimeMin 0.40 min nEvals 483 Final parameters -6.48817730 -40.87053680 44.73067856 0.26869830 -0.55279166 -0.06000530 Final cost -1.078430418798719 --------------------------------- mri_coreg utimesec 113.939678 mri_coreg stimesec 0.579911 mri_coreg ru_maxrss 422124 mri_coreg ru_ixrss 0 mri_coreg ru_idrss 0 mri_coreg ru_isrss 0 mri_coreg ru_minflt 265510 mri_coreg ru_majflt 0 mri_coreg ru_nswap 0 mri_coreg ru_inblock 0 mri_coreg ru_oublock 0 mri_coreg ru_msgsnd 0 mri_coreg ru_msgrcv 0 mri_coreg ru_nsignals 0 mri_coreg ru_nvcsw 129 mri_coreg ru_nivcsw 218 Final RefRAS-to-MovRAS 0.99995 -0.00105 -0.00965 -6.48818; 0.00109 0.99999 0.00469 -40.87054; 0.00964 -0.00470 0.99994 44.73068; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox 0.29090 -0.00281 0.00030 -5.20012; 0.00095 0.06726 -0.28303 59.97077; -0.00183 -0.19457 -0.04625 38.48653; 0.00000 0.00000 0.00000 1.00000; Final parameters -6.4882 -40.8705 44.7307 0.2687 -0.5528 -0.0600 nhits = 106099 out of 16777216, Percent Overlap: 40.5 mri_coreg RunTimeSec 114.6 sec To check run: tkregisterfv --mov bold/tmp.bbregister.6365/template.nii --targ /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/brainmask.mgz --reg bold/tmp.bbregister.6365/mri_coreg.lta --s fsf01anat --surfs mri_coreg done mri_segreg --mov bold/tmp.bbregister.6365/template.nii --init-reg bold/tmp.bbregister.6365/reg.init.dat --out-reg bold/tmp.bbregister.6365/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.112 2014/02/25 19:06:37 greve Exp $ setenv SUBJECTS_DIR /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects cd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01 mri_segreg --mov bold/tmp.bbregister.6365/template.nii --init-reg bold/tmp.bbregister.6365/reg.init.dat --out-reg bold/tmp.bbregister.6365/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Linux hostname transfer machine x86_64 user zkaufman movvol bold/tmp.bbregister.6365/template.nii regfile bold/tmp.bbregister.6365/reg.init.dat subject fsf01anat dof 6 outregfile bold/tmp.bbregister.6365/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1459543723 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99995 -0.00105 -0.00965 0.98232; 0.00914 -0.23123 0.97286 -37.86047; 0.00325 0.97290 0.23121 -1.62868; 0.00000 0.00000 0.00000 1.00000; Loading mov Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 1.083311 1 -25.0 -25.0 25.0 1.051309 2 -25.0 25.0 -25.0 1.054864 3 -25.0 25.0 25.0 1.081770 4 25.0 -25.0 -25.0 1.067926 5 25.0 -25.0 25.0 1.050873 6 25.0 25.0 -25.0 1.030024 7 25.0 25.0 25.0 1.084266 REL: 8 0.696003 8.504343 1.063043 rel = 0.654727 Initial costs ---------------- Number of surface hits 3040 WM Intensity 858.6377 +/- 209.8749 Ctx Intensity 868.9119 +/- 243.4205 Pct Contrast -0.6755 +/- 22.6146 Cost 0.6960 RelCost 0.6547 WARNING: initial G-W contrast is negative, but expecting positive. If the mov data has a T1 contrast, re-run with --T1 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 1.0755 1.0755 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 1.0629 1.0629 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 1.0062 1.0062 0.0 5 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 4.0000 0.9908 0.9908 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.9492 0.9492 0.0 18 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 -4.0000 0.9448 0.9448 0.0 30 -4.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.9355 0.9355 0.0 31 -4.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.9241 0.9241 0.0 33 -4.0000 -4.0000 0.0000 -4.0000 4.0000 -4.0000 0.9222 0.9222 0.0 34 -4.0000 -4.0000 0.0000 -4.0000 4.0000 0.0000 0.9048 0.9048 0.0 40 -4.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.8986 0.8986 0.0 273 0.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.8425 0.8425 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.7947 0.7947 0.0 282 0.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.7454 0.7454 0.0 283 0.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.6102 0.6102 0.0 Brute Force -------------------------- Min cost was 0.610218 Number of iterations 729 Search time 1.399000 sec Parameters at best (transmm, rotdeg) 0.000 -4.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 -4 2 0 3 0 4 0 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000100 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.610218 6 0.382 -4.000 0.000 0.000 0.000 0.000 0.6088949457 8 0.276 -4.000 0.000 0.000 0.000 0.000 0.6088196475 9 0.315 -4.000 0.000 0.000 0.000 0.000 0.6087799486 11 0.341 -4.000 0.000 0.000 0.000 0.000 0.6087733692 12 0.329 -4.000 0.000 0.000 0.000 0.000 0.6087612813 14 0.324 -4.000 0.000 0.000 0.000 0.000 0.6087549140 20 0.324 -3.000 0.000 0.000 0.000 0.000 0.5746081690 30 0.324 -3.021 0.000 0.000 0.000 0.000 0.5745843566 31 0.324 -3.034 0.000 0.000 0.000 0.000 0.5745490332 34 0.324 -3.036 0.000 0.000 0.000 0.000 0.5745438653 36 0.324 -3.037 0.000 0.000 0.000 0.000 0.5745411536 43 0.324 -3.037 -0.139 0.000 0.000 0.000 0.5745334091 44 0.324 -3.037 -0.071 0.000 0.000 0.000 0.5745215456 45 0.324 -3.037 -0.078 0.000 0.000 0.000 0.5745187304 46 0.324 -3.037 -0.096 0.000 0.000 0.000 0.5745154637 47 0.324 -3.037 -0.098 0.000 0.000 0.000 0.5745153552 49 0.324 -3.037 -0.099 0.000 0.000 0.000 0.5745153198 57 0.324 -3.037 -0.100 -0.201 0.000 0.000 0.5741958771 58 0.324 -3.037 -0.100 -0.168 0.000 0.000 0.5741640610 62 0.324 -3.037 -0.100 -0.169 0.000 0.000 0.5741637986 69 0.324 -3.037 -0.100 -0.169 0.382 0.000 0.5691101744 70 0.324 -3.037 -0.100 -0.169 0.459 0.000 0.5687130027 72 0.324 -3.037 -0.100 -0.169 0.443 0.000 0.5686866622 73 0.324 -3.037 -0.100 -0.169 0.444 0.000 0.5686864233 74 0.324 -3.037 -0.100 -0.169 0.445 0.000 0.5686863014 88 0.324 -3.037 -0.100 -0.169 0.445 0.027 0.5686260322 103 0.321 -3.045 -0.099 -0.167 0.441 0.027 0.5686241973 105 0.322 -3.043 -0.100 -0.168 0.443 0.027 0.5686235116 106 0.322 -3.042 -0.100 -0.168 0.443 0.027 0.5686234854 107 0.323 -3.041 -0.100 -0.168 0.443 0.027 0.5686229253 powell nthiter 1: fret = 0.568623 115 0.188 -3.041 -0.100 -0.168 0.443 0.027 0.5680738566 116 0.201 -3.041 -0.100 -0.168 0.443 0.027 0.5679567597 117 0.236 -3.041 -0.100 -0.168 0.443 0.027 0.5678070430 119 0.238 -3.041 -0.100 -0.168 0.443 0.027 0.5678052689 120 0.240 -3.041 -0.100 -0.168 0.443 0.027 0.5678035783 122 0.244 -3.041 -0.100 -0.168 0.443 0.027 0.5678028566 123 0.243 -3.041 -0.100 -0.168 0.443 0.027 0.5678027463 131 0.243 -3.041 -0.100 -0.168 0.443 0.114 0.5676332257 134 0.243 -3.041 -0.100 -0.168 0.443 0.108 0.5676315694 136 0.243 -3.041 -0.100 -0.168 0.443 0.107 0.5676315551 147 0.243 -3.041 -0.106 -0.168 0.443 0.107 0.5676297126 148 0.243 -3.041 -0.107 -0.168 0.443 0.107 0.5676291650 149 0.243 -3.041 -0.119 -0.168 0.443 0.107 0.5676270460 150 0.243 -3.041 -0.116 -0.168 0.443 0.107 0.5676261695 151 0.243 -3.041 -0.115 -0.168 0.443 0.107 0.5676260540 159 0.243 -3.041 -0.115 -0.029 0.443 0.107 0.5666409292 160 0.243 -3.041 -0.115 0.008 0.443 0.107 0.5666355895 161 0.243 -3.041 -0.115 -0.008 0.443 0.107 0.5666240413 164 0.243 -3.041 -0.115 -0.007 0.443 0.107 0.5666240305 172 0.243 -3.041 -0.115 -0.007 0.404 0.107 0.5665818302 173 0.243 -3.041 -0.115 -0.007 0.407 0.107 0.5665814958 174 0.243 -3.041 -0.115 -0.007 0.408 0.107 0.5665813884 189 0.244 -3.038 -0.115 -0.008 0.409 0.107 0.5665780062 190 0.246 -3.032 -0.116 -0.009 0.412 0.107 0.5665745281 193 0.246 -3.031 -0.116 -0.009 0.412 0.107 0.5665742939 powell nthiter 2: fret = 0.566574 201 0.150 -3.031 -0.116 -0.009 0.412 0.107 0.5665409139 202 0.194 -3.031 -0.116 -0.009 0.412 0.107 0.5663031664 203 0.197 -3.031 -0.116 -0.009 0.412 0.107 0.5662995016 204 0.206 -3.031 -0.116 -0.009 0.412 0.107 0.5662934947 206 0.205 -3.031 -0.116 -0.009 0.412 0.107 0.5662931920 214 0.205 -3.031 -0.116 -0.009 0.412 0.098 0.5662739078 215 0.205 -3.031 -0.116 -0.009 0.412 0.021 0.5662487535 217 0.205 -3.031 -0.116 -0.009 0.412 0.052 0.5662394047 218 0.205 -3.031 -0.116 -0.009 0.412 0.048 0.5662380703 219 0.205 -3.031 -0.116 -0.009 0.412 0.043 0.5662366346 221 0.205 -3.031 -0.116 -0.009 0.412 0.041 0.5662361231 222 0.205 -3.031 -0.116 -0.009 0.412 0.040 0.5662359616 223 0.205 -3.031 -0.116 -0.009 0.412 0.038 0.5662358682 231 0.205 -3.031 -0.113 -0.009 0.412 0.038 0.5662227771 232 0.205 -3.031 -0.063 -0.009 0.412 0.038 0.5661138356 235 0.205 -3.031 -0.070 -0.009 0.412 0.038 0.5661103308 236 0.205 -3.031 -0.071 -0.009 0.412 0.038 0.5661102844 249 0.205 -3.031 -0.072 0.091 0.412 0.038 0.5659033885 251 0.205 -3.031 -0.072 0.059 0.412 0.038 0.5658567785 252 0.205 -3.031 -0.072 0.061 0.412 0.038 0.5658565120 262 0.205 -3.031 -0.072 0.061 0.398 0.038 0.5658481006 264 0.205 -3.031 -0.072 0.061 0.404 0.038 0.5658320693 273 0.218 -2.992 -0.076 0.054 0.422 0.039 0.5657713063 274 0.216 -2.997 -0.075 0.055 0.419 0.039 0.5657109693 276 0.215 -3.002 -0.075 0.056 0.417 0.039 0.5657084187 277 0.215 -3.001 -0.075 0.055 0.418 0.039 0.5657057140 278 0.215 -3.000 -0.075 0.055 0.418 0.039 0.5657034651 279 0.216 -2.999 -0.075 0.055 0.419 0.039 0.5657016512 280 0.185 -2.967 -0.035 0.119 0.425 -0.030 0.5655312015 powell nthiter 3: fret = 0.565702 341 0.201 -2.999 -0.051 0.072 0.404 0.012 0.5655245601 344 0.201 -2.999 -0.051 0.072 0.399 0.012 0.5655244770 346 0.201 -2.999 -0.051 0.072 0.401 0.012 0.5655209827 348 0.201 -2.999 -0.051 0.072 0.400 0.012 0.5655202100 357 0.202 -2.996 -0.051 0.071 0.402 0.012 0.5655033387 358 0.204 -2.991 -0.052 0.071 0.404 0.013 0.5654914325 360 0.203 -2.993 -0.052 0.071 0.403 0.013 0.5654874315 powell nthiter 4: fret = 0.565487 374 0.204 -2.993 -0.052 0.071 0.403 0.013 0.5654870053 382 0.204 -2.993 -0.052 0.071 0.403 0.009 0.5654826995 384 0.204 -2.993 -0.052 0.071 0.403 0.007 0.5654818649 395 0.204 -2.993 -0.046 0.071 0.403 0.007 0.5654803965 406 0.204 -2.993 -0.047 0.085 0.403 0.007 0.5654715163 407 0.204 -2.993 -0.047 0.083 0.403 0.007 0.5654712014 417 0.204 -2.993 -0.047 0.083 0.402 0.007 0.5654697103 429 0.205 -2.991 -0.047 0.083 0.403 0.007 0.5654611619 430 0.206 -2.986 -0.048 0.082 0.405 0.007 0.5654397630 Powell done niters = 4 Computing relative cost 0 -25.0 -25.0 -25.0 1.046751 1 -25.0 -25.0 25.0 1.049925 2 -25.0 25.0 -25.0 1.073495 3 -25.0 25.0 25.0 1.083916 4 25.0 -25.0 -25.0 1.047432 5 25.0 -25.0 25.0 1.043519 6 25.0 25.0 -25.0 1.023743 7 25.0 25.0 25.0 1.041117 REL: 8 0.565440 8.409899 1.051237 rel = 0.53788 Number of iterations 4 Min cost was 0.565440 Number of FunctionCalls 435 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.832000 sec Parameters at optimum (transmm) 0.20611 -2.98644 -0.04755 Parameters at optimum (rotdeg) 0.08215 0.40505 0.00728 Final costs ---------------- Number of surface hits 3040 WM Intensity 823.4812 +/- 226.6387 Ctx Intensity 852.8414 +/- 261.7289 Pct Contrast 1.3812 +/- 22.7389 Cost 0.5654 RelCost 0.6547 Reg at min cost was 0.99995 0.00586 -0.00813 1.18132; 0.00927 -0.23262 0.97252 -40.84442; -0.00381 0.97255 0.23266 -1.73742; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/tmp.bbregister.6365/bbr.pass1.dat, type = 14 Original Reg 0.99995 -0.00105 -0.00965 0.98232; 0.00914 -0.23123 0.97286 -37.86047; 0.00325 0.97290 0.23121 -1.62868; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00000 -0.00691 -0.00152 -0.19900; -0.00012 0.00139 0.00033 2.98394; 0.00706 0.00035 -0.00146 0.10874; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 3.002696 Computing change in rh position Surface-RMS-Diff-mm 3.006413 0.085604 3.234398 WARNING: initial G-W contrast was negative, but expected positive. If the mov data has a T1 contrast, re-run with --T1 mri_segreg done mri_segreg --mov bold/tmp.bbregister.6365/template.nii --init-reg bold/tmp.bbregister.6365/bbr.pass1.dat --out-reg bold/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/tmp.bbregister.6365/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.112 2014/02/25 19:06:37 greve Exp $ setenv SUBJECTS_DIR /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects cd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01 mri_segreg --mov bold/tmp.bbregister.6365/template.nii --init-reg bold/tmp.bbregister.6365/bbr.pass1.dat --out-reg bold/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/tmp.bbregister.6365/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname transfer machine x86_64 user zkaufman movvol bold/tmp.bbregister.6365/template.nii regfile bold/tmp.bbregister.6365/bbr.pass1.dat subject fsf01anat dof 6 outregfile bold/register.dof6.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1459147969 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99995 0.00586 -0.00813 1.18132; 0.00927 -0.23262 0.97252 -40.84442; -0.00381 0.97255 0.23266 -1.73742; 0.00000 0.00000 0.00000 1.00000; Loading mov Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 1.033917 1 -25.0 -25.0 25.0 1.054409 2 -25.0 25.0 -25.0 1.061950 3 -25.0 25.0 25.0 1.071155 4 25.0 -25.0 -25.0 1.042408 5 25.0 -25.0 25.0 1.034931 6 25.0 25.0 -25.0 1.033287 7 25.0 25.0 25.0 1.061837 REL: 8 0.572625 8.393893 1.049237 rel = 0.545754 Initial costs ---------------- Number of surface hits 304441 WM Intensity 824.7969 +/- 224.4640 Ctx Intensity 853.3974 +/- 259.6470 Pct Contrast 1.3784 +/- 23.5542 Cost 0.5726 RelCost 0.5458 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.5700 0.5700 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.5694 0.5694 0.0 2 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.5684 0.5684 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.5679 0.5679 0.0 5 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1000 0.5676 0.5676 0.0 14 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.1000 0.5673 0.5673 0.0 85 -0.1000 0.0000 -0.1000 -0.1000 0.0000 0.0000 0.5669 0.5669 0.0 92 -0.1000 0.0000 -0.1000 0.0000 -0.1000 0.1000 0.5665 0.5665 0.0 94 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.0000 0.5662 0.5662 0.0 95 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.1000 0.5661 0.5661 0.0 185 -0.1000 0.1000 -0.1000 0.1000 0.0000 0.1000 0.5659 0.5659 0.0 187 -0.1000 0.1000 -0.1000 0.1000 0.1000 0.0000 0.5658 0.5658 0.0 334 0.0000 0.0000 -0.1000 0.0000 -0.1000 0.0000 0.5655 0.5655 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.5654 0.5654 0.0 427 0.0000 0.1000 -0.1000 0.1000 0.0000 0.0000 0.5654 0.5654 0.0 Brute Force -------------------------- Min cost was 0.565439 Number of iterations 729 Search time 1.400000 sec Parameters at best (transmm, rotdeg) 0.000 0.100 -0.100 0.100 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0.1 2 -0.1 3 0.1 4 0 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000000 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.574334 7 -0.152 0.100 -0.100 0.100 0.000 0.000 0.5740838514 8 -0.115 0.100 -0.100 0.100 0.000 0.000 0.5740361834 9 -0.108 0.100 -0.100 0.100 0.000 0.000 0.5740341107 11 -0.107 0.100 -0.100 0.100 0.000 0.000 0.5740340539 18 -0.107 0.482 -0.100 0.100 0.000 0.000 0.5732433597 19 -0.107 0.333 -0.100 0.100 0.000 0.000 0.5728437757 20 -0.107 0.342 -0.100 0.100 0.000 0.000 0.5728343078 21 -0.107 0.357 -0.100 0.100 0.000 0.000 0.5728218038 24 -0.107 0.374 -0.100 0.100 0.000 0.000 0.5728191235 25 -0.107 0.369 -0.100 0.100 0.000 0.000 0.5728180167 26 -0.107 0.368 -0.100 0.100 0.000 0.000 0.5728179701 35 -0.107 0.367 0.282 0.100 0.000 0.000 0.5724629506 36 -0.107 0.367 0.110 0.100 0.000 0.000 0.5717696334 37 -0.107 0.367 0.111 0.100 0.000 0.000 0.5717693458 38 -0.107 0.367 0.117 0.100 0.000 0.000 0.5717690940 40 -0.107 0.367 0.115 0.100 0.000 0.000 0.5717688895 47 -0.107 0.367 0.115 -0.518 0.000 0.000 0.5621395859 49 -0.107 0.367 0.115 -0.592 0.000 0.000 0.5619647560 52 -0.107 0.367 0.115 -0.591 0.000 0.000 0.5619646731 60 -0.107 0.367 0.115 -0.591 -0.083 0.000 0.5617906006 61 -0.107 0.367 0.115 -0.591 -0.076 0.000 0.5617872865 62 -0.107 0.367 0.115 -0.591 -0.073 0.000 0.5617867623 71 -0.107 0.367 0.115 -0.591 -0.073 -0.227 0.5612106612 powell nthiter 1: fret = 0.561211 87 -0.173 0.367 0.115 -0.591 -0.073 -0.227 0.5611533745 88 -0.156 0.367 0.115 -0.591 -0.073 -0.227 0.5611454858 89 -0.155 0.367 0.115 -0.591 -0.073 -0.227 0.5611454157 90 -0.154 0.367 0.115 -0.591 -0.073 -0.227 0.5611454088 99 -0.154 0.484 0.115 -0.591 -0.073 -0.227 0.5608218206 101 -0.154 0.493 0.115 -0.591 -0.073 -0.227 0.5608209513 103 -0.154 0.490 0.115 -0.591 -0.073 -0.227 0.5608204314 112 -0.154 0.489 0.140 -0.591 -0.073 -0.227 0.5608048442 121 -0.154 0.489 0.139 -0.655 -0.073 -0.227 0.5607661379 122 -0.154 0.489 0.139 -0.637 -0.073 -0.227 0.5607644810 123 -0.154 0.489 0.139 -0.643 -0.073 -0.227 0.5607631156 124 -0.154 0.489 0.139 -0.645 -0.073 -0.227 0.5607630528 132 -0.154 0.489 0.139 -0.645 -0.109 -0.227 0.5607085328 134 -0.154 0.489 0.139 -0.645 -0.112 -0.227 0.5607080568 143 -0.154 0.489 0.139 -0.645 -0.112 -0.260 0.5606905357 144 -0.154 0.489 0.139 -0.645 -0.112 -0.266 0.5606903635 150 -0.154 0.489 0.139 -0.645 -0.112 -0.270 0.5606902735 152 -0.154 0.489 0.139 -0.645 -0.112 -0.268 0.5606902497 powell nthiter 2: fret = 0.560690 160 -0.188 0.489 0.139 -0.645 -0.112 -0.268 0.5606870293 161 -0.173 0.489 0.139 -0.645 -0.112 -0.268 0.5606806368 170 -0.173 0.506 0.139 -0.645 -0.112 -0.268 0.5606800873 171 -0.173 0.498 0.139 -0.645 -0.112 -0.268 0.5606791202 181 -0.173 0.499 0.127 -0.645 -0.112 -0.268 0.5606763680 191 -0.173 0.499 0.129 -0.642 -0.112 -0.268 0.5606760673 192 -0.173 0.499 0.129 -0.640 -0.112 -0.268 0.5606760156 193 -0.173 0.499 0.129 -0.639 -0.112 -0.268 0.5606757540 198 -0.173 0.499 0.129 -0.635 -0.112 -0.268 0.5606754372 207 -0.173 0.499 0.129 -0.635 -0.117 -0.268 0.5606750492 217 -0.173 0.499 0.129 -0.635 -0.117 -0.272 0.5606739954 218 -0.173 0.499 0.129 -0.635 -0.117 -0.279 0.5606734052 powell nthiter 3: fret = 0.560673 229 -0.174 0.499 0.129 -0.635 -0.117 -0.280 0.5606732722 230 -0.175 0.499 0.129 -0.635 -0.117 -0.280 0.5606732242 239 -0.175 0.497 0.129 -0.635 -0.117 -0.280 0.5606729538 241 -0.175 0.493 0.129 -0.635 -0.117 -0.280 0.5606727874 242 -0.175 0.492 0.129 -0.635 -0.117 -0.280 0.5606727718 243 -0.175 0.491 0.129 -0.635 -0.117 -0.280 0.5606727681 269 -0.175 0.491 0.129 -0.628 -0.117 -0.280 0.5606705370 270 -0.175 0.491 0.129 -0.625 -0.117 -0.280 0.5606704198 271 -0.175 0.491 0.129 -0.626 -0.117 -0.280 0.5606703453 279 -0.175 0.491 0.129 -0.626 -0.118 -0.280 0.5606702392 280 -0.175 0.491 0.129 -0.626 -0.119 -0.280 0.5606699522 286 -0.175 0.491 0.129 -0.626 -0.121 -0.280 0.5606698293 powell nthiter 4: fret = 0.560670 305 -0.176 0.491 0.129 -0.626 -0.121 -0.280 0.5606697719 306 -0.177 0.491 0.129 -0.626 -0.121 -0.280 0.5606697693 317 -0.178 0.486 0.129 -0.626 -0.121 -0.280 0.5606697219 318 -0.178 0.489 0.129 -0.626 -0.121 -0.280 0.5606695357 powell nthiter 5: fret = 0.560670 Powell done niters = 5 Computing relative cost 0 -25.0 -25.0 -25.0 1.035909 1 -25.0 -25.0 25.0 1.053714 2 -25.0 25.0 -25.0 1.061847 3 -25.0 25.0 25.0 1.073981 4 25.0 -25.0 -25.0 1.048710 5 25.0 -25.0 25.0 1.040168 6 25.0 25.0 -25.0 1.030810 7 25.0 25.0 25.0 1.063426 REL: 8 0.560670 8.408567 1.051071 rel = 0.533427 Number of iterations 5 Min cost was 0.560670 Number of FunctionCalls 419 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 50.472000 sec Parameters at optimum (transmm) -0.17708 0.48899 0.12883 Parameters at optimum (rotdeg) -0.62551 -0.12050 -0.28116 Final costs ---------------- Number of surface hits 304441 WM Intensity 828.8717 +/- 218.1828 Ctx Intensity 860.1954 +/- 253.4915 Pct Contrast 1.7561 +/- 22.8229 Cost 0.5607 RelCost 0.5458 Reg at min cost was 0.99999 0.00272 -0.00381 0.80644; 0.00432 -0.22201 0.97504 -40.37728; -0.00180 0.97504 0.22201 -1.16010; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/register.dof6.dat, type = 14 Original Reg 0.99995 0.00586 -0.00813 1.18132; 0.00927 -0.23262 0.97252 -40.84442; -0.00381 0.97255 0.23266 -1.73742; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00004 0.00314 -0.00432 0.37489; 0.00495 -0.01062 -0.00251 -0.46714; -0.00200 -0.00249 0.01065 -0.57732; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.738681 Computing change in rh position Surface-RMS-Diff-mm 0.710759 0.368009 1.646569 mri_segreg done MinCost: 0.560670 828.871695 860.195415 1.756131 tkregister2_cmdl --mov bold/template.nii.gz --reg bold/register.dof6.dat --noedit --ltaout bold/register.dof6.lta tkregister_tcl /usr/local/freesurfer/dev/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume bold/template.nii.gz reg file bold/register.dof6.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.131 2016/03/24 17:39:56 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- 0.99999 0.00272 -0.00381 0.80644; 0.00432 -0.22201 0.97504 -40.37728; -0.00180 0.97504 0.22201 -1.16010; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: loading target /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/orig.mgz Ttarg: -------------------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading movable bold/template.nii.gz Tmov: -------------------- -3.43750 0.00000 0.00000 110.00000; 0.00000 0.00000 5.00000 -75.00000; 0.00000 -3.43750 0.00000 109.99999; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 0.99999 0.00272 -0.00381 0.80644; 0.00432 -0.22201 0.97504 -40.37728; -0.00180 0.97504 0.22201 -1.16010; 0.00000 0.00000 0.00000 1.00000; Determinant -1 subject = fsf01anat RegMat --------------------------- 0.99999 0.00272 -0.00381 0.80644; 0.00432 -0.22201 0.97504 -40.37728; -0.00180 0.97504 0.22201 -1.16010; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Sun Mar 27 21:37:27 EDT 2016 Ended at Sun Mar 27 21:40:38 EDT 2016 BBR-Run-Time-Sec 191 bbregister Done To check results, run: tkregister2 --mov bold/template.nii.gz --reg bold/register.dof6.dat --surf Run: 001 ---------------- Sun Mar 27 21:40:38 EDT 2016 -------------------------------------- /autofs/cluster/pubftp/data/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.7323 Log file is bold/001/register.dof6.dat.log Sun Mar 27 21:40:38 EDT 2016 setenv SUBJECTS_DIR /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects cd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01 /usr/local/freesurfer/dev/bin/bbregister --s fsf01anat --init-coreg --6 --bold --mov bold/001/template.nii.gz --reg bold/001/register.dof6.dat --lta bold/001/register.dof6.lta --init-reg-out bold/001/init.register.dof6.dat $Id: bbregister,v 1.74 2016/02/17 21:07:31 greve Exp $ Linux transfer 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer/dev mri_convert bold/001/template.nii.gz bold/001/tmp.bbregister.7323/template.nii mri_convert.bin bold/001/template.nii.gz bold/001/tmp.bbregister.7323/template.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from bold/001/template.nii.gz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.973976, -0.226651) k_ras = (-2.36491e-18, -0.226651, 0.973976) writing to bold/001/tmp.bbregister.7323/template.nii... mri_coreg --s fsf01anat --mov bold/001/tmp.bbregister.7323/template.nii --regdat bold/001/tmp.bbregister.7323/reg.init.dat --reg bold/001/tmp.bbregister.7323/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 freadFloat: fread failed $Id: mri_coreg.c,v 1.26 2016/01/20 23:42:39 greve Exp $ cwd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01 cmdline mri_coreg --s fsf01anat --mov bold/001/tmp.bbregister.7323/template.nii --regdat bold/001/tmp.bbregister.7323/reg.init.dat --reg bold/001/tmp.bbregister.7323/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 sysname Linux hostname transfer machine x86_64 user zkaufman dof 6 nsep 1 cras0 1 ftol 0.000100 linmintol 0.010000 bf 1 bflim 30.000000 bfnsamp 30 SmoothRef 0 SatPct 99.990000 MovOOB 0 Reading in mov bold/001/tmp.bbregister.7323/template.nii Reading in ref /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/brainmask.mgz freadFloat: fread failed Reading in and applying refmask /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/aparc+aseg.mgz Setting cras translation parameters to align centers Creating random numbers for coordinate dithering Performing intensity dithering Initial parameters -6.0223 -45.2577 79.2380 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Separation list (1): 4 min = 4 DoSmoothing 1 DoCoordDither 1 DoIntensityDither 1 nitersmax 4 ftol 1.000e-04 linmintol 1.000e-02 SatPct 99.990000 Hist FWHM 7.000000 7.000000 nthreads 1 movsat = 1714.3334 mov gstd 0.9989 0.9989 0.0000 Smoothing mov refsat = 118.0000 ref gstd 1.8914 1.8914 1.8914 Smoothing ref COREGpreproc() done Testing if mov and target overlap Init cost -1.0211907209 nhits = 106280 out of 16777216, Percent Overlap: 40.5 Initial RefRAS-to-MovRAS 1.00000 0.00000 0.00000 -6.02228; 0.00000 1.00000 0.00000 -45.25770; 0.00000 0.00000 1.00000 79.23798; 0.00000 0.00000 0.00000 1.00000; Initial RefVox-to-MovVox 0.29091 -0.00000 -0.00000 -5.59091; -0.00000 0.06593 -0.28334 59.21896; 0.00000 -0.19480 -0.04533 45.11600; 0.00000 0.00000 0.00000 1.00000; sep = 4 ----------------------------------- COREGoptBruteForce() 30 1 30 Turning on MovOOB for BruteForce Search #BF# sep= 4 iter=0 lim=30.0 delta=2.00 -6.02228 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0504159 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6 Starting OpenPowel2(), sep = 4 InitialCost -1.0719541311 #@# 4 188 -6.02228 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0719541 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.071954 #@# 4 193 -6.64031 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0719982 #@# 4 195 -6.42368 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0720158 #@# 4 198 -6.36391 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0720164 #@# 4 201 -6.34980 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0720165 #@# 4 205 -6.34980 -36.87573 49.23798 4.00000 0.00000 0.00000 -1.0744008 #@# 4 208 -6.34980 -40.53706 49.23798 4.00000 0.00000 0.00000 -1.0759999 #@# 4 210 -6.34980 -39.59051 49.23798 4.00000 0.00000 0.00000 -1.0763069 #@# 4 211 -6.34980 -39.48524 49.23798 4.00000 0.00000 0.00000 -1.0763090 #@# 4 212 -6.34980 -39.50470 49.23798 4.00000 0.00000 0.00000 -1.0763118 #@# 4 221 -6.34980 -39.50470 49.14936 4.00000 0.00000 0.00000 -1.0763154 #@# 4 222 -6.34980 -39.50470 49.13935 4.00000 0.00000 0.00000 -1.0763171 #@# 4 231 -6.34980 -39.50470 49.13935 3.38197 0.00000 0.00000 -1.0764904 #@# 4 233 -6.34980 -39.50470 49.13935 3.49223 0.00000 0.00000 -1.0765028 #@# 4 234 -6.34980 -39.50470 49.13935 3.52561 0.00000 0.00000 -1.0765045 #@# 4 236 -6.34980 -39.50470 49.13935 3.51561 0.00000 0.00000 -1.0765049 #@# 4 237 -6.34980 -39.50470 49.13935 3.50561 0.00000 0.00000 -1.0765057 #@# 4 244 -6.34980 -39.50470 49.13935 3.50561 0.13342 0.00000 -1.0765141 #@# 4 246 -6.34980 -39.50470 49.13935 3.50561 0.11799 0.00000 -1.0765142 #@# 4 254 -6.34980 -39.50470 49.13935 3.50561 0.11799 -0.18203 -1.0765320 #@# 4 257 -6.34980 -39.50470 49.13935 3.50561 0.11799 -0.17203 -1.0765326 #@# 4 265 -6.37596 -39.84391 49.13148 3.46613 0.12741 -0.18577 -1.0765558 #@# 4 266 -6.37268 -39.80144 49.13247 3.47107 0.12623 -0.18405 -1.0765580 powell nthiter 1: fret = -1.076558 #@# 4 274 -6.38890 -39.80144 49.13247 3.47107 0.12623 -0.18405 -1.0765586 #@# 4 275 -6.41432 -39.80144 49.13247 3.47107 0.12623 -0.18405 -1.0765587 #@# 4 278 -6.43432 -39.80144 49.13247 3.47107 0.12623 -0.18405 -1.0765595 #@# 4 296 -6.43432 -39.80144 48.51443 3.47107 0.12623 -0.18405 -1.0766954 #@# 4 298 -6.43432 -39.80144 48.53483 3.47107 0.12623 -0.18405 -1.0766957 #@# 4 299 -6.43432 -39.80144 48.54483 3.47107 0.12623 -0.18405 -1.0766963 #@# 4 308 -6.43432 -39.80144 48.54483 2.85304 0.12623 -0.18405 -1.0767852 #@# 4 310 -6.43432 -39.80144 48.54483 3.05311 0.12623 -0.18405 -1.0768225 #@# 4 311 -6.43432 -39.80144 48.54483 3.07104 0.12623 -0.18405 -1.0768234 #@# 4 320 -6.43432 -39.80144 48.54483 3.07104 -0.03917 -0.18405 -1.0768281 #@# 4 321 -6.43432 -39.80144 48.54483 3.07104 -0.04917 -0.18405 -1.0768285 #@# 4 324 -6.43432 -39.80144 48.54483 3.07104 -0.06163 -0.18405 -1.0768286 #@# 4 325 -6.43432 -39.80144 48.54483 3.07104 -0.07163 -0.18405 -1.0768287 #@# 4 334 -6.45092 -40.01678 48.53983 3.04597 -0.08174 -0.19277 -1.0768327 #@# 4 335 -6.44572 -39.94929 48.54139 3.05382 -0.08361 -0.19004 -1.0768330 #@# 4 337 -6.54164 -40.39388 47.94343 2.60204 -0.28521 -0.20804 -1.0770371 #@# 4 340 -6.69684 -41.11325 46.97591 1.87103 -0.61140 -0.23718 -1.0771599 #@# 4 346 -6.67134 -40.99509 47.13483 1.99110 -0.55782 -0.23240 -1.0771701 #@# 4 347 -6.66953 -40.98666 47.14616 1.99966 -0.55400 -0.23205 -1.0771704 powell nthiter 2: fret = -1.077170 #@# 4 355 -6.28756 -40.98666 47.14616 1.99966 -0.55400 -0.23205 -1.0771829 #@# 4 356 -6.45323 -40.98666 47.14616 1.99966 -0.55400 -0.23205 -1.0771980 #@# 4 357 -6.44323 -40.98666 47.14616 1.99966 -0.55400 -0.23205 -1.0771983 #@# 4 367 -6.43213 -40.98666 47.14616 1.99966 -0.55400 -0.20730 -1.0772012 #@# 4 369 -6.43213 -40.98666 47.14616 1.99966 -0.55400 -0.19130 -1.0772020 #@# 4 370 -6.43213 -40.98666 47.14616 1.99966 -0.55400 -0.18130 -1.0772022 #@# 4 377 -6.38192 -40.33559 47.16128 2.07545 -0.57209 -0.15493 -1.0773158 #@# 4 381 -6.37151 -40.20062 47.16441 2.09116 -0.57584 -0.14946 -1.0773164 #@# 4 382 -6.37504 -40.24644 47.16335 2.08583 -0.57456 -0.15132 -1.0773177 #@# 4 383 -6.37832 -40.28891 47.16236 2.08089 -0.57338 -0.15304 -1.0773191 #@# 4 390 -6.37832 -40.28891 47.16236 2.19769 -0.57338 -0.15304 -1.0773278 #@# 4 400 -6.37832 -40.28891 47.16236 2.19769 -0.19142 -0.15304 -1.0773637 #@# 4 401 -6.37832 -40.28891 47.16236 2.19769 -0.01061 -0.15304 -1.0773693 #@# 4 402 -6.37832 -40.28891 47.16236 2.19769 0.03750 -0.15304 -1.0773698 #@# 4 408 -6.47424 -40.73350 46.56440 1.74590 -0.16410 -0.17105 -1.0774988 #@# 4 417 -6.47180 -40.72219 46.57962 1.75740 -0.15897 -0.17059 -1.0774992 #@# 4 419 -6.47276 -40.72663 46.57364 1.75288 -0.16099 -0.17077 -1.0774993 powell nthiter 3: fret = -1.077499 #@# 4 427 -6.49168 -40.72663 46.57364 1.75288 -0.16099 -0.17077 -1.0775008 #@# 4 445 -6.46515 -40.38260 46.58163 1.79293 -0.17054 -0.15683 -1.0775325 #@# 4 448 -6.46187 -40.34013 46.58261 1.79787 -0.17172 -0.15511 -1.0775337 #@# 4 459 -6.46187 -40.34013 46.58261 1.81916 -0.17172 -0.15511 -1.0775342 #@# 4 468 -6.46187 -40.34013 46.58261 1.81916 -0.22158 -0.15511 -1.0775393 #@# 4 469 -6.46187 -40.34013 46.58261 1.81916 -0.43860 -0.15511 -1.0775400 #@# 4 470 -6.46187 -40.34013 46.58261 1.81916 -0.33451 -0.15511 -1.0775418 #@# 4 471 -6.46187 -40.34013 46.58261 1.81916 -0.34451 -0.15511 -1.0775422 #@# 4 475 -6.55779 -40.78473 45.98465 1.36737 -0.54610 -0.17312 -1.0775452 #@# 4 479 -6.52115 -40.61491 46.21305 1.53994 -0.46910 -0.16624 -1.0775739 #@# 4 483 -6.51923 -40.60601 46.22501 1.54897 -0.46507 -0.16588 -1.0775740 #@# 4 484 -6.51721 -40.59665 46.23761 1.55849 -0.46082 -0.16550 -1.0775748 #@# 4 485 -6.51596 -40.59086 46.24539 1.56437 -0.45820 -0.16527 -1.0775765 Powell done niters total = 3 OptTimeSec 24.2 sec OptTimeMin 0.40 min nEvals 486 Final parameters -6.51596308 -40.59085846 46.24539185 1.56437409 -0.45819777 -0.16526955 Final cost -1.077576544779150 --------------------------------- mri_coreg utimesec 113.811697 mri_coreg stimesec 0.634903 mri_coreg ru_maxrss 422120 mri_coreg ru_ixrss 0 mri_coreg ru_idrss 0 mri_coreg ru_isrss 0 mri_coreg ru_minflt 266590 mri_coreg ru_majflt 0 mri_coreg ru_nswap 0 mri_coreg ru_inblock 0 mri_coreg ru_oublock 0 mri_coreg ru_msgsnd 0 mri_coreg ru_msgrcv 0 mri_coreg ru_nsignals 0 mri_coreg ru_nvcsw 48 mri_coreg ru_nivcsw 233 Final RefRAS-to-MovRAS 0.99996 -0.00288 -0.00800 -6.51596; 0.00310 0.99962 0.02730 -40.59086; 0.00792 -0.02732 0.99960 46.24539; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox 0.29090 -0.00233 0.00084 -5.27552; 0.00140 0.07364 -0.28143 58.99800; -0.00140 -0.19348 -0.05064 38.90063; 0.00000 0.00000 0.00000 1.00000; Final parameters -6.5160 -40.5909 46.2454 1.5644 -0.4582 -0.1653 nhits = 106066 out of 16777216, Percent Overlap: 40.5 mri_coreg RunTimeSec 114.5 sec To check run: tkregisterfv --mov bold/001/tmp.bbregister.7323/template.nii --targ /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/brainmask.mgz --reg bold/001/tmp.bbregister.7323/mri_coreg.lta --s fsf01anat --surfs mri_coreg done mri_segreg --mov bold/001/tmp.bbregister.7323/template.nii --init-reg bold/001/tmp.bbregister.7323/reg.init.dat --out-reg bold/001/tmp.bbregister.7323/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.112 2014/02/25 19:06:37 greve Exp $ setenv SUBJECTS_DIR /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects cd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01 mri_segreg --mov bold/001/tmp.bbregister.7323/template.nii --init-reg bold/001/tmp.bbregister.7323/reg.init.dat --out-reg bold/001/tmp.bbregister.7323/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Linux hostname transfer machine x86_64 user zkaufman movvol bold/001/tmp.bbregister.7323/template.nii regfile bold/001/tmp.bbregister.7323/reg.init.dat subject fsf01anat dof 6 outregfile bold/001/tmp.bbregister.7323/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1459133830 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99996 -0.00288 -0.00800 0.79362; 0.00701 -0.25318 0.96739 -37.62688; 0.00482 0.96742 0.25315 -1.99570; 0.00000 0.00000 0.00000 1.00000; Loading mov Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 1.091030 1 -25.0 -25.0 25.0 1.054789 2 -25.0 25.0 -25.0 1.072374 3 -25.0 25.0 25.0 1.071854 4 25.0 -25.0 -25.0 1.053108 5 25.0 -25.0 25.0 1.051902 6 25.0 25.0 -25.0 1.032281 7 25.0 25.0 25.0 1.064927 REL: 8 0.741129 8.492266 1.061533 rel = 0.698168 Initial costs ---------------- Number of surface hits 3040 WM Intensity 855.3245 +/- 209.5971 Ctx Intensity 857.9055 +/- 239.0958 Pct Contrast -1.3471 +/- 21.9053 Cost 0.7411 RelCost 0.6982 WARNING: initial G-W contrast is negative, but expecting positive. If the mov data has a T1 contrast, re-run with --T1 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 1.0755 1.0755 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 1.0380 1.0380 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 1.0152 1.0152 0.0 5 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 4.0000 1.0011 1.0011 0.0 6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 1.0006 1.0006 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.9613 0.9613 0.0 18 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 -4.0000 0.9509 0.9509 0.0 30 -4.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.9324 0.9324 0.0 34 -4.0000 -4.0000 0.0000 -4.0000 4.0000 0.0000 0.9215 0.9215 0.0 40 -4.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.9087 0.9087 0.0 273 0.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.8170 0.8170 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.7728 0.7728 0.0 282 0.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.7334 0.7334 0.0 283 0.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.6066 0.6066 0.0 Brute Force -------------------------- Min cost was 0.606586 Number of iterations 729 Search time 1.390000 sec Parameters at best (transmm, rotdeg) 0.000 -4.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 -4 2 0 3 0 4 0 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000100 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.606586 7 0.066 -4.000 0.000 0.000 0.000 0.000 0.6062284744 9 0.078 -4.000 0.000 0.000 0.000 0.000 0.6062084021 11 0.077 -4.000 0.000 0.000 0.000 0.000 0.6062080631 14 0.077 -3.000 0.000 0.000 0.000 0.000 0.5911750249 20 0.077 -2.999 0.000 0.000 0.000 0.000 0.5911741576 21 0.077 -2.990 0.000 0.000 0.000 0.000 0.5911666665 23 0.077 -2.986 0.000 0.000 0.000 0.000 0.5911666121 24 0.077 -2.988 0.000 0.000 0.000 0.000 0.5911665914 25 0.077 -2.989 0.000 0.000 0.000 0.000 0.5911665783 32 0.077 -2.989 -0.081 0.000 0.000 0.000 0.5910502958 33 0.077 -2.989 -0.086 0.000 0.000 0.000 0.5910246040 34 0.077 -2.989 -0.289 0.000 0.000 0.000 0.5894910382 37 0.077 -2.989 -0.310 0.000 0.000 0.000 0.5894845029 38 0.077 -2.989 -0.301 0.000 0.000 0.000 0.5894757486 41 0.077 -2.989 -0.299 0.000 0.000 0.000 0.5894752072 47 0.077 -2.989 -0.299 -0.618 0.000 0.000 0.5840612358 48 0.077 -2.989 -0.299 -1.000 0.000 0.000 0.5837877173 49 0.077 -2.989 -0.299 -0.854 0.000 0.000 0.5832733231 50 0.077 -2.989 -0.299 -0.829 0.000 0.000 0.5832206346 52 0.077 -2.989 -0.299 -0.805 0.000 0.000 0.5831866416 54 0.077 -2.989 -0.299 -0.803 0.000 0.000 0.5831835268 56 0.077 -2.989 -0.299 -0.798 0.000 0.000 0.5831774762 66 0.077 -2.989 -0.299 -0.798 0.156 0.000 0.5824563477 67 0.077 -2.989 -0.299 -0.798 0.160 0.000 0.5824445317 69 0.077 -2.989 -0.299 -0.798 0.201 0.000 0.5823838314 73 0.077 -2.989 -0.299 -0.798 0.202 0.000 0.5823837361 82 0.077 -2.989 -0.299 -0.798 0.202 0.011 0.5823759210 83 0.077 -2.989 -0.299 -0.798 0.202 0.012 0.5823758510 powell nthiter 1: fret = 0.582376 92 0.208 -2.989 -0.299 -0.798 0.202 0.012 0.5817083693 93 0.224 -2.989 -0.299 -0.798 0.202 0.012 0.5816498022 109 0.224 -2.965 -0.299 -0.798 0.202 0.012 0.5815972125 111 0.224 -2.967 -0.299 -0.798 0.202 0.012 0.5815971409 118 0.224 -2.967 0.083 -0.798 0.202 0.012 0.5779825349 119 0.224 -2.967 0.125 -0.798 0.202 0.012 0.5776512064 120 0.224 -2.967 0.345 -0.798 0.202 0.012 0.5774362066 121 0.224 -2.967 0.254 -0.798 0.202 0.012 0.5767839647 123 0.224 -2.967 0.253 -0.798 0.202 0.012 0.5767838318 131 0.224 -2.967 0.253 -0.934 0.202 0.012 0.5767136750 132 0.224 -2.967 0.253 -0.882 0.202 0.012 0.5766593687 133 0.224 -2.967 0.253 -0.880 0.202 0.012 0.5766570831 134 0.224 -2.967 0.253 -0.849 0.202 0.012 0.5766276192 139 0.224 -2.967 0.253 -0.848 0.202 0.012 0.5766269157 141 0.224 -2.967 0.253 -0.847 0.202 0.012 0.5766264777 148 0.224 -2.967 0.253 -0.847 0.273 0.012 0.5761817590 149 0.224 -2.967 0.253 -0.847 0.302 0.012 0.5761157809 150 0.224 -2.967 0.253 -0.847 0.317 0.012 0.5761107539 151 0.224 -2.967 0.253 -0.847 0.313 0.012 0.5761103305 161 0.224 -2.967 0.253 -0.847 0.313 -0.237 0.5753880894 162 0.224 -2.967 0.253 -0.847 0.313 -0.219 0.5753198208 163 0.224 -2.967 0.253 -0.847 0.313 -0.162 0.5750734898 164 0.224 -2.967 0.253 -0.847 0.313 -0.095 0.5750461053 165 0.224 -2.967 0.253 -0.847 0.313 -0.122 0.5750031327 166 0.224 -2.967 0.253 -0.847 0.313 -0.124 0.5750020595 168 0.224 -2.967 0.253 -0.847 0.313 -0.126 0.5750019348 powell nthiter 2: fret = 0.575002 179 0.245 -2.967 0.253 -0.847 0.313 -0.126 0.5749931670 180 0.236 -2.967 0.253 -0.847 0.313 -0.126 0.5749865621 181 0.237 -2.967 0.253 -0.847 0.313 -0.126 0.5749863135 190 0.238 -2.585 0.253 -0.847 0.313 -0.126 0.5737294716 191 0.238 -2.613 0.253 -0.847 0.313 -0.126 0.5733581688 192 0.238 -2.741 0.253 -0.847 0.313 -0.126 0.5731019269 194 0.238 -2.702 0.253 -0.847 0.313 -0.126 0.5729946273 195 0.238 -2.696 0.253 -0.847 0.313 -0.126 0.5729917427 196 0.238 -2.694 0.253 -0.847 0.313 -0.126 0.5729915673 204 0.238 -2.694 0.170 -0.847 0.313 -0.126 0.5729650848 205 0.238 -2.694 0.208 -0.847 0.313 -0.126 0.5727941122 206 0.238 -2.694 0.210 -0.847 0.313 -0.126 0.5727918004 207 0.238 -2.694 0.215 -0.847 0.313 -0.126 0.5727903233 208 0.238 -2.694 0.214 -0.847 0.313 -0.126 0.5727902177 218 0.238 -2.694 0.214 -0.885 0.313 -0.126 0.5727347502 219 0.238 -2.694 0.214 -0.873 0.313 -0.126 0.5727215961 221 0.238 -2.694 0.214 -0.870 0.313 -0.126 0.5727215641 224 0.238 -2.694 0.214 -0.871 0.313 -0.126 0.5727213214 225 0.238 -2.694 0.214 -0.872 0.313 -0.126 0.5727212996 233 0.238 -2.694 0.214 -0.872 0.380 -0.126 0.5725384737 235 0.238 -2.694 0.214 -0.872 0.359 -0.126 0.5724816420 244 0.238 -2.694 0.214 -0.872 0.359 -0.244 0.5722659064 245 0.238 -2.694 0.214 -0.872 0.359 -0.220 0.5721382936 247 0.238 -2.694 0.214 -0.872 0.359 -0.210 0.5721288352 248 0.238 -2.694 0.214 -0.872 0.359 -0.211 0.5721285019 249 0.238 -2.694 0.214 -0.872 0.359 -0.212 0.5721284982 powell nthiter 3: fret = 0.572128 261 0.251 -2.694 0.214 -0.872 0.359 -0.212 0.5721268545 262 0.245 -2.694 0.214 -0.872 0.359 -0.212 0.5721263911 263 0.247 -2.694 0.214 -0.872 0.359 -0.212 0.5721261892 273 0.247 -2.686 0.214 -0.872 0.359 -0.212 0.5721196467 274 0.247 -2.685 0.214 -0.872 0.359 -0.212 0.5721194444 275 0.247 -2.684 0.214 -0.872 0.359 -0.212 0.5721194427 284 0.247 -2.684 0.189 -0.872 0.359 -0.212 0.5720285823 286 0.247 -2.684 0.188 -0.872 0.359 -0.212 0.5720282467 287 0.247 -2.684 0.187 -0.872 0.359 -0.212 0.5720281917 297 0.247 -2.684 0.187 -0.896 0.359 -0.212 0.5719820945 299 0.247 -2.684 0.187 -0.894 0.359 -0.212 0.5719819454 311 0.247 -2.684 0.187 -0.894 0.369 -0.212 0.5719638925 312 0.247 -2.684 0.187 -0.894 0.370 -0.212 0.5719635060 313 0.247 -2.684 0.187 -0.894 0.371 -0.212 0.5719633947 324 0.247 -2.684 0.187 -0.894 0.371 -0.215 0.5719596491 326 0.247 -2.684 0.187 -0.894 0.371 -0.219 0.5719594195 330 0.256 -2.674 0.161 -0.916 0.383 -0.226 0.5719197605 336 0.252 -2.678 0.171 -0.907 0.378 -0.224 0.5719164947 337 0.254 -2.676 0.167 -0.911 0.380 -0.225 0.5719163309 338 0.253 -2.677 0.168 -0.909 0.379 -0.224 0.5719163070 339 0.253 -2.677 0.168 -0.909 0.379 -0.224 0.5719162257 341 0.253 -2.677 0.168 -0.910 0.379 -0.224 0.5719161766 344 0.253 -2.677 0.168 -0.910 0.379 -0.224 0.5719161519 powell nthiter 4: fret = 0.571916 353 0.261 -2.677 0.168 -0.910 0.379 -0.224 0.5719063789 365 0.260 -2.687 0.168 -0.910 0.379 -0.224 0.5718940157 368 0.260 -2.688 0.168 -0.910 0.379 -0.224 0.5718939767 388 0.260 -2.688 0.168 -0.908 0.379 -0.224 0.5718927247 390 0.260 -2.688 0.168 -0.907 0.379 -0.224 0.5718925026 400 0.260 -2.688 0.168 -0.907 0.377 -0.224 0.5718906748 402 0.260 -2.688 0.168 -0.907 0.378 -0.224 0.5718905732 409 0.261 -2.687 0.163 -0.911 0.380 -0.226 0.5718875429 411 0.261 -2.687 0.163 -0.910 0.380 -0.226 0.5718875190 413 0.261 -2.687 0.164 -0.910 0.379 -0.225 0.5718873484 414 0.261 -2.687 0.164 -0.910 0.379 -0.226 0.5718871917 Powell done niters = 4 Computing relative cost 0 -25.0 -25.0 -25.0 1.046795 1 -25.0 -25.0 25.0 1.059148 2 -25.0 25.0 -25.0 1.058524 3 -25.0 25.0 25.0 1.068570 4 25.0 -25.0 -25.0 1.050597 5 25.0 -25.0 25.0 1.058344 6 25.0 25.0 -25.0 1.008646 7 25.0 25.0 25.0 1.039732 REL: 8 0.571887 8.390356 1.048795 rel = 0.545281 Number of iterations 4 Min cost was 0.571887 Number of FunctionCalls 417 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.799000 sec Parameters at optimum (transmm) 0.26102 -2.68671 0.16381 Parameters at optimum (rotdeg) -0.91016 0.37946 -0.22558 Final costs ---------------- Number of surface hits 3040 WM Intensity 823.1487 +/- 219.0824 Ctx Intensity 850.7398 +/- 251.0629 Pct Contrast 1.2975 +/- 21.2306 Cost 0.5719 RelCost 0.6982 Reg at min cost was 0.99999 0.00261 -0.00260 0.89712; 0.00314 -0.23779 0.97131 -40.34334; -0.00192 0.97131 0.23780 -1.23918; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/001/tmp.bbregister.7323/bbr.pass1.dat, type = 14 Original Reg 0.99996 -0.00288 -0.00800 0.79362; 0.00701 -0.25318 0.96739 -37.62688; 0.00482 0.96742 0.25315 -1.99570; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00003 -0.00550 -0.00540 -0.10350; 0.00386 -0.01539 -0.00392 2.71645; 0.00673 -0.00390 0.01535 -0.75653; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 2.828482 Computing change in rh position Surface-RMS-Diff-mm 2.899287 0.678971 4.298419 WARNING: initial G-W contrast was negative, but expected positive. If the mov data has a T1 contrast, re-run with --T1 mri_segreg done mri_segreg --mov bold/001/tmp.bbregister.7323/template.nii --init-reg bold/001/tmp.bbregister.7323/bbr.pass1.dat --out-reg bold/001/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/001/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/001/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/001/tmp.bbregister.7323/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.112 2014/02/25 19:06:37 greve Exp $ setenv SUBJECTS_DIR /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects cd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01 mri_segreg --mov bold/001/tmp.bbregister.7323/template.nii --init-reg bold/001/tmp.bbregister.7323/bbr.pass1.dat --out-reg bold/001/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/001/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/001/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/001/tmp.bbregister.7323/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname transfer machine x86_64 user zkaufman movvol bold/001/tmp.bbregister.7323/template.nii regfile bold/001/tmp.bbregister.7323/bbr.pass1.dat subject fsf01anat dof 6 outregfile bold/001/register.dof6.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1459888130 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99999 0.00261 -0.00260 0.89712; 0.00314 -0.23779 0.97131 -40.34334; -0.00192 0.97131 0.23780 -1.23918; 0.00000 0.00000 0.00000 1.00000; Loading mov Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 1.041968 1 -25.0 -25.0 25.0 1.059150 2 -25.0 25.0 -25.0 1.061925 3 -25.0 25.0 25.0 1.067526 4 25.0 -25.0 -25.0 1.044055 5 25.0 -25.0 25.0 1.037784 6 25.0 25.0 -25.0 1.029330 7 25.0 25.0 25.0 1.059843 REL: 8 0.575895 8.401582 1.050198 rel = 0.548368 Initial costs ---------------- Number of surface hits 304441 WM Intensity 824.4612 +/- 216.4690 Ctx Intensity 852.2073 +/- 248.1521 Pct Contrast 1.4860 +/- 21.7327 Cost 0.5759 RelCost 0.5484 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.5758 0.5758 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.5754 0.5754 0.0 2 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.5750 0.5750 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.5749 0.5749 0.0 5 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1000 0.5741 0.5741 0.0 32 -0.1000 -0.1000 0.0000 -0.1000 0.0000 0.1000 0.5738 0.5738 0.0 41 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.1000 0.5733 0.5733 0.0 121 -0.1000 0.0000 0.0000 0.0000 0.0000 0.0000 0.5730 0.5730 0.0 122 -0.1000 0.0000 0.0000 0.0000 0.0000 0.1000 0.5724 0.5724 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.5719 0.5719 0.0 Brute Force -------------------------- Min cost was 0.571887 Number of iterations 729 Search time 1.389000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000000 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.575895 7 -0.179 0.000 0.000 0.000 0.000 0.000 0.5752653415 8 -0.169 0.000 0.000 0.000 0.000 0.000 0.5752605206 10 -0.167 0.000 0.000 0.000 0.000 0.000 0.5752604991 18 -0.167 -0.124 0.000 0.000 0.000 0.000 0.5749283431 20 -0.167 -0.123 0.000 0.000 0.000 0.000 0.5749282754 23 -0.167 -0.116 0.000 0.000 0.000 0.000 0.5749281752 24 -0.167 -0.118 0.000 0.000 0.000 0.000 0.5749281119 34 -0.167 -0.120 -0.066 0.000 0.000 0.000 0.5748104146 35 -0.167 -0.120 -0.067 0.000 0.000 0.000 0.5748102314 36 -0.167 -0.120 -0.069 0.000 0.000 0.000 0.5748101899 39 -0.167 -0.120 -0.068 0.000 0.000 0.000 0.5748101682 46 -0.167 -0.120 -0.068 0.066 0.000 0.000 0.5747279731 47 -0.167 -0.120 -0.068 0.065 0.000 0.000 0.5747277809 48 -0.167 -0.120 -0.068 0.062 0.000 0.000 0.5747273292 59 -0.167 -0.120 -0.068 0.060 -0.130 0.000 0.5742703125 60 -0.167 -0.120 -0.068 0.060 -0.126 0.000 0.5742702276 62 -0.167 -0.120 -0.068 0.060 -0.127 0.000 0.5742702108 70 -0.167 -0.120 -0.068 0.060 -0.127 -0.135 0.5740538576 72 -0.167 -0.120 -0.068 0.060 -0.127 -0.123 0.5740517557 73 -0.167 -0.120 -0.068 0.060 -0.127 -0.124 0.5740515949 powell nthiter 1: fret = 0.574052 83 -0.177 -0.120 -0.068 0.060 -0.127 -0.124 0.5740498590 85 -0.178 -0.120 -0.068 0.060 -0.127 -0.124 0.5740498430 87 -0.179 -0.120 -0.068 0.060 -0.127 -0.124 0.5740498351 97 -0.179 -0.146 -0.068 0.060 -0.127 -0.124 0.5740408555 99 -0.179 -0.141 -0.068 0.060 -0.127 -0.124 0.5740394896 100 -0.179 -0.139 -0.068 0.060 -0.127 -0.124 0.5740392308 103 -0.179 -0.138 -0.068 0.060 -0.127 -0.124 0.5740391210 111 -0.179 -0.138 -0.076 0.060 -0.127 -0.124 0.5740381369 112 -0.179 -0.138 -0.075 0.060 -0.127 -0.124 0.5740380875 121 -0.179 -0.138 -0.075 0.067 -0.127 -0.124 0.5740370003 130 -0.179 -0.138 -0.075 0.067 -0.147 -0.124 0.5740299009 131 -0.179 -0.138 -0.075 0.067 -0.143 -0.124 0.5740290835 132 -0.179 -0.138 -0.075 0.067 -0.142 -0.124 0.5740290639 142 -0.179 -0.138 -0.075 0.067 -0.142 -0.121 0.5740290133 powell nthiter 2: fret = 0.574029 153 -0.177 -0.138 -0.075 0.067 -0.142 -0.122 0.5740289562 165 -0.176 -0.141 -0.075 0.067 -0.142 -0.122 0.5740288872 167 -0.176 -0.140 -0.075 0.067 -0.142 -0.122 0.5740288792 175 -0.176 -0.140 -0.076 0.067 -0.142 -0.122 0.5740288603 202 -0.176 -0.140 -0.076 0.067 -0.142 -0.120 0.5740288189 powell nthiter 3: fret = 0.574029 218 -0.180 -0.140 -0.076 0.067 -0.142 -0.120 0.5740287982 220 -0.178 -0.140 -0.076 0.067 -0.142 -0.120 0.5740286976 230 -0.178 -0.141 -0.076 0.067 -0.142 -0.120 0.5740286646 powell nthiter 4: fret = 0.574029 Powell done niters = 4 Computing relative cost 0 -25.0 -25.0 -25.0 1.042605 1 -25.0 -25.0 25.0 1.059107 2 -25.0 25.0 -25.0 1.061220 3 -25.0 25.0 25.0 1.067018 4 25.0 -25.0 -25.0 1.041190 5 25.0 -25.0 25.0 1.038381 6 25.0 25.0 -25.0 1.026362 7 25.0 25.0 25.0 1.058163 REL: 8 0.574029 8.394046 1.049256 rel = 0.547082 Number of iterations 4 Min cost was 0.574029 Number of FunctionCalls 327 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 39.169000 sec Parameters at optimum (transmm) -0.17750 -0.14145 -0.07556 Parameters at optimum (rotdeg) 0.06718 -0.14231 -0.11978 Final costs ---------------- Number of surface hits 304441 WM Intensity 822.8239 +/- 217.8386 Ctx Intensity 850.7266 +/- 249.7037 Pct Contrast 1.4813 +/- 21.8878 Cost 0.5740 RelCost 0.5484 Reg at min cost was 1.00000 -0.00030 -0.00116 0.63848; 0.00106 -0.23893 0.97104 -40.48510; 0.00057 0.97104 0.23893 -1.35981; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/001/register.dof6.dat, type = 14 Original Reg 0.99999 0.00261 -0.00260 0.89712; 0.00314 -0.23779 0.97131 -40.34334; -0.00192 0.97131 0.23780 -1.23918; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00001 0.00291 -0.00144 0.25864; 0.00209 0.00114 0.00028 0.14176; -0.00249 0.00028 -0.00113 0.12063; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.268551 Computing change in rh position Surface-RMS-Diff-mm 0.278744 0.119083 0.560626 mri_segreg done MinCost: 0.574029 822.823927 850.726610 1.481314 tkregister2_cmdl --mov bold/001/template.nii.gz --reg bold/001/register.dof6.dat --noedit --ltaout bold/001/register.dof6.lta tkregister_tcl /usr/local/freesurfer/dev/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume bold/001/template.nii.gz reg file bold/001/register.dof6.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.131 2016/03/24 17:39:56 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- 1.00000 -0.00030 -0.00116 0.63848; 0.00106 -0.23893 0.97104 -40.48510; 0.00057 0.97104 0.23893 -1.35981; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: loading target /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/orig.mgz Ttarg: -------------------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading movable bold/001/template.nii.gz Tmov: -------------------- -3.43750 0.00000 0.00000 110.00000; 0.00000 0.00000 5.00000 -75.00000; 0.00000 -3.43750 0.00000 109.99999; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 1.00000 -0.00030 -0.00116 0.63848; 0.00106 -0.23893 0.97104 -40.48510; 0.00057 0.97104 0.23893 -1.35981; 0.00000 0.00000 0.00000 1.00000; Determinant -1 subject = fsf01anat RegMat --------------------------- 1.00000 -0.00030 -0.00116 0.63848; 0.00106 -0.23893 0.97104 -40.48510; 0.00057 0.97104 0.23893 -1.35981; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Sun Mar 27 21:40:38 EDT 2016 Ended at Sun Mar 27 21:43:35 EDT 2016 BBR-Run-Time-Sec 177 bbregister Done To check results, run: tkregister2 --mov bold/001/template.nii.gz --reg bold/001/register.dof6.dat --surf Run: 002 ---------------- Sun Mar 27 21:43:35 EDT 2016 -------------------------------------- /autofs/cluster/pubftp/data/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.8216 Log file is bold/002/register.dof6.dat.log Sun Mar 27 21:43:35 EDT 2016 setenv SUBJECTS_DIR /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects cd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01 /usr/local/freesurfer/dev/bin/bbregister --s fsf01anat --init-coreg --6 --bold --mov bold/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 1.74 2016/02/17 21:07:31 greve Exp $ Linux transfer 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer/dev mri_convert bold/002/template.nii.gz bold/002/tmp.bbregister.8216/template.nii mri_convert.bin bold/002/template.nii.gz bold/002/tmp.bbregister.8216/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.8216/template.nii... mri_coreg --s fsf01anat --mov bold/002/tmp.bbregister.8216/template.nii --regdat bold/002/tmp.bbregister.8216/reg.init.dat --reg bold/002/tmp.bbregister.8216/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 freadFloat: fread failed $Id: mri_coreg.c,v 1.26 2016/01/20 23:42:39 greve Exp $ cwd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01 cmdline mri_coreg --s fsf01anat --mov bold/002/tmp.bbregister.8216/template.nii --regdat bold/002/tmp.bbregister.8216/reg.init.dat --reg bold/002/tmp.bbregister.8216/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 sysname Linux hostname transfer machine x86_64 user zkaufman dof 6 nsep 1 cras0 1 ftol 0.000100 linmintol 0.010000 bf 1 bflim 30.000000 bfnsamp 30 SmoothRef 0 SatPct 99.990000 MovOOB 0 Reading in mov bold/002/tmp.bbregister.8216/template.nii Reading in ref /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/brainmask.mgz freadFloat: fread failed Reading in and applying refmask /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/aparc+aseg.mgz Setting cras translation parameters to align centers Creating random numbers for coordinate dithering Performing intensity dithering Initial parameters -6.0223 -45.2577 79.2380 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Separation list (1): 4 min = 4 DoSmoothing 1 DoCoordDither 1 DoIntensityDither 1 nitersmax 4 ftol 1.000e-04 linmintol 1.000e-02 SatPct 99.990000 Hist FWHM 7.000000 7.000000 nthreads 1 movsat = 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 -1.0208344040 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 -1.0503549 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6 Starting OpenPowel2(), sep = 4 InitialCost -1.0718224049 #@# 4 188 -6.02228 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0718224 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.071822 #@# 4 193 -6.64031 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0719349 #@# 4 195 -6.59165 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0719365 #@# 4 198 -6.61507 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0719366 #@# 4 202 -6.61507 -36.87573 49.23798 4.00000 0.00000 0.00000 -1.0745635 #@# 4 205 -6.61507 -41.17706 49.23798 4.00000 0.00000 0.00000 -1.0759979 #@# 4 207 -6.61507 -39.72627 49.23798 4.00000 0.00000 0.00000 -1.0767008 #@# 4 208 -6.61507 -39.60749 49.23798 4.00000 0.00000 0.00000 -1.0767057 #@# 4 210 -6.61507 -39.61750 49.23798 4.00000 0.00000 0.00000 -1.0767063 #@# 4 212 -6.61507 -39.63502 49.23798 4.00000 0.00000 0.00000 -1.0767068 #@# 4 213 -6.61507 -39.64502 49.23798 4.00000 0.00000 0.00000 -1.0767070 #@# 4 218 -6.61507 -39.64502 48.61994 4.00000 0.00000 0.00000 -1.0768584 #@# 4 221 -6.61507 -39.64502 48.67850 4.00000 0.00000 0.00000 -1.0768603 #@# 4 226 -6.61507 -39.64502 48.69041 4.00000 0.00000 0.00000 -1.0768607 #@# 4 233 -6.61507 -39.64502 48.69041 3.69351 0.00000 0.00000 -1.0769408 #@# 4 243 -6.61507 -39.64502 48.69041 3.69351 0.11487 0.00000 -1.0769414 #@# 4 244 -6.61507 -39.64502 48.69041 3.69351 0.07907 0.00000 -1.0769424 #@# 4 245 -6.61507 -39.64502 48.69041 3.69351 0.06327 0.00000 -1.0769441 #@# 4 254 -6.61507 -39.64502 48.69041 3.69351 0.05327 -0.11267 -1.0769488 #@# 4 255 -6.61507 -39.64502 48.69041 3.69351 0.05327 -0.07416 -1.0769519 #@# 4 256 -6.61507 -39.64502 48.69041 3.69351 0.05327 -0.06416 -1.0769525 #@# 4 266 -6.64182 -39.84299 48.66570 3.67968 0.05568 -0.06706 -1.0769551 #@# 4 267 -6.63195 -39.76992 48.67482 3.68479 0.05479 -0.06599 -1.0769573 powell nthiter 1: fret = -1.076957 #@# 4 284 -6.63195 -39.76992 48.67482 3.68479 0.05479 -0.11174 -1.0769575 #@# 4 295 -6.63195 -39.76992 48.05679 3.68479 0.05479 -0.10174 -1.0770384 #@# 4 297 -6.63195 -39.76992 48.22495 3.68479 0.05479 -0.10174 -1.0770584 #@# 4 298 -6.63195 -39.76992 48.24800 3.68479 0.05479 -0.10174 -1.0770628 #@# 4 309 -6.63195 -39.76992 48.24800 3.40638 0.05479 -0.10174 -1.0771101 #@# 4 310 -6.63195 -39.76992 48.24800 3.41702 0.05479 -0.10174 -1.0771109 #@# 4 331 -6.63788 -39.81379 48.24252 3.41395 0.05532 -0.10238 -1.0771112 #@# 4 332 -6.64380 -39.85767 48.23705 3.41089 0.05585 -0.10302 -1.0771115 #@# 4 333 -6.67254 -40.07031 47.78368 3.12826 0.05844 -0.14188 -1.0772173 #@# 4 336 -6.71902 -40.41438 47.05012 2.67096 0.06261 -0.20474 -1.0773371 #@# 4 339 -6.74358 -40.59613 46.66264 2.42940 0.06482 -0.23795 -1.0773462 #@# 4 341 -6.73429 -40.52739 46.80918 2.52076 0.06399 -0.22539 -1.0773517 #@# 4 342 -6.73401 -40.52527 46.81372 2.52358 0.06396 -0.22501 -1.0773519 #@# 4 346 -6.73372 -40.52314 46.81825 2.52641 0.06393 -0.22462 -1.0773520 powell nthiter 2: fret = -1.077352 #@# 4 353 -6.35147 -40.52102 46.82278 2.52923 0.06391 -0.22423 -1.0773767 #@# 4 354 -6.50145 -40.52102 46.82278 2.52923 0.06391 -0.22423 -1.0774014 #@# 4 372 -6.45092 -40.14699 46.86946 2.55536 0.05937 -0.21876 -1.0774232 #@# 4 382 -6.47105 -40.29596 46.85087 2.36651 0.06118 -0.22094 -1.0774385 #@# 4 383 -6.47105 -40.29596 46.85087 2.38684 0.06118 -0.22094 -1.0774398 #@# 4 384 -6.47105 -40.29596 46.85087 2.41066 0.06118 -0.22094 -1.0774417 #@# 4 395 -6.47105 -40.29596 46.85087 2.41066 0.08931 -0.22094 -1.0774440 #@# 4 399 -6.49978 -40.50860 46.39751 2.12803 0.09189 -0.25979 -1.0774601 #@# 4 404 -6.49429 -40.46799 46.48409 2.18201 0.09140 -0.25237 -1.0774612 #@# 4 407 -6.49509 -40.47392 46.47146 2.17414 0.09147 -0.25345 -1.0774614 powell nthiter 3: fret = -1.077461 #@# 4 418 -6.47534 -40.47392 46.47146 2.17414 0.09147 -0.25345 -1.0774621 #@# 4 439 -6.43065 -40.24802 46.49965 2.18992 0.08873 -0.25015 -1.0774789 #@# 4 441 -6.43658 -40.29189 46.49417 2.18685 0.08926 -0.25079 -1.0774796 #@# 4 469 -6.44755 -40.37312 46.32101 2.07890 0.09025 -0.26563 -1.0774847 #@# 4 470 -6.44691 -40.36834 46.33119 2.08525 0.09019 -0.26476 -1.0774853 #@# 4 472 -6.44572 -40.35956 46.34992 2.09692 0.09008 -0.26316 -1.0774854 #@# 4 473 -6.44620 -40.36312 46.34232 2.09218 0.09012 -0.26381 -1.0774865 Powell done niters total = 3 OptTimeSec 23.1 sec OptTimeMin 0.39 min nEvals 474 Final parameters -6.44620275 -40.36312103 46.34231567 2.09218264 0.09012368 -0.26380762 Final cost -1.077486459939647 --------------------------------- mri_coreg utimesec 112.763857 mri_coreg stimesec 0.577912 mri_coreg ru_maxrss 422120 mri_coreg ru_ixrss 0 mri_coreg ru_idrss 0 mri_coreg ru_isrss 0 mri_coreg ru_minflt 262272 mri_coreg ru_majflt 0 mri_coreg ru_nswap 0 mri_coreg ru_inblock 0 mri_coreg ru_oublock 0 mri_coreg ru_msgsnd 0 mri_coreg ru_msgrcv 0 mri_coreg ru_nsignals 0 mri_coreg ru_nvcsw 48 mri_coreg ru_nivcsw 212 Final RefRAS-to-MovRAS 0.99999 -0.00460 0.00157 -6.44620; 0.00454 0.99932 0.03651 -40.36312; -0.00174 -0.03650 0.99933 46.34232; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox 0.29091 0.00046 0.00134 -5.60242; 0.00117 0.07623 -0.28074 58.65872; 0.00054 -0.19301 -0.05241 38.71618; 0.00000 0.00000 0.00000 1.00000; Final parameters -6.4462 -40.3631 46.3423 2.0922 0.0901 -0.2638 nhits = 105996 out of 16777216, Percent Overlap: 40.4 mri_coreg RunTimeSec 113.4 sec To check run: tkregisterfv --mov bold/002/tmp.bbregister.8216/template.nii --targ /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/brainmask.mgz --reg bold/002/tmp.bbregister.8216/mri_coreg.lta --s fsf01anat --surfs mri_coreg done mri_segreg --mov bold/002/tmp.bbregister.8216/template.nii --init-reg bold/002/tmp.bbregister.8216/reg.init.dat --out-reg bold/002/tmp.bbregister.8216/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.112 2014/02/25 19:06:37 greve Exp $ setenv SUBJECTS_DIR /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects cd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01 mri_segreg --mov bold/002/tmp.bbregister.8216/template.nii --init-reg bold/002/tmp.bbregister.8216/reg.init.dat --out-reg bold/002/tmp.bbregister.8216/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Linux hostname transfer machine x86_64 user zkaufman movvol bold/002/tmp.bbregister.8216/template.nii regfile bold/002/tmp.bbregister.8216/reg.init.dat subject fsf01anat dof 6 outregfile bold/002/tmp.bbregister.8216/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 1459251226 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99999 -0.00460 0.00157 0.46915; -0.00272 -0.26205 0.96505 -38.13902; 0.00403 0.96504 0.26206 -2.17302; 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 1.074729 1 -25.0 -25.0 25.0 1.051907 2 -25.0 25.0 -25.0 1.067790 3 -25.0 25.0 25.0 1.069653 4 25.0 -25.0 -25.0 1.050159 5 25.0 -25.0 25.0 1.068417 6 25.0 25.0 -25.0 1.030957 7 25.0 25.0 25.0 1.061691 REL: 8 0.701297 8.475304 1.059413 rel = 0.661968 Initial costs ---------------- Number of surface hits 3040 WM Intensity 849.3710 +/- 206.7691 Ctx Intensity 857.4528 +/- 235.1353 Pct Contrast -0.6538 +/- 21.1345 Cost 0.7013 RelCost 0.6620 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 1.0714 1.0714 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 1.0529 1.0529 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 1.0177 1.0177 0.0 5 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 4.0000 0.9893 0.9893 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.9779 0.9779 0.0 8 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 4.0000 0.9658 0.9658 0.0 18 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 -4.0000 0.9462 0.9462 0.0 33 -4.0000 -4.0000 0.0000 -4.0000 4.0000 -4.0000 0.9396 0.9396 0.0 34 -4.0000 -4.0000 0.0000 -4.0000 4.0000 0.0000 0.9260 0.9260 0.0 39 -4.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.9157 0.9157 0.0 40 -4.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.9065 0.9065 0.0 273 0.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.8496 0.8496 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.8065 0.8065 0.0 282 0.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.7663 0.7663 0.0 283 0.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.6195 0.6195 0.0 Brute Force -------------------------- Min cost was 0.619521 Number of iterations 729 Search time 1.386000 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 = 0.619521 8 0.052 -4.000 0.000 0.000 0.000 0.000 0.6192315294 10 0.100 -4.000 0.000 0.000 0.000 0.000 0.6191724077 11 0.096 -4.000 0.000 0.000 0.000 0.000 0.6191718859 12 0.095 -4.000 0.000 0.000 0.000 0.000 0.6191718595 13 0.094 -4.000 0.000 0.000 0.000 0.000 0.6191717677 17 0.093 -4.000 0.000 0.000 0.000 0.000 0.6191717354 19 0.093 -3.000 0.000 0.000 0.000 0.000 0.5888402214 22 0.093 -2.382 0.000 0.000 0.000 0.000 0.5852215621 24 0.093 -2.581 0.000 0.000 0.000 0.000 0.5841867824 25 0.093 -2.580 0.000 0.000 0.000 0.000 0.5841754873 26 0.093 -2.518 0.000 0.000 0.000 0.000 0.5839802364 28 0.093 -2.531 0.000 0.000 0.000 0.000 0.5839200071 29 0.093 -2.539 0.000 0.000 0.000 0.000 0.5839067332 31 0.093 -2.537 0.000 0.000 0.000 0.000 0.5839021403 33 0.093 -2.538 0.000 0.000 0.000 0.000 0.5839007442 42 0.093 -2.538 -0.005 0.000 0.000 0.000 0.5838999106 43 0.093 -2.538 -0.003 0.000 0.000 0.000 0.5838992203 52 0.093 -2.538 -0.003 -0.137 0.000 0.000 0.5831161379 54 0.093 -2.538 -0.003 -0.108 0.000 0.000 0.5830386948 57 0.093 -2.538 -0.003 -0.104 0.000 0.000 0.5830369094 58 0.093 -2.538 -0.003 -0.103 0.000 0.000 0.5830369056 65 0.093 -2.538 -0.003 -0.103 0.382 0.000 0.5825666541 66 0.093 -2.538 -0.003 -0.103 0.207 0.000 0.5822679643 68 0.093 -2.538 -0.003 -0.103 0.128 0.000 0.5819977149 69 0.093 -2.538 -0.003 -0.103 0.093 0.000 0.5819512677 72 0.093 -2.538 -0.003 -0.103 0.087 0.000 0.5819476405 74 0.093 -2.538 -0.003 -0.103 0.088 0.000 0.5819469479 81 0.093 -2.538 -0.003 -0.103 0.088 0.382 0.5794954486 85 0.093 -2.538 -0.003 -0.103 0.088 0.379 0.5794916054 86 0.093 -2.538 -0.003 -0.103 0.088 0.374 0.5794887143 88 0.093 -2.538 -0.003 -0.103 0.088 0.373 0.5794885800 powell nthiter 1: fret = 0.579489 97 0.135 -2.538 -0.003 -0.103 0.088 0.373 0.5791607900 98 0.183 -2.538 -0.003 -0.103 0.088 0.373 0.5789931972 100 0.187 -2.538 -0.003 -0.103 0.088 0.373 0.5789919910 110 0.187 -2.517 -0.003 -0.103 0.088 0.373 0.5789144307 111 0.187 -2.509 -0.003 -0.103 0.088 0.373 0.5788985824 121 0.187 -2.509 -0.045 -0.103 0.088 0.373 0.5787029347 122 0.187 -2.509 -0.083 -0.103 0.088 0.373 0.5786726938 123 0.187 -2.509 -0.073 -0.103 0.088 0.373 0.5786612507 124 0.187 -2.509 -0.070 -0.103 0.088 0.373 0.5786598255 126 0.187 -2.509 -0.069 -0.103 0.088 0.373 0.5786590362 128 0.187 -2.509 -0.068 -0.103 0.088 0.373 0.5786586472 137 0.187 -2.509 -0.068 -0.058 0.088 0.373 0.5784014595 141 0.187 -2.509 -0.068 -0.039 0.088 0.373 0.5783808848 143 0.187 -2.509 -0.068 -0.042 0.088 0.373 0.5783798438 144 0.187 -2.509 -0.068 -0.043 0.088 0.373 0.5783798273 152 0.187 -2.509 -0.068 -0.043 0.233 0.373 0.5775691277 153 0.187 -2.509 -0.068 -0.043 0.227 0.373 0.5775657708 154 0.187 -2.509 -0.068 -0.043 0.223 0.373 0.5775640366 168 0.187 -2.509 -0.068 -0.043 0.223 0.358 0.5775418059 170 0.187 -2.509 -0.068 -0.043 0.223 0.349 0.5775352362 171 0.187 -2.509 -0.068 -0.043 0.223 0.348 0.5775349185 172 0.187 -2.509 -0.068 -0.043 0.223 0.346 0.5775342602 174 0.187 -2.509 -0.068 -0.043 0.223 0.345 0.5775341321 powell nthiter 2: fret = 0.577534 183 0.207 -2.509 -0.068 -0.043 0.223 0.345 0.5773671198 184 0.269 -2.509 -0.068 -0.043 0.223 0.345 0.5773465341 186 0.240 -2.509 -0.068 -0.043 0.223 0.345 0.5772464059 187 0.239 -2.509 -0.068 -0.043 0.223 0.345 0.5772458041 189 0.238 -2.509 -0.068 -0.043 0.223 0.345 0.5772454014 197 0.238 -2.510 -0.068 -0.043 0.223 0.345 0.5772381297 198 0.238 -2.527 -0.068 -0.043 0.223 0.345 0.5772160453 200 0.238 -2.524 -0.068 -0.043 0.223 0.345 0.5772128924 201 0.238 -2.522 -0.068 -0.043 0.223 0.345 0.5772122773 203 0.238 -2.521 -0.068 -0.043 0.223 0.345 0.5772118901 204 0.238 -2.520 -0.068 -0.043 0.223 0.345 0.5772116408 213 0.238 -2.520 0.001 -0.043 0.223 0.345 0.5770800449 215 0.238 -2.520 -0.024 -0.043 0.223 0.345 0.5770192560 227 0.238 -2.520 -0.024 -0.044 0.223 0.345 0.5770189997 235 0.238 -2.520 -0.024 -0.044 0.269 0.345 0.5769073872 236 0.238 -2.520 -0.024 -0.044 0.268 0.345 0.5769065765 237 0.238 -2.520 -0.024 -0.044 0.263 0.345 0.5769060505 239 0.238 -2.520 -0.024 -0.044 0.265 0.345 0.5769058137 251 0.238 -2.520 -0.024 -0.044 0.265 0.346 0.5769054435 powell nthiter 3: fret = 0.576905 265 0.247 -2.520 -0.024 -0.044 0.265 0.347 0.5768904227 275 0.248 -2.521 -0.024 -0.044 0.265 0.347 0.5768868190 276 0.248 -2.537 -0.024 -0.044 0.265 0.347 0.5768808121 278 0.248 -2.531 -0.024 -0.044 0.265 0.347 0.5768775802 289 0.248 -2.532 -0.022 -0.044 0.265 0.347 0.5768773847 299 0.248 -2.532 -0.022 -0.040 0.265 0.347 0.5768771487 300 0.248 -2.532 -0.022 -0.042 0.265 0.347 0.5768767782 301 0.248 -2.532 -0.022 -0.043 0.265 0.347 0.5768767225 308 0.248 -2.532 -0.022 -0.043 0.276 0.347 0.5768713474 309 0.248 -2.532 -0.022 -0.043 0.275 0.347 0.5768711240 319 0.248 -2.532 -0.022 -0.043 0.275 0.352 0.5768697970 Powell done niters = 3 Computing relative cost 0 -25.0 -25.0 -25.0 1.055362 1 -25.0 -25.0 25.0 1.052615 2 -25.0 25.0 -25.0 1.065683 3 -25.0 25.0 25.0 1.080333 4 25.0 -25.0 -25.0 1.061283 5 25.0 -25.0 25.0 1.048964 6 25.0 25.0 -25.0 1.015041 7 25.0 25.0 25.0 1.036502 REL: 8 0.576870 8.415783 1.051973 rel = 0.548369 Number of iterations 3 Min cost was 0.576870 Number of FunctionCalls 324 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.622000 sec Parameters at optimum (transmm) 0.24849 -2.53183 -0.02215 Parameters at optimum (rotdeg) -0.04262 0.27451 0.35242 Final costs ---------------- Number of surface hits 3040 WM Intensity 819.5308 +/- 220.2267 Ctx Intensity 845.7718 +/- 250.8758 Pct Contrast 1.2641 +/- 21.5617 Cost 0.5769 RelCost 0.6620 Reg at min cost was 0.99999 0.00163 -0.00311 0.94194; 0.00343 -0.26132 0.96524 -40.66891; -0.00076 0.96525 0.26133 -2.16902; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/002/tmp.bbregister.8216/bbr.pass1.dat, type = 14 Original Reg 0.99999 -0.00460 0.00157 0.46915; -0.00272 -0.26205 0.96505 -38.13902; 0.00403 0.96504 0.26206 -2.17302; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00001 -0.00623 0.00469 -0.47280; -0.00615 -0.00072 -0.00019 2.52989; 0.00479 -0.00021 0.00073 -0.00400; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 2.712676 Computing change in rh position Surface-RMS-Diff-mm 2.550597 0.194105 2.954893 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.8216/template.nii --init-reg bold/002/tmp.bbregister.8216/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.8216/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.112 2014/02/25 19:06:37 greve Exp $ setenv SUBJECTS_DIR /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects cd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01 mri_segreg --mov bold/002/tmp.bbregister.8216/template.nii --init-reg bold/002/tmp.bbregister.8216/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.8216/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname transfer machine x86_64 user zkaufman movvol bold/002/tmp.bbregister.8216/template.nii regfile bold/002/tmp.bbregister.8216/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 1459770015 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99999 0.00163 -0.00311 0.94194; 0.00343 -0.26132 0.96524 -40.66891; -0.00076 0.96525 0.26133 -2.16902; 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 1.044124 1 -25.0 -25.0 25.0 1.059863 2 -25.0 25.0 -25.0 1.058965 3 -25.0 25.0 25.0 1.063359 4 25.0 -25.0 -25.0 1.035627 5 25.0 -25.0 25.0 1.041665 6 25.0 25.0 -25.0 1.032164 7 25.0 25.0 25.0 1.059059 REL: 8 0.585388 8.394826 1.049353 rel = 0.557856 Initial costs ---------------- Number of surface hits 304441 WM Intensity 821.4523 +/- 217.7281 Ctx Intensity 848.2581 +/- 248.1382 Pct Contrast 1.4413 +/- 21.8614 Cost 0.5854 RelCost 0.5579 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.5798 0.5798 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.5789 0.5789 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.5786 0.5786 0.0 28 -0.1000 -0.1000 0.0000 -0.1000 -0.1000 0.0000 0.5781 0.5781 0.0 31 -0.1000 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.5778 0.5778 0.0 109 -0.1000 0.0000 0.0000 -0.1000 -0.1000 0.0000 0.5778 0.5778 0.0 118 -0.1000 0.0000 0.0000 0.0000 -0.1000 0.0000 0.5777 0.5777 0.0 274 0.0000 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.5777 0.5777 0.0 283 0.0000 -0.1000 0.0000 0.0000 0.0000 0.0000 0.5774 0.5774 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.5769 0.5769 0.0 Brute Force -------------------------- Min cost was 0.576870 Number of iterations 729 Search time 1.409000 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 = 0.585388 7 -0.193 0.000 0.000 0.000 0.000 0.000 0.5848983126 8 -0.163 0.000 0.000 0.000 0.000 0.000 0.5848773659 9 -0.160 0.000 0.000 0.000 0.000 0.000 0.5848768811 12 -0.159 0.000 0.000 0.000 0.000 0.000 0.5848768645 19 -0.159 -0.056 0.000 0.000 0.000 0.000 0.5848349526 20 -0.159 -0.045 0.000 0.000 0.000 0.000 0.5848334132 21 -0.159 -0.047 0.000 0.000 0.000 0.000 0.5848332127 30 -0.159 -0.048 0.060 0.000 0.000 0.000 0.5847736040 31 -0.159 -0.048 0.051 0.000 0.000 0.000 0.5847687304 32 -0.159 -0.048 0.047 0.000 0.000 0.000 0.5847683639 41 -0.159 -0.048 0.048 -0.302 0.000 0.000 0.5831120361 42 -0.159 -0.048 0.048 -0.303 0.000 0.000 0.5831116563 43 -0.159 -0.048 0.048 -0.315 0.000 0.000 0.5831115255 45 -0.159 -0.048 0.048 -0.309 0.000 0.000 0.5831107631 55 -0.159 -0.048 0.048 -0.308 -0.046 0.000 0.5829994981 57 -0.159 -0.048 0.048 -0.308 -0.057 0.000 0.5829956989 59 -0.159 -0.048 0.048 -0.308 -0.058 0.000 0.5829956958 66 -0.159 -0.048 0.048 -0.308 -0.058 -0.618 0.5805096899 68 -0.159 -0.048 0.048 -0.308 -0.058 -0.511 0.5803175224 69 -0.159 -0.048 0.048 -0.308 -0.058 -0.459 0.5803063548 70 -0.159 -0.048 0.048 -0.308 -0.058 -0.474 0.5803056487 71 -0.159 -0.048 0.048 -0.308 -0.058 -0.470 0.5803056486 72 -0.159 -0.048 0.048 -0.308 -0.058 -0.472 0.5803056038 74 -0.159 -0.048 0.048 -0.308 -0.058 -0.471 0.5803054524 powell nthiter 1: fret = 0.580305 82 -0.266 -0.048 0.048 -0.308 -0.058 -0.471 0.5800093472 83 -0.280 -0.048 0.048 -0.308 -0.058 -0.471 0.5800051676 98 -0.282 0.039 0.048 -0.308 -0.058 -0.471 0.5798871710 99 -0.282 0.031 0.048 -0.308 -0.058 -0.471 0.5798865647 103 -0.282 0.027 0.048 -0.308 -0.058 -0.471 0.5798863255 104 -0.282 0.024 0.048 -0.308 -0.058 -0.471 0.5798862797 106 -0.282 0.025 0.048 -0.308 -0.058 -0.471 0.5798862691 113 -0.282 0.025 0.085 -0.308 -0.058 -0.471 0.5798736144 114 -0.282 0.025 0.074 -0.308 -0.058 -0.471 0.5798705115 115 -0.282 0.025 0.073 -0.308 -0.058 -0.471 0.5798704906 123 -0.282 0.025 0.073 -0.321 -0.058 -0.471 0.5798644084 124 -0.282 0.025 0.073 -0.328 -0.058 -0.471 0.5798627554 126 -0.282 0.025 0.073 -0.338 -0.058 -0.471 0.5798603129 130 -0.282 0.025 0.073 -0.342 -0.058 -0.471 0.5798599482 131 -0.282 0.025 0.073 -0.343 -0.058 -0.471 0.5798598454 140 -0.282 0.025 0.073 -0.343 -0.097 -0.471 0.5798161910 141 -0.282 0.025 0.073 -0.343 -0.098 -0.471 0.5798153923 142 -0.282 0.025 0.073 -0.343 -0.110 -0.471 0.5798130764 143 -0.282 0.025 0.073 -0.343 -0.111 -0.471 0.5798130658 144 -0.282 0.025 0.073 -0.343 -0.112 -0.471 0.5798129085 157 -0.282 0.025 0.073 -0.343 -0.112 -0.586 0.5796557316 159 -0.282 0.025 0.073 -0.343 -0.112 -0.583 0.5796554872 162 -0.282 0.025 0.073 -0.343 -0.112 -0.578 0.5796553764 powell nthiter 2: fret = 0.579655 173 -0.293 0.025 0.073 -0.343 -0.112 -0.578 0.5796435441 174 -0.312 0.025 0.073 -0.343 -0.112 -0.578 0.5796348469 176 -0.311 0.025 0.073 -0.343 -0.112 -0.578 0.5796348170 187 -0.310 0.049 0.073 -0.343 -0.112 -0.578 0.5796032413 188 -0.310 0.066 0.073 -0.343 -0.112 -0.578 0.5795929137 189 -0.310 0.073 0.073 -0.343 -0.112 -0.578 0.5795922171 200 -0.310 0.071 0.075 -0.343 -0.112 -0.578 0.5795921954 209 -0.310 0.071 0.075 -0.376 -0.112 -0.578 0.5795799538 210 -0.310 0.071 0.075 -0.371 -0.112 -0.578 0.5795782400 212 -0.310 0.071 0.075 -0.370 -0.112 -0.578 0.5795782162 220 -0.310 0.071 0.075 -0.370 -0.115 -0.578 0.5795773774 221 -0.310 0.071 0.075 -0.370 -0.119 -0.578 0.5795769165 223 -0.310 0.071 0.075 -0.370 -0.118 -0.578 0.5795768940 231 -0.310 0.071 0.075 -0.370 -0.118 -0.601 0.5795756225 232 -0.310 0.071 0.075 -0.370 -0.118 -0.592 0.5795751630 233 -0.310 0.071 0.075 -0.370 -0.118 -0.593 0.5795750961 powell nthiter 3: fret = 0.579575 244 -0.314 0.071 0.075 -0.370 -0.118 -0.594 0.5795748604 255 -0.313 0.075 0.075 -0.370 -0.118 -0.594 0.5795743929 264 -0.313 0.076 0.079 -0.370 -0.118 -0.594 0.5795743502 265 -0.313 0.076 0.077 -0.370 -0.118 -0.594 0.5795742975 275 -0.313 0.076 0.076 -0.365 -0.118 -0.594 0.5795741471 277 -0.313 0.076 0.076 -0.367 -0.118 -0.594 0.5795740408 294 -0.313 0.076 0.076 -0.367 -0.117 -0.602 0.5795738264 301 -0.316 0.080 0.077 -0.364 -0.115 -0.609 0.5795735083 powell nthiter 4: fret = 0.579574 309 -0.317 0.076 0.076 -0.367 -0.117 -0.602 0.5795733837 310 -0.318 0.076 0.076 -0.367 -0.117 -0.602 0.5795733445 311 -0.319 0.076 0.076 -0.367 -0.117 -0.602 0.5795733071 327 -0.320 0.077 0.076 -0.367 -0.117 -0.602 0.5795732957 336 -0.320 0.077 0.074 -0.367 -0.117 -0.602 0.5795732460 351 -0.320 0.077 0.073 -0.365 -0.117 -0.602 0.5795729178 368 -0.320 0.077 0.073 -0.365 -0.117 -0.604 0.5795726913 369 -0.320 0.077 0.073 -0.365 -0.117 -0.608 0.5795722814 371 -0.320 0.077 0.073 -0.365 -0.117 -0.614 0.5795721369 372 -0.320 0.077 0.073 -0.365 -0.117 -0.613 0.5795720359 374 -0.327 0.078 0.070 -0.363 -0.117 -0.624 0.5795702969 387 -0.327 0.078 0.070 -0.363 -0.117 -0.624 0.5795702810 388 -0.327 0.078 0.070 -0.363 -0.117 -0.624 0.5795702683 powell nthiter 5: fret = 0.579570 400 -0.331 0.078 0.070 -0.363 -0.117 -0.624 0.5795701396 415 -0.331 0.085 0.070 -0.363 -0.117 -0.624 0.5795697983 416 -0.331 0.082 0.070 -0.363 -0.117 -0.624 0.5795692785 426 -0.331 0.081 0.069 -0.363 -0.117 -0.624 0.5795692444 436 -0.331 0.081 0.068 -0.360 -0.117 -0.624 0.5795685952 437 -0.331 0.081 0.068 -0.356 -0.117 -0.624 0.5795685126 439 -0.331 0.081 0.068 -0.358 -0.117 -0.624 0.5795683624 447 -0.331 0.081 0.068 -0.358 -0.123 -0.624 0.5795668048 449 -0.331 0.081 0.068 -0.358 -0.122 -0.624 0.5795668047 463 -0.331 0.081 0.068 -0.358 -0.122 -0.624 0.5795667962 464 -0.331 0.081 0.068 -0.358 -0.122 -0.624 0.5795667801 powell nthiter 6: fret = 0.579567 476 -0.329 0.081 0.068 -0.358 -0.122 -0.624 0.5795667538 486 -0.329 0.084 0.068 -0.358 -0.122 -0.624 0.5795667226 488 -0.329 0.083 0.068 -0.358 -0.122 -0.624 0.5795666462 497 -0.329 0.082 0.067 -0.358 -0.122 -0.624 0.5795666254 516 -0.329 0.082 0.067 -0.358 -0.123 -0.624 0.5795665861 517 -0.329 0.082 0.067 -0.358 -0.124 -0.624 0.5795665420 523 -0.329 0.082 0.067 -0.358 -0.126 -0.624 0.5795664955 540 -0.329 0.082 0.067 -0.358 -0.126 -0.624 0.5795664803 powell nthiter 7: fret = 0.579566 Powell done niters = 7 Computing relative cost 0 -25.0 -25.0 -25.0 1.045638 1 -25.0 -25.0 25.0 1.056579 2 -25.0 25.0 -25.0 1.055536 3 -25.0 25.0 25.0 1.065014 4 25.0 -25.0 -25.0 1.036060 5 25.0 -25.0 25.0 1.039382 6 25.0 25.0 -25.0 1.023601 7 25.0 25.0 25.0 1.053313 REL: 8 0.579567 8.375122 1.046890 rel = 0.553608 Number of iterations 7 Min cost was 0.579567 Number of FunctionCalls 609 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 72.814000 sec Parameters at optimum (transmm) -0.32808 0.08248 0.06722 Parameters at optimum (rotdeg) -0.35878 -0.12631 -0.62388 Final costs ---------------- Number of surface hits 304441 WM Intensity 821.4983 +/- 216.3940 Ctx Intensity 849.5079 +/- 247.0991 Pct Contrast 1.5364 +/- 21.7383 Cost 0.5796 RelCost 0.5579 Reg at min cost was 0.99997 -0.00328 0.00685 0.17506; -0.00746 -0.25525 0.96685 -40.60711; 0.00143 0.96687 0.25527 -1.84502; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/002/register.dof6.dat, type = 14 Original Reg 0.99999 0.00163 -0.00311 0.94194; 0.00343 -0.26132 0.96524 -40.66891; -0.00076 0.96525 0.26133 -2.16902; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00002 0.00491 -0.00997 0.76688; 0.01089 -0.00607 -0.00160 -0.06180; -0.00218 -0.00162 0.00606 -0.32400; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.627115 Computing change in rh position Surface-RMS-Diff-mm 0.664017 0.289815 1.330995 mri_segreg done MinCost: 0.579567 821.498253 849.507892 1.536366 tkregister2_cmdl --mov bold/002/template.nii.gz --reg bold/002/register.dof6.dat --noedit --ltaout bold/002/register.dof6.lta tkregister_tcl /usr/local/freesurfer/dev/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume bold/002/template.nii.gz reg file bold/002/register.dof6.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.131 2016/03/24 17:39:56 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- 0.99997 -0.00328 0.00685 0.17506; -0.00746 -0.25525 0.96685 -40.60711; 0.00143 0.96687 0.25527 -1.84502; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: loading target /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/orig.mgz Ttarg: -------------------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading movable bold/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 -------- 0.99997 -0.00328 0.00685 0.17506; -0.00746 -0.25525 0.96685 -40.60711; 0.00143 0.96687 0.25527 -1.84502; 0.00000 0.00000 0.00000 1.00000; Determinant -1 subject = fsf01anat RegMat --------------------------- 0.99997 -0.00328 0.00685 0.17506; -0.00746 -0.25525 0.96685 -40.60711; 0.00143 0.96687 0.25527 -1.84502; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Sun Mar 27 21:43:35 EDT 2016 Ended at Sun Mar 27 21:47:05 EDT 2016 BBR-Run-Time-Sec 210 bbregister Done To check results, run: tkregister2 --mov bold/002/template.nii.gz --reg bold/002/register.dof6.dat --surf Run: 003 ---------------- Sun Mar 27 21:47:05 EDT 2016 -------------------------------------- /autofs/cluster/pubftp/data/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.9239 Log file is bold/003/register.dof6.dat.log Sun Mar 27 21:47:05 EDT 2016 setenv SUBJECTS_DIR /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects cd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01 /usr/local/freesurfer/dev/bin/bbregister --s fsf01anat --init-coreg --6 --bold --mov bold/003/template.nii.gz --reg bold/003/register.dof6.dat --lta bold/003/register.dof6.lta --init-reg-out bold/003/init.register.dof6.dat $Id: bbregister,v 1.74 2016/02/17 21:07:31 greve Exp $ Linux transfer 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer/dev mri_convert bold/003/template.nii.gz bold/003/tmp.bbregister.9239/template.nii mri_convert.bin bold/003/template.nii.gz bold/003/tmp.bbregister.9239/template.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from bold/003/template.nii.gz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.973976, -0.226651) k_ras = (-2.36491e-18, -0.226651, 0.973976) writing to bold/003/tmp.bbregister.9239/template.nii... mri_coreg --s fsf01anat --mov bold/003/tmp.bbregister.9239/template.nii --regdat bold/003/tmp.bbregister.9239/reg.init.dat --reg bold/003/tmp.bbregister.9239/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 freadFloat: fread failed $Id: mri_coreg.c,v 1.26 2016/01/20 23:42:39 greve Exp $ cwd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01 cmdline mri_coreg --s fsf01anat --mov bold/003/tmp.bbregister.9239/template.nii --regdat bold/003/tmp.bbregister.9239/reg.init.dat --reg bold/003/tmp.bbregister.9239/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 sysname Linux hostname transfer machine x86_64 user zkaufman dof 6 nsep 1 cras0 1 ftol 0.000100 linmintol 0.010000 bf 1 bflim 30.000000 bfnsamp 30 SmoothRef 0 SatPct 99.990000 MovOOB 0 Reading in mov bold/003/tmp.bbregister.9239/template.nii Reading in ref /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/brainmask.mgz freadFloat: fread failed Reading in and applying refmask /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/aparc+aseg.mgz Setting cras translation parameters to align centers Creating random numbers for coordinate dithering Performing intensity dithering Initial parameters -6.0223 -45.2577 79.2380 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Separation list (1): 4 min = 4 DoSmoothing 1 DoCoordDither 1 DoIntensityDither 1 nitersmax 4 ftol 1.000e-04 linmintol 1.000e-02 SatPct 99.990000 Hist FWHM 7.000000 7.000000 nthreads 1 movsat = 1708.3334 mov gstd 0.9989 0.9989 0.0000 Smoothing mov refsat = 118.0000 ref gstd 1.8914 1.8914 1.8914 Smoothing ref COREGpreproc() done Testing if mov and target overlap Init cost -1.0202975942 nhits = 106280 out of 16777216, Percent Overlap: 40.5 Initial RefRAS-to-MovRAS 1.00000 0.00000 0.00000 -6.02228; 0.00000 1.00000 0.00000 -45.25770; 0.00000 0.00000 1.00000 79.23798; 0.00000 0.00000 0.00000 1.00000; Initial RefVox-to-MovVox 0.29091 -0.00000 -0.00000 -5.59091; -0.00000 0.06593 -0.28334 59.21896; 0.00000 -0.19480 -0.04533 45.11600; 0.00000 0.00000 0.00000 1.00000; sep = 4 ----------------------------------- COREGoptBruteForce() 30 1 30 Turning on MovOOB for BruteForce Search #BF# sep= 4 iter=0 lim=30.0 delta=2.00 -6.02228 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0499788 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6 Starting OpenPowel2(), sep = 4 InitialCost -1.0710277557 #@# 4 188 -6.02228 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0710278 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.071028 #@# 4 191 -7.64031 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0713971 #@# 4 192 -7.20970 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0714792 #@# 4 196 -7.17804 -35.25770 49.23798 4.00000 0.00000 0.00000 -1.0714808 #@# 4 202 -7.16804 -36.87573 49.23798 4.00000 0.00000 0.00000 -1.0740036 #@# 4 205 -7.16804 -40.14709 49.23798 4.00000 0.00000 0.00000 -1.0760239 #@# 4 207 -7.16804 -39.66540 49.23798 4.00000 0.00000 0.00000 -1.0760907 #@# 4 209 -7.16804 -39.69576 49.23798 4.00000 0.00000 0.00000 -1.0760912 #@# 4 211 -7.16804 -39.71626 49.23798 4.00000 0.00000 0.00000 -1.0760921 #@# 4 214 -7.16804 -39.72625 49.23798 4.00000 0.00000 0.00000 -1.0760937 #@# 4 217 -7.16804 -39.72625 47.61994 4.00000 0.00000 0.00000 -1.0762608 #@# 4 218 -7.16804 -39.72625 48.27965 4.00000 0.00000 0.00000 -1.0763843 #@# 4 222 -7.16804 -39.72625 48.26255 4.00000 0.00000 0.00000 -1.0763875 #@# 4 227 -7.16804 -39.72625 48.19618 4.00000 0.00000 0.00000 -1.0763898 #@# 4 228 -7.16804 -39.72625 48.20618 4.00000 0.00000 0.00000 -1.0763899 #@# 4 233 -7.16804 -39.72625 48.20618 3.38197 0.00000 0.00000 -1.0765280 #@# 4 235 -7.16804 -39.72625 48.20618 3.55769 0.00000 0.00000 -1.0765572 #@# 4 236 -7.16804 -39.72625 48.20618 3.56769 0.00000 0.00000 -1.0765582 #@# 4 238 -7.16804 -39.72625 48.20618 3.57769 0.00000 0.00000 -1.0765584 #@# 4 246 -7.16804 -39.72625 48.20618 3.57769 -0.26120 0.00000 -1.0765694 #@# 4 251 -7.16804 -39.72625 48.20618 3.57769 -0.28120 0.00000 -1.0765697 #@# 4 257 -7.16804 -39.72625 48.20618 3.57769 -0.28120 -0.61803 -1.0767374 #@# 4 259 -7.16804 -39.72625 48.20618 3.57769 -0.28120 -0.46037 -1.0767633 #@# 4 261 -7.16804 -39.72625 48.20618 3.57769 -0.28120 -0.49442 -1.0767654 #@# 4 264 -7.16804 -39.72625 48.20618 3.57769 -0.28120 -0.48413 -1.0767661 powell nthiter 1: fret = -1.076766 #@# 4 273 -7.02185 -39.72625 48.20618 3.57769 -0.28120 -0.48413 -1.0767806 #@# 4 274 -7.03185 -39.72625 48.20618 3.57769 -0.28120 -0.48413 -1.0767807 #@# 4 275 -7.04185 -39.72625 48.20618 3.57769 -0.28120 -0.48413 -1.0767813 #@# 4 284 -7.04185 -39.89198 48.20618 3.57769 -0.28120 -0.48413 -1.0767962 #@# 4 287 -7.04185 -39.90197 48.20618 3.57769 -0.28120 -0.48413 -1.0767970 #@# 4 292 -7.04185 -39.90197 47.58815 3.57769 -0.28120 -0.48413 -1.0768745 #@# 4 299 -7.04185 -39.90197 47.60170 3.57769 -0.28120 -0.48413 -1.0768762 #@# 4 305 -7.04185 -39.90197 47.60170 2.95966 -0.28120 -0.48413 -1.0769082 #@# 4 307 -7.04185 -39.90197 47.60170 3.23260 -0.28120 -0.48413 -1.0769733 #@# 4 308 -7.04185 -39.90197 47.60170 3.24260 -0.28120 -0.48413 -1.0769756 #@# 4 310 -7.04185 -39.90197 47.60170 3.28445 -0.28120 -0.48413 -1.0769801 #@# 4 330 -7.04185 -39.90197 47.60170 3.28445 -0.28120 -0.56028 -1.0769842 #@# 4 331 -7.04185 -39.90197 47.60170 3.28445 -0.28120 -0.54787 -1.0769848 #@# 4 333 -6.91566 -40.07769 46.99722 2.99120 -0.28120 -0.61160 -1.0771338 #@# 4 336 -6.71148 -40.36202 46.01915 2.51671 -0.28120 -0.71472 -1.0771655 #@# 4 337 -6.78855 -40.25469 46.38836 2.69583 -0.28120 -0.67579 -1.0771891 #@# 4 341 -6.77987 -40.26678 46.34677 2.67565 -0.28120 -0.68018 -1.0771896 #@# 4 342 -6.78113 -40.26502 46.35282 2.67858 -0.28120 -0.67954 -1.0771897 #@# 4 343 -6.78285 -40.26263 46.36103 2.68257 -0.28120 -0.67868 -1.0771898 #@# 4 344 -6.78503 -40.25960 46.37147 2.68763 -0.28120 -0.67757 -1.0771900 powell nthiter 2: fret = -1.077190 #@# 4 353 -6.77503 -40.25960 46.37147 2.68763 -0.28120 -0.67757 -1.0771902 #@# 4 364 -6.77503 -40.16743 46.37147 2.68763 -0.28120 -0.67757 -1.0771923 #@# 4 374 -6.77503 -40.16743 46.75343 2.68763 -0.28120 -0.67757 -1.0772008 #@# 4 375 -6.77503 -40.16743 46.58694 2.68763 -0.28120 -0.67757 -1.0772063 #@# 4 376 -6.77503 -40.16743 46.60578 2.68763 -0.28120 -0.67757 -1.0772073 #@# 4 378 -6.77503 -40.16743 46.61578 2.68763 -0.28120 -0.67757 -1.0772086 #@# 4 386 -6.77503 -40.16743 46.61578 2.68763 -0.28120 -0.77400 -1.0772150 #@# 4 398 -6.77503 -40.16743 46.61578 2.68763 -0.37044 -0.77400 -1.0772165 #@# 4 401 -6.77503 -40.16743 46.61578 2.68763 -0.31161 -0.77400 -1.0772182 #@# 4 408 -6.72683 -40.23455 46.38489 2.57562 -0.31161 -0.79835 -1.0772325 Powell done niters total = 2 OptTimeSec 18.1 sec OptTimeMin 0.30 min nEvals 412 Final parameters -6.72682571 -40.23455048 46.38489151 2.57562280 -0.31161472 -0.79834813 Final cost -1.077232506625936 --------------------------------- mri_coreg utimesec 107.507656 mri_coreg stimesec 0.536918 mri_coreg ru_maxrss 422120 mri_coreg ru_ixrss 0 mri_coreg ru_idrss 0 mri_coreg ru_isrss 0 mri_coreg ru_minflt 239950 mri_coreg ru_majflt 0 mri_coreg ru_nswap 0 mri_coreg ru_inblock 0 mri_coreg ru_oublock 0 mri_coreg ru_msgsnd 0 mri_coreg ru_msgrcv 0 mri_coreg ru_nsignals 0 mri_coreg ru_nvcsw 47 mri_coreg ru_nivcsw 123 Final RefRAS-to-MovRAS 0.99989 -0.01393 -0.00544 -6.72683; 0.01416 0.99889 0.04494 -40.23455; 0.00481 -0.04501 0.99897 46.38489; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox 0.29088 -0.00158 0.00405 -5.50132; 0.00433 0.07860 -0.28006 57.90867; -0.00029 -0.19256 -0.05405 38.90065; 0.00000 0.00000 0.00000 1.00000; Final parameters -6.7268 -40.2346 46.3849 2.5756 -0.3116 -0.7983 nhits = 105924 out of 16777216, Percent Overlap: 40.4 mri_coreg RunTimeSec 108.1 sec To check run: tkregisterfv --mov bold/003/tmp.bbregister.9239/template.nii --targ /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/brainmask.mgz --reg bold/003/tmp.bbregister.9239/mri_coreg.lta --s fsf01anat --surfs mri_coreg done mri_segreg --mov bold/003/tmp.bbregister.9239/template.nii --init-reg bold/003/tmp.bbregister.9239/reg.init.dat --out-reg bold/003/tmp.bbregister.9239/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.112 2014/02/25 19:06:37 greve Exp $ setenv SUBJECTS_DIR /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects cd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01 mri_segreg --mov bold/003/tmp.bbregister.9239/template.nii --init-reg bold/003/tmp.bbregister.9239/reg.init.dat --out-reg bold/003/tmp.bbregister.9239/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Linux hostname transfer machine x86_64 user zkaufman movvol bold/003/tmp.bbregister.9239/template.nii regfile bold/003/tmp.bbregister.9239/reg.init.dat subject fsf01anat dof 6 outregfile bold/003/tmp.bbregister.9239/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1459445017 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99989 -0.01393 -0.00544 -0.16222; 0.00147 -0.27024 0.96279 -38.51289; 0.01488 0.96269 0.27019 -2.32548; 0.00000 0.00000 0.00000 1.00000; Loading mov Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 1.064490 1 -25.0 -25.0 25.0 1.053749 2 -25.0 25.0 -25.0 1.068206 3 -25.0 25.0 25.0 1.069813 4 25.0 -25.0 -25.0 1.061733 5 25.0 -25.0 25.0 1.041060 6 25.0 25.0 -25.0 1.037284 7 25.0 25.0 25.0 1.063876 REL: 8 0.712841 8.460211 1.057526 rel = 0.674065 Initial costs ---------------- Number of surface hits 3040 WM Intensity 848.1464 +/- 206.9645 Ctx Intensity 853.5742 +/- 234.8119 Pct Contrast -1.0428 +/- 20.9501 Cost 0.7128 RelCost 0.6741 WARNING: initial G-W contrast is negative, but expecting positive. If the mov data has a T1 contrast, re-run with --T1 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 1.0661 1.0661 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 1.0498 1.0498 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 1.0052 1.0052 0.0 5 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 4.0000 0.9773 0.9773 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.9715 0.9715 0.0 8 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 4.0000 0.9548 0.9548 0.0 18 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 -4.0000 0.9470 0.9470 0.0 30 -4.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.9254 0.9254 0.0 34 -4.0000 -4.0000 0.0000 -4.0000 4.0000 0.0000 0.9160 0.9160 0.0 40 -4.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.8973 0.8973 0.0 273 0.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.8276 0.8276 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.7740 0.7740 0.0 282 0.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.7555 0.7555 0.0 283 0.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.6114 0.6114 0.0 Brute Force -------------------------- Min cost was 0.611427 Number of iterations 729 Search time 1.424000 sec Parameters at best (transmm, rotdeg) 0.000 -4.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 -4 2 0 3 0 4 0 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000100 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.611427 7 0.086 -4.000 0.000 0.000 0.000 0.000 0.6110832010 9 0.069 -4.000 0.000 0.000 0.000 0.000 0.6110689071 10 0.073 -4.000 0.000 0.000 0.000 0.000 0.6110668926 11 0.074 -4.000 0.000 0.000 0.000 0.000 0.6110667963 14 0.074 -3.000 0.000 0.000 0.000 0.000 0.5762751272 19 0.074 -2.780 0.000 0.000 0.000 0.000 0.5750879568 22 0.074 -2.766 0.000 0.000 0.000 0.000 0.5750816091 23 0.074 -2.768 0.000 0.000 0.000 0.000 0.5750813194 34 0.074 -2.769 -0.007 0.000 0.000 0.000 0.5750800698 36 0.074 -2.769 -0.005 0.000 0.000 0.000 0.5750795277 37 0.074 -2.769 -0.004 0.000 0.000 0.000 0.5750793737 45 0.074 -2.769 -0.004 -0.188 0.000 0.000 0.5731449330 46 0.074 -2.769 -0.004 -0.231 0.000 0.000 0.5730869485 47 0.074 -2.769 -0.004 -0.227 0.000 0.000 0.5730854129 48 0.074 -2.769 -0.004 -0.225 0.000 0.000 0.5730847681 59 0.074 -2.769 -0.004 -0.225 -0.068 0.000 0.5725784834 61 0.074 -2.769 -0.004 -0.225 -0.090 0.000 0.5725432845 62 0.074 -2.769 -0.004 -0.225 -0.092 0.000 0.5725428360 70 0.074 -2.769 -0.004 -0.225 -0.092 -0.283 0.5717403601 71 0.074 -2.769 -0.004 -0.225 -0.092 -0.279 0.5717324154 73 0.074 -2.769 -0.004 -0.225 -0.092 -0.259 0.5717052529 74 0.074 -2.769 -0.004 -0.225 -0.092 -0.247 0.5716930073 77 0.074 -2.769 -0.004 -0.225 -0.092 -0.245 0.5716893200 78 0.074 -2.769 -0.004 -0.225 -0.092 -0.243 0.5716861491 powell nthiter 1: fret = 0.571686 101 0.075 -2.769 -0.004 -0.225 -0.092 -0.243 0.5716853711 102 0.086 -2.769 -0.004 -0.225 -0.092 -0.243 0.5716718018 105 0.106 -2.769 -0.004 -0.225 -0.092 -0.243 0.5716494029 107 0.110 -2.769 -0.004 -0.225 -0.092 -0.243 0.5716479167 108 0.111 -2.769 -0.004 -0.225 -0.092 -0.243 0.5716477313 109 0.114 -2.769 -0.004 -0.225 -0.092 -0.243 0.5716473342 111 0.113 -2.769 -0.004 -0.225 -0.092 -0.243 0.5716471628 136 0.113 -2.769 0.052 -0.225 -0.092 -0.243 0.5715540922 140 0.113 -2.769 0.049 -0.225 -0.092 -0.243 0.5715535052 150 0.113 -2.769 0.048 -0.250 -0.092 -0.243 0.5714838203 151 0.113 -2.769 0.048 -0.252 -0.092 -0.243 0.5714830893 159 0.113 -2.769 0.048 -0.252 -0.126 -0.243 0.5710646421 161 0.113 -2.769 0.048 -0.252 -0.170 -0.243 0.5710512642 162 0.113 -2.769 0.048 -0.252 -0.149 -0.243 0.5709812709 176 0.113 -2.771 0.048 -0.251 -0.149 -0.242 0.5709718280 powell nthiter 2: fret = 0.570972 191 0.112 -2.771 0.048 -0.251 -0.149 -0.242 0.5709712708 212 0.112 -2.771 0.016 -0.251 -0.149 -0.242 0.5709397252 215 0.112 -2.771 0.020 -0.251 -0.149 -0.242 0.5709384474 217 0.112 -2.771 0.019 -0.251 -0.149 -0.242 0.5709383487 218 0.112 -2.771 0.018 -0.251 -0.149 -0.242 0.5709382848 226 0.112 -2.771 0.018 -0.290 -0.149 -0.242 0.5709004748 230 0.112 -2.771 0.018 -0.291 -0.149 -0.242 0.5708999470 232 0.112 -2.771 0.018 -0.294 -0.149 -0.242 0.5708994141 233 0.112 -2.771 0.018 -0.295 -0.149 -0.242 0.5708993348 244 0.112 -2.771 0.018 -0.295 -0.155 -0.242 0.5708983296 245 0.112 -2.771 0.018 -0.295 -0.152 -0.242 0.5708972395 259 0.112 -2.777 0.018 -0.294 -0.152 -0.241 0.5708932587 260 0.112 -2.775 0.018 -0.294 -0.152 -0.241 0.5708779739 powell nthiter 3: fret = 0.570878 272 0.113 -2.775 0.018 -0.294 -0.152 -0.241 0.5708765324 273 0.114 -2.775 0.018 -0.294 -0.152 -0.241 0.5708752883 294 0.114 -2.775 0.012 -0.294 -0.152 -0.241 0.5708694707 295 0.114 -2.775 0.006 -0.294 -0.152 -0.241 0.5708683940 296 0.114 -2.775 0.008 -0.294 -0.152 -0.241 0.5708681606 304 0.114 -2.775 0.008 -0.309 -0.152 -0.241 0.5708675109 305 0.114 -2.775 0.008 -0.302 -0.152 -0.241 0.5708647982 307 0.114 -2.775 0.008 -0.303 -0.152 -0.241 0.5708647687 320 0.114 -2.775 0.008 -0.303 -0.154 -0.241 0.5708639190 321 0.114 -2.775 0.008 -0.303 -0.155 -0.241 0.5708638899 335 0.114 -2.776 0.008 -0.303 -0.155 -0.241 0.5708613627 Powell done niters = 3 Computing relative cost 0 -25.0 -25.0 -25.0 1.035794 1 -25.0 -25.0 25.0 1.061384 2 -25.0 25.0 -25.0 1.067881 3 -25.0 25.0 25.0 1.084840 4 25.0 -25.0 -25.0 1.045115 5 25.0 -25.0 25.0 1.043826 6 25.0 25.0 -25.0 1.005493 7 25.0 25.0 25.0 1.033448 REL: 8 0.570861 8.377779 1.047222 rel = 0.545119 Number of iterations 3 Min cost was 0.570861 Number of FunctionCalls 337 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.659000 sec Parameters at optimum (transmm) 0.11433 -2.77582 0.00807 Parameters at optimum (rotdeg) -0.30293 -0.15539 -0.24108 Final costs ---------------- Number of surface hits 3040 WM Intensity 815.0247 +/- 221.7895 Ctx Intensity 841.8167 +/- 253.2951 Pct Contrast 1.1337 +/- 22.0110 Cost 0.5709 RelCost 0.6741 Reg at min cost was 0.99984 -0.01766 -0.00210 -0.20423; -0.00266 -0.26507 0.96423 -41.29947; 0.01759 0.96407 0.26508 -2.11419; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/003/tmp.bbregister.9239/bbr.pass1.dat, type = 14 Original Reg 0.99989 -0.01393 -0.00544 -0.16222; 0.00147 -0.27024 0.96279 -38.51289; 0.01488 0.96269 0.27019 -2.32548; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00005 0.00373 -0.00334 0.04201; 0.00413 -0.00517 -0.00143 2.78658; -0.00270 -0.00137 0.00511 -0.21129; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 2.726874 Computing change in rh position Surface-RMS-Diff-mm 2.836810 0.269703 3.367713 WARNING: initial G-W contrast was negative, but expected positive. If the mov data has a T1 contrast, re-run with --T1 mri_segreg done mri_segreg --mov bold/003/tmp.bbregister.9239/template.nii --init-reg bold/003/tmp.bbregister.9239/bbr.pass1.dat --out-reg bold/003/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/003/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/003/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/003/tmp.bbregister.9239/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.112 2014/02/25 19:06:37 greve Exp $ setenv SUBJECTS_DIR /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects cd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01 mri_segreg --mov bold/003/tmp.bbregister.9239/template.nii --init-reg bold/003/tmp.bbregister.9239/bbr.pass1.dat --out-reg bold/003/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/003/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/003/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/003/tmp.bbregister.9239/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname transfer machine x86_64 user zkaufman movvol bold/003/tmp.bbregister.9239/template.nii regfile bold/003/tmp.bbregister.9239/bbr.pass1.dat subject fsf01anat dof 6 outregfile bold/003/register.dof6.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1460084016 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99984 -0.01766 -0.00210 -0.20423; -0.00266 -0.26507 0.96423 -41.29947; 0.01759 0.96407 0.26508 -2.11419; 0.00000 0.00000 0.00000 1.00000; Loading mov Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 1.037860 1 -25.0 -25.0 25.0 1.050974 2 -25.0 25.0 -25.0 1.056127 3 -25.0 25.0 25.0 1.065740 4 25.0 -25.0 -25.0 1.029204 5 25.0 -25.0 25.0 1.033160 6 25.0 25.0 -25.0 1.018567 7 25.0 25.0 25.0 1.056295 REL: 8 0.586631 8.347926 1.043491 rel = 0.562182 Initial costs ---------------- Number of surface hits 304441 WM Intensity 817.0696 +/- 218.7005 Ctx Intensity 843.7289 +/- 248.8705 Pct Contrast 1.3464 +/- 21.8518 Cost 0.5866 RelCost 0.5622 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.5742 0.5742 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.5735 0.5735 0.0 2 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.5733 0.5733 0.0 5 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1000 0.5729 0.5729 0.0 11 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.1000 0.5729 0.5729 0.0 13 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.5727 0.5727 0.0 14 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.1000 0.5727 0.5727 0.0 24 -0.1000 -0.1000 -0.1000 0.1000 0.1000 -0.1000 0.5725 0.5725 0.0 25 -0.1000 -0.1000 -0.1000 0.1000 0.1000 0.0000 0.5725 0.5725 0.0 41 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.1000 0.5723 0.5723 0.0 85 -0.1000 0.0000 -0.1000 -0.1000 0.0000 0.0000 0.5720 0.5720 0.0 86 -0.1000 0.0000 -0.1000 -0.1000 0.0000 0.1000 0.5719 0.5719 0.0 93 -0.1000 0.0000 -0.1000 0.0000 0.0000 -0.1000 0.5718 0.5718 0.0 94 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.0000 0.5716 0.5716 0.0 105 -0.1000 0.0000 -0.1000 0.1000 0.1000 -0.1000 0.5715 0.5715 0.0 121 -0.1000 0.0000 0.0000 0.0000 0.0000 0.0000 0.5714 0.5714 0.0 186 -0.1000 0.1000 -0.1000 0.1000 0.1000 -0.1000 0.5713 0.5713 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.5709 0.5709 0.0 Brute Force -------------------------- Min cost was 0.570861 Number of iterations 729 Search time 1.389000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000000 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.586631 7 -0.084 0.000 0.000 0.000 0.000 0.000 0.5864572238 8 -0.086 0.000 0.000 0.000 0.000 0.000 0.5864550790 10 -0.135 0.000 0.000 0.000 0.000 0.000 0.5864488077 11 -0.114 0.000 0.000 0.000 0.000 0.000 0.5864396257 20 -0.114 0.135 0.000 0.000 0.000 0.000 0.5860444851 21 -0.114 0.137 0.000 0.000 0.000 0.000 0.5860433769 22 -0.114 0.148 0.000 0.000 0.000 0.000 0.5860424187 24 -0.114 0.144 0.000 0.000 0.000 0.000 0.5860420319 33 -0.114 0.143 -0.167 0.000 0.000 0.000 0.5854810982 35 -0.114 0.143 -0.172 0.000 0.000 0.000 0.5854804344 37 -0.114 0.143 -0.173 0.000 0.000 0.000 0.5854804221 42 -0.114 0.143 -0.173 -0.618 0.000 0.000 0.5849595337 44 -0.114 0.143 -0.173 -0.335 0.000 0.000 0.5835658191 45 -0.114 0.143 -0.173 -0.333 0.000 0.000 0.5835656485 46 -0.114 0.143 -0.173 -0.331 0.000 0.000 0.5835653514 50 -0.114 0.143 -0.173 -0.324 0.000 0.000 0.5835652076 51 -0.114 0.143 -0.173 -0.327 0.000 0.000 0.5835651162 52 -0.114 0.143 -0.173 -0.328 0.000 0.000 0.5835650546 60 -0.114 0.143 -0.173 -0.328 0.004 0.000 0.5835583925 61 -0.114 0.143 -0.173 -0.328 0.032 0.000 0.5835332284 63 -0.114 0.143 -0.173 -0.328 0.034 0.000 0.5835331527 69 -0.114 0.143 -0.173 -0.328 0.035 0.000 0.5835329896 76 -0.114 0.143 -0.173 -0.328 0.035 -0.082 0.5834538650 80 -0.114 0.143 -0.173 -0.328 0.035 -0.083 0.5834537841 powell nthiter 1: fret = 0.583454 88 -0.078 0.143 -0.173 -0.328 0.035 -0.083 0.5834342311 89 -0.084 0.143 -0.173 -0.328 0.035 -0.083 0.5834334407 98 -0.083 0.253 -0.173 -0.328 0.035 -0.083 0.5832112554 99 -0.083 0.249 -0.173 -0.328 0.035 -0.083 0.5832101233 100 -0.083 0.244 -0.173 -0.328 0.035 -0.083 0.5832092276 102 -0.083 0.245 -0.173 -0.328 0.035 -0.083 0.5832091998 111 -0.083 0.246 -0.167 -0.328 0.035 -0.083 0.5832083397 120 -0.083 0.246 -0.166 -0.383 0.035 -0.083 0.5831861851 121 -0.083 0.246 -0.166 -0.366 0.035 -0.083 0.5831809294 123 -0.083 0.246 -0.166 -0.369 0.035 -0.083 0.5831808315 134 -0.083 0.246 -0.166 -0.370 0.029 -0.083 0.5831798754 143 -0.083 0.246 -0.166 -0.370 0.030 -0.091 0.5831790286 144 -0.083 0.246 -0.166 -0.370 0.030 -0.092 0.5831788717 158 -0.079 0.260 -0.165 -0.376 0.029 -0.093 0.5831763662 powell nthiter 2: fret = 0.583176 170 -0.084 0.259 -0.165 -0.375 0.029 -0.093 0.5831749836 171 -0.088 0.259 -0.165 -0.375 0.029 -0.093 0.5831748069 172 -0.087 0.259 -0.165 -0.375 0.029 -0.093 0.5831747961 180 -0.086 0.259 -0.165 -0.375 0.029 -0.092 0.5831746524 190 -0.086 0.259 -0.167 -0.375 0.029 -0.092 0.5831741571 191 -0.086 0.259 -0.172 -0.375 0.029 -0.092 0.5831736691 193 -0.086 0.259 -0.171 -0.375 0.029 -0.092 0.5831735941 203 -0.086 0.259 -0.170 -0.377 0.029 -0.092 0.5831734131 212 -0.086 0.259 -0.170 -0.377 0.030 -0.092 0.5831734022 220 -0.083 0.266 -0.169 -0.380 0.030 -0.093 0.5831726812 powell nthiter 3: fret = 0.583173 238 -0.084 0.267 -0.169 -0.380 0.029 -0.093 0.5831723398 239 -0.090 0.267 -0.169 -0.380 0.029 -0.093 0.5831719801 241 -0.088 0.267 -0.169 -0.380 0.029 -0.093 0.5831718957 250 -0.087 0.267 -0.169 -0.380 0.029 -0.092 0.5831718312 251 -0.087 0.267 -0.169 -0.380 0.029 -0.090 0.5831716930 258 -0.087 0.267 -0.169 -0.380 0.029 -0.091 0.5831716275 266 -0.087 0.267 -0.174 -0.380 0.029 -0.091 0.5831712317 268 -0.087 0.267 -0.173 -0.380 0.029 -0.091 0.5831711905 276 -0.087 0.267 -0.173 -0.389 0.029 -0.091 0.5831710092 277 -0.087 0.267 -0.173 -0.385 0.029 -0.091 0.5831708236 278 -0.087 0.267 -0.173 -0.386 0.029 -0.091 0.5831707726 295 -0.086 0.270 -0.173 -0.387 0.029 -0.091 0.5831700523 296 -0.085 0.274 -0.173 -0.389 0.029 -0.092 0.5831694443 307 -0.087 0.281 -0.176 -0.398 0.029 -0.090 0.5831671965 314 -0.087 0.282 -0.177 -0.399 0.029 -0.090 0.5831669310 316 -0.087 0.282 -0.177 -0.399 0.029 -0.090 0.5831668655 powell nthiter 4: fret = 0.583167 329 -0.096 0.282 -0.177 -0.399 0.029 -0.090 0.5831663616 331 -0.092 0.282 -0.177 -0.399 0.029 -0.090 0.5831660062 powell nthiter 5: fret = 0.583166 404 -0.092 0.282 -0.176 -0.399 0.029 -0.090 0.5831659980 Powell done niters = 5 Computing relative cost 0 -25.0 -25.0 -25.0 1.037328 1 -25.0 -25.0 25.0 1.053696 2 -25.0 25.0 -25.0 1.052743 3 -25.0 25.0 25.0 1.065192 4 25.0 -25.0 -25.0 1.030789 5 25.0 -25.0 25.0 1.033511 6 25.0 25.0 -25.0 1.016194 7 25.0 25.0 25.0 1.055953 REL: 8 0.583166 8.345408 1.043176 rel = 0.559029 Number of iterations 5 Min cost was 0.583166 Number of FunctionCalls 460 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 55.127000 sec Parameters at optimum (transmm) -0.09225 0.28190 -0.17709 Parameters at optimum (rotdeg) -0.39935 0.02875 -0.08970 Final costs ---------------- Number of surface hits 304441 WM Intensity 819.2719 +/- 215.1285 Ctx Intensity 846.2816 +/- 245.7675 Pct Contrast 1.3831 +/- 21.6201 Cost 0.5832 RelCost 0.5622 Reg at min cost was 0.99985 -0.01758 -0.00046 -0.36207; -0.00410 -0.25832 0.96605 -41.03093; 0.01710 0.96590 0.25835 -2.00327; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/003/register.dof6.dat, type = 14 Original Reg 0.99984 -0.01766 -0.00210 -0.20423; -0.00266 -0.26507 0.96423 -41.29947; 0.01759 0.96407 0.26508 -2.11419; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00000 -0.00008 -0.00164 0.15784; 0.00144 -0.00675 -0.00183 -0.26854; 0.00048 -0.00183 0.00673 -0.11092; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.434600 Computing change in rh position Surface-RMS-Diff-mm 0.417951 0.186093 0.922594 mri_segreg done MinCost: 0.583166 819.271929 846.281568 1.383141 tkregister2_cmdl --mov bold/003/template.nii.gz --reg bold/003/register.dof6.dat --noedit --ltaout bold/003/register.dof6.lta tkregister_tcl /usr/local/freesurfer/dev/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume bold/003/template.nii.gz reg file bold/003/register.dof6.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.131 2016/03/24 17:39:56 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- 0.99985 -0.01758 -0.00046 -0.36207; -0.00410 -0.25832 0.96605 -41.03093; 0.01710 0.96590 0.25835 -2.00327; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: loading target /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/orig.mgz Ttarg: -------------------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading movable bold/003/template.nii.gz Tmov: -------------------- -3.43750 0.00000 0.00000 110.00000; 0.00000 0.00000 5.00000 -75.00000; 0.00000 -3.43750 0.00000 109.99999; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 0.99985 -0.01758 -0.00046 -0.36207; -0.00410 -0.25832 0.96605 -41.03093; 0.01710 0.96590 0.25835 -2.00327; 0.00000 0.00000 0.00000 1.00000; Determinant -1 subject = fsf01anat RegMat --------------------------- 0.99985 -0.01758 -0.00046 -0.36207; -0.00410 -0.25832 0.96605 -41.03093; 0.01710 0.96590 0.25835 -2.00327; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Sun Mar 27 21:47:05 EDT 2016 Ended at Sun Mar 27 21:50:11 EDT 2016 BBR-Run-Time-Sec 186 bbregister Done To check results, run: tkregister2 --mov bold/003/template.nii.gz --reg bold/003/register.dof6.dat --surf Run: 004 ---------------- Sun Mar 27 21:50:11 EDT 2016 -------------------------------------- /autofs/cluster/pubftp/data/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.10182 Log file is bold/004/register.dof6.dat.log Sun Mar 27 21:50:11 EDT 2016 setenv SUBJECTS_DIR /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects cd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01 /usr/local/freesurfer/dev/bin/bbregister --s fsf01anat --init-coreg --6 --bold --mov bold/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 1.74 2016/02/17 21:07:31 greve Exp $ Linux transfer 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer/dev mri_convert bold/004/template.nii.gz bold/004/tmp.bbregister.10182/template.nii mri_convert.bin bold/004/template.nii.gz bold/004/tmp.bbregister.10182/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.10182/template.nii... mri_coreg --s fsf01anat --mov bold/004/tmp.bbregister.10182/template.nii --regdat bold/004/tmp.bbregister.10182/reg.init.dat --reg bold/004/tmp.bbregister.10182/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 freadFloat: fread failed $Id: mri_coreg.c,v 1.26 2016/01/20 23:42:39 greve Exp $ cwd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01 cmdline mri_coreg --s fsf01anat --mov bold/004/tmp.bbregister.10182/template.nii --regdat bold/004/tmp.bbregister.10182/reg.init.dat --reg bold/004/tmp.bbregister.10182/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 sysname Linux hostname transfer machine x86_64 user zkaufman dof 6 nsep 1 cras0 1 ftol 0.000100 linmintol 0.010000 bf 1 bflim 30.000000 bfnsamp 30 SmoothRef 0 SatPct 99.990000 MovOOB 0 Reading in mov bold/004/tmp.bbregister.10182/template.nii Reading in ref /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/brainmask.mgz freadFloat: fread failed Reading in and applying refmask /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/aparc+aseg.mgz Setting cras translation parameters to align centers Creating random numbers for coordinate dithering Performing intensity dithering Initial parameters -6.0223 -45.2577 79.2380 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Separation list (1): 4 min = 4 DoSmoothing 1 DoCoordDither 1 DoIntensityDither 1 nitersmax 4 ftol 1.000e-04 linmintol 1.000e-02 SatPct 99.990000 Hist FWHM 7.000000 7.000000 nthreads 1 movsat = 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 -1.0203497499 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 -1.0499884 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6 Starting OpenPowel2(), sep = 4 InitialCost -1.0708916187 #@# 4 188 -8.02228 -35.25770 49.23798 4.00000 -2.00000 0.00000 -1.0708916 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.070892 #@# 4 194 -7.64031 -35.25770 49.23798 4.00000 -2.00000 0.00000 -1.0709071 #@# 4 195 -7.77817 -35.25770 49.23798 4.00000 -2.00000 0.00000 -1.0709195 #@# 4 200 -7.77817 -36.87573 49.23798 4.00000 -2.00000 0.00000 -1.0732599 #@# 4 203 -7.77817 -39.98059 49.23798 4.00000 -2.00000 0.00000 -1.0753539 #@# 4 205 -7.77817 -39.84149 49.23798 4.00000 -2.00000 0.00000 -1.0753565 #@# 4 206 -7.77817 -39.87265 49.23798 4.00000 -2.00000 0.00000 -1.0753576 #@# 4 207 -7.77817 -39.89194 49.23798 4.00000 -2.00000 0.00000 -1.0753590 #@# 4 209 -7.77817 -39.90194 49.23798 4.00000 -2.00000 0.00000 -1.0753592 #@# 4 213 -7.77817 -39.90194 47.61994 4.00000 -2.00000 0.00000 -1.0759000 #@# 4 214 -7.77817 -39.90194 47.87240 4.00000 -2.00000 0.00000 -1.0759512 #@# 4 219 -7.77817 -39.90194 47.91168 4.00000 -2.00000 0.00000 -1.0759517 #@# 4 222 -7.77817 -39.90194 47.93502 4.00000 -2.00000 0.00000 -1.0759526 #@# 4 229 -7.77817 -39.90194 47.93502 3.38197 -2.00000 0.00000 -1.0760587 #@# 4 231 -7.77817 -39.90194 47.93502 3.57218 -2.00000 0.00000 -1.0760833 #@# 4 232 -7.77817 -39.90194 47.93502 3.56218 -2.00000 0.00000 -1.0760840 #@# 4 233 -7.77817 -39.90194 47.93502 3.53506 -2.00000 0.00000 -1.0760846 #@# 4 236 -7.77817 -39.90194 47.93502 3.52506 -2.00000 0.00000 -1.0760849 #@# 4 239 -7.77817 -39.90194 47.93502 3.52506 -1.00000 0.00000 -1.0762094 #@# 4 252 -7.77817 -39.90194 47.93502 3.52506 -1.00000 -0.61803 -1.0762370 #@# 4 254 -7.77817 -39.90194 47.93502 3.52506 -1.00000 -0.33698 -1.0763111 #@# 4 255 -7.77817 -39.90194 47.93502 3.52506 -1.00000 -0.32698 -1.0763112 powell nthiter 1: fret = -1.076311 #@# 4 263 -7.39620 -39.90194 47.93502 3.52506 -1.00000 -0.32698 -1.0763468 #@# 4 264 -7.51062 -39.90194 47.93502 3.52506 -1.00000 -0.32698 -1.0763528 #@# 4 274 -7.51062 -40.03887 47.93502 3.52506 -1.00000 -0.32698 -1.0763602 #@# 4 276 -7.51062 -39.98687 47.93502 3.52506 -1.00000 -0.32698 -1.0763603 #@# 4 278 -7.51062 -40.01094 47.93502 3.52506 -1.00000 -0.32698 -1.0763611 #@# 4 285 -7.51062 -40.01094 47.31698 3.52506 -1.00000 -0.32698 -1.0763919 #@# 4 287 -7.51062 -40.01094 47.55783 3.52506 -1.00000 -0.32698 -1.0764216 #@# 4 297 -7.51062 -40.01094 47.55783 3.23717 -1.00000 -0.32698 -1.0764997 #@# 4 306 -7.51062 -40.01094 47.55783 3.23717 -0.61803 -0.32698 -1.0765086 #@# 4 307 -7.51062 -40.01094 47.55783 3.23717 -0.71445 -0.32698 -1.0765111 #@# 4 308 -7.51062 -40.01094 47.55783 3.23717 -0.74133 -0.32698 -1.0765117 #@# 4 310 -7.51062 -40.01094 47.55783 3.23717 -0.77907 -0.32698 -1.0765119 #@# 4 312 -7.51062 -40.01094 47.55783 3.23717 -0.80239 -0.32698 -1.0765121 #@# 4 314 -7.51062 -40.01094 47.55783 3.23717 -0.79239 -0.32698 -1.0765122 #@# 4 321 -7.51062 -40.01094 47.55783 3.23717 -0.79239 -0.53073 -1.0765570 #@# 4 322 -7.51062 -40.01094 47.55783 3.23717 -0.79239 -0.54149 -1.0765579 #@# 4 326 -7.24307 -40.11993 47.18064 2.94927 -0.58478 -0.75600 -1.0767590 #@# 4 329 -6.81017 -40.29630 46.57034 2.48345 -0.24886 -1.10308 -1.0769871 #@# 4 330 -6.20476 -40.54293 45.71684 1.83200 0.22092 -1.58847 -1.0770749 #@# 4 331 -6.31058 -40.49982 45.86603 1.94587 0.13880 -1.50363 -1.0770855 #@# 4 336 -6.30246 -40.50313 45.85458 1.93713 0.14510 -1.51014 -1.0770868 powell nthiter 2: fret = -1.077087 #@# 4 346 -6.24198 -40.50422 45.85081 1.93426 0.14718 -1.51228 -1.0770910 #@# 4 348 -6.25198 -40.50422 45.85081 1.93426 0.14718 -1.51228 -1.0770912 #@# 4 356 -6.25198 -40.72304 45.85081 1.93426 0.14718 -1.51228 -1.0770961 #@# 4 357 -6.25198 -40.65836 45.85081 1.93426 0.14718 -1.51228 -1.0770994 #@# 4 359 -6.25198 -40.67276 45.85081 1.93426 0.14718 -1.51228 -1.0771002 #@# 4 386 -6.25198 -40.67276 45.85081 1.93426 -0.47086 -1.51228 -1.0771352 #@# 4 388 -6.25198 -40.67276 45.85081 1.93426 -0.32358 -1.51228 -1.0771396 #@# 4 390 -6.25198 -40.67276 45.85081 1.93426 -0.37401 -1.51228 -1.0771431 Powell done niters total = 2 OptTimeSec 17.5 sec OptTimeMin 0.29 min nEvals 403 Final parameters -6.25198269 -40.67275620 45.85080719 1.93425500 -0.36400908 -1.51228023 Final cost -1.077143045158469 --------------------------------- mri_coreg utimesec 109.061420 mri_coreg stimesec 0.557915 mri_coreg ru_maxrss 422124 mri_coreg ru_ixrss 0 mri_coreg ru_idrss 0 mri_coreg ru_isrss 0 mri_coreg ru_minflt 236714 mri_coreg ru_majflt 0 mri_coreg ru_nswap 0 mri_coreg ru_inblock 0 mri_coreg ru_oublock 0 mri_coreg ru_msgsnd 0 mri_coreg ru_msgrcv 0 mri_coreg ru_nsignals 0 mri_coreg ru_nvcsw 48 mri_coreg ru_nivcsw 204 Final RefRAS-to-MovRAS 0.99963 -0.02639 -0.00635 -6.25198; 0.02659 0.99908 0.03375 -40.67276; 0.00546 -0.03391 0.99941 45.85081; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox 0.29080 -0.00185 0.00768 -5.84847; 0.00789 0.07546 -0.28084 57.93825; 0.00014 -0.19315 -0.05189 38.66851; 0.00000 0.00000 0.00000 1.00000; Final parameters -6.2520 -40.6728 45.8508 1.9343 -0.3640 -1.5123 nhits = 105986 out of 16777216, Percent Overlap: 40.4 mri_coreg RunTimeSec 109.6 sec To check run: tkregisterfv --mov bold/004/tmp.bbregister.10182/template.nii --targ /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/brainmask.mgz --reg bold/004/tmp.bbregister.10182/mri_coreg.lta --s fsf01anat --surfs mri_coreg done mri_segreg --mov bold/004/tmp.bbregister.10182/template.nii --init-reg bold/004/tmp.bbregister.10182/reg.init.dat --out-reg bold/004/tmp.bbregister.10182/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.112 2014/02/25 19:06:37 greve Exp $ setenv SUBJECTS_DIR /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects cd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01 mri_segreg --mov bold/004/tmp.bbregister.10182/template.nii --init-reg bold/004/tmp.bbregister.10182/reg.init.dat --out-reg bold/004/tmp.bbregister.10182/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Linux hostname transfer machine x86_64 user zkaufman movvol bold/004/tmp.bbregister.10182/template.nii regfile bold/004/tmp.bbregister.10182/reg.init.dat subject fsf01anat dof 6 outregfile bold/004/tmp.bbregister.10182/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 1459602735 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99963 -0.02639 -0.00635 -0.41348; -0.00071 -0.25947 0.96575 -38.39435; 0.02714 0.96539 0.25939 -2.26805; 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 1.072113 1 -25.0 -25.0 25.0 1.055222 2 -25.0 25.0 -25.0 1.070797 3 -25.0 25.0 25.0 1.071522 4 25.0 -25.0 -25.0 1.051892 5 25.0 -25.0 25.0 1.046639 6 25.0 25.0 -25.0 1.038996 7 25.0 25.0 25.0 1.043091 REL: 8 0.736458 8.450271 1.056284 rel = 0.697216 Initial costs ---------------- Number of surface hits 3040 WM Intensity 854.7604 +/- 206.4629 Ctx Intensity 857.9380 +/- 234.5218 Pct Contrast -1.3390 +/- 21.1493 Cost 0.7365 RelCost 0.6972 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 1.0702 1.0702 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 1.0526 1.0526 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 1.0183 1.0183 0.0 4 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.0000 1.0100 1.0100 0.0 5 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 4.0000 0.9869 0.9869 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.9654 0.9654 0.0 8 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 4.0000 0.9549 0.9549 0.0 18 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 -4.0000 0.9472 0.9472 0.0 30 -4.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.9343 0.9343 0.0 33 -4.0000 -4.0000 0.0000 -4.0000 4.0000 -4.0000 0.9279 0.9279 0.0 34 -4.0000 -4.0000 0.0000 -4.0000 4.0000 0.0000 0.9039 0.9039 0.0 39 -4.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.9022 0.9022 0.0 40 -4.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.8773 0.8773 0.0 273 0.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.8385 0.8385 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.7806 0.7806 0.0 282 0.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.7611 0.7611 0.0 283 0.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.6051 0.6051 0.0 Brute Force -------------------------- Min cost was 0.605117 Number of iterations 729 Search time 1.404000 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 = 0.605117 6 0.382 -4.000 0.000 0.000 0.000 0.000 0.6028346868 8 0.253 -4.000 0.000 0.000 0.000 0.000 0.6013973767 9 0.235 -4.000 0.000 0.000 0.000 0.000 0.6013890613 10 0.241 -4.000 0.000 0.000 0.000 0.000 0.6013835310 11 0.242 -4.000 0.000 0.000 0.000 0.000 0.6013832748 12 0.243 -4.000 0.000 0.000 0.000 0.000 0.6013832562 15 0.243 -3.000 0.000 0.000 0.000 0.000 0.5909781130 22 0.243 -2.910 0.000 0.000 0.000 0.000 0.5908128171 24 0.243 -2.934 0.000 0.000 0.000 0.000 0.5908104590 25 0.243 -2.923 0.000 0.000 0.000 0.000 0.5908054797 27 0.243 -2.924 0.000 0.000 0.000 0.000 0.5908054187 36 0.243 -2.924 -0.280 0.000 0.000 0.000 0.5880212945 38 0.243 -2.924 -0.252 0.000 0.000 0.000 0.5879658965 40 0.243 -2.924 -0.231 0.000 0.000 0.000 0.5879626795 41 0.243 -2.924 -0.239 0.000 0.000 0.000 0.5879577926 43 0.243 -2.924 -0.237 0.000 0.000 0.000 0.5879567580 45 0.243 -2.924 -0.236 0.000 0.000 0.000 0.5879565032 50 0.243 -2.924 -0.236 -0.618 0.000 0.000 0.5817865773 52 0.243 -2.924 -0.236 -0.706 0.000 0.000 0.5814076086 53 0.243 -2.924 -0.236 -0.754 0.000 0.000 0.5812425829 54 0.243 -2.924 -0.236 -0.848 0.000 0.000 0.5811280987 55 0.243 -2.924 -0.236 -0.839 0.000 0.000 0.5811253027 57 0.243 -2.924 -0.236 -0.838 0.000 0.000 0.5811252929 64 0.243 -2.924 -0.236 -0.838 0.382 0.000 0.5780079155 65 0.243 -2.924 -0.236 -0.838 0.312 0.000 0.5776301055 66 0.243 -2.924 -0.236 -0.838 0.285 0.000 0.5776290554 67 0.243 -2.924 -0.236 -0.838 0.298 0.000 0.5776262111 70 0.243 -2.924 -0.236 -0.838 0.301 0.000 0.5776260656 71 0.243 -2.924 -0.236 -0.838 0.302 0.000 0.5776260608 79 0.243 -2.924 -0.236 -0.838 0.302 -0.063 0.5775688251 83 0.243 -2.924 -0.236 -0.838 0.302 -0.071 0.5775661365 84 0.243 -2.924 -0.236 -0.838 0.302 -0.074 0.5775653956 85 0.243 -2.924 -0.236 -0.838 0.302 -0.082 0.5775646048 89 0.243 -2.924 -0.236 -0.838 0.302 -0.080 0.5775644440 powell nthiter 1: fret = 0.577564 97 0.034 -2.924 -0.236 -0.838 0.302 -0.080 0.5757723028 98 0.003 -2.924 -0.236 -0.838 0.302 -0.080 0.5756573558 99 -0.074 -2.924 -0.236 -0.838 0.302 -0.080 0.5755823493 101 -0.055 -2.924 -0.236 -0.838 0.302 -0.080 0.5755604640 102 -0.049 -2.924 -0.236 -0.838 0.302 -0.080 0.5755603161 103 -0.052 -2.924 -0.236 -0.838 0.302 -0.080 0.5755599872 105 -0.051 -2.924 -0.236 -0.838 0.302 -0.080 0.5755599817 111 -0.051 -2.543 -0.236 -0.838 0.302 -0.080 0.5755459374 112 -0.051 -2.733 -0.236 -0.838 0.302 -0.080 0.5744721472 114 -0.051 -2.698 -0.236 -0.838 0.302 -0.080 0.5744141623 116 -0.051 -2.697 -0.236 -0.838 0.302 -0.080 0.5744137303 117 -0.051 -2.691 -0.236 -0.838 0.302 -0.080 0.5744126972 119 -0.051 -2.692 -0.236 -0.838 0.302 -0.080 0.5744126876 127 -0.051 -2.692 -0.094 -0.838 0.302 -0.080 0.5739106506 128 -0.051 -2.692 -0.098 -0.838 0.302 -0.080 0.5739047811 129 -0.051 -2.692 -0.115 -0.838 0.302 -0.080 0.5738836674 132 -0.051 -2.692 -0.116 -0.838 0.302 -0.080 0.5738833731 140 -0.051 -2.692 -0.116 -0.933 0.302 -0.080 0.5735864138 143 -0.051 -2.692 -0.116 -0.934 0.302 -0.080 0.5735858335 153 -0.051 -2.692 -0.116 -0.934 0.322 -0.080 0.5733075230 154 -0.051 -2.692 -0.116 -0.934 0.414 -0.080 0.5730251214 156 -0.051 -2.692 -0.116 -0.934 0.404 -0.080 0.5730033370 157 -0.051 -2.692 -0.116 -0.934 0.392 -0.080 0.5729832913 159 -0.051 -2.692 -0.116 -0.934 0.380 -0.080 0.5729744890 160 -0.051 -2.692 -0.116 -0.934 0.379 -0.080 0.5729741133 161 -0.051 -2.692 -0.116 -0.934 0.374 -0.080 0.5729736696 162 -0.051 -2.692 -0.116 -0.934 0.376 -0.080 0.5729733453 163 -0.051 -2.692 -0.116 -0.934 0.377 -0.080 0.5729733398 175 -0.051 -2.692 -0.116 -0.934 0.377 -0.082 0.5729729319 176 -0.051 -2.692 -0.116 -0.934 0.377 -0.083 0.5729728620 powell nthiter 2: fret = 0.572973 185 -0.026 -2.692 -0.116 -0.934 0.377 -0.083 0.5727797486 186 0.034 -2.692 -0.116 -0.934 0.377 -0.083 0.5726444144 187 0.022 -2.692 -0.116 -0.934 0.377 -0.083 0.5726302888 197 0.022 -2.711 -0.116 -0.934 0.377 -0.083 0.5726173300 198 0.022 -2.713 -0.116 -0.934 0.377 -0.083 0.5726150147 202 0.022 -2.726 -0.116 -0.934 0.377 -0.083 0.5726087188 205 0.022 -2.724 -0.116 -0.934 0.377 -0.083 0.5726084638 215 0.022 -2.724 -0.081 -0.934 0.377 -0.083 0.5725593631 216 0.022 -2.724 -0.084 -0.934 0.377 -0.083 0.5725542188 217 0.022 -2.724 -0.091 -0.934 0.377 -0.083 0.5725504697 218 0.022 -2.724 -0.090 -0.934 0.377 -0.083 0.5725503885 228 0.022 -2.724 -0.089 -0.880 0.377 -0.083 0.5724435245 231 0.022 -2.724 -0.089 -0.882 0.377 -0.083 0.5724432586 233 0.022 -2.724 -0.089 -0.881 0.377 -0.083 0.5724431612 241 0.022 -2.724 -0.089 -0.881 0.462 -0.083 0.5722497714 243 0.022 -2.724 -0.089 -0.881 0.429 -0.083 0.5721451700 244 0.022 -2.724 -0.089 -0.881 0.430 -0.083 0.5721449726 254 0.022 -2.724 -0.089 -0.881 0.430 -0.103 0.5721342976 255 0.022 -2.724 -0.089 -0.881 0.430 -0.102 0.5721337200 256 0.022 -2.724 -0.089 -0.881 0.430 -0.098 0.5721331423 powell nthiter 3: fret = 0.572133 268 0.021 -2.724 -0.089 -0.881 0.430 -0.098 0.5721330481 278 0.021 -2.710 -0.089 -0.881 0.430 -0.098 0.5721133991 279 0.021 -2.707 -0.089 -0.881 0.430 -0.098 0.5721126331 280 0.021 -2.706 -0.089 -0.881 0.430 -0.098 0.5721125889 288 0.021 -2.706 -0.005 -0.881 0.430 -0.098 0.5720335031 289 0.021 -2.706 -0.027 -0.881 0.430 -0.098 0.5719949343 290 0.021 -2.706 -0.036 -0.881 0.430 -0.098 0.5719886287 293 0.021 -2.706 -0.032 -0.881 0.430 -0.098 0.5719883966 294 0.021 -2.706 -0.034 -0.881 0.430 -0.098 0.5719880909 304 0.021 -2.706 -0.034 -0.863 0.430 -0.098 0.5719877244 306 0.021 -2.706 -0.034 -0.872 0.430 -0.098 0.5719851888 307 0.021 -2.706 -0.034 -0.871 0.430 -0.098 0.5719850142 317 0.021 -2.706 -0.034 -0.871 0.451 -0.098 0.5719434321 318 0.021 -2.706 -0.034 -0.871 0.450 -0.098 0.5719425524 319 0.021 -2.706 -0.034 -0.871 0.447 -0.098 0.5719416852 330 0.021 -2.706 -0.034 -0.871 0.447 -0.063 0.5719156484 332 0.021 -2.706 -0.034 -0.871 0.447 -0.072 0.5719102092 334 0.021 -2.706 -0.034 -0.871 0.447 -0.073 0.5719100676 336 0.020 -2.688 0.022 -0.860 0.464 -0.048 0.5717590035 343 0.020 -2.685 0.031 -0.859 0.467 -0.044 0.5717489676 344 0.020 -2.684 0.033 -0.858 0.468 -0.043 0.5717472018 347 0.020 -2.684 0.034 -0.858 0.468 -0.043 0.5717471921 348 0.020 -2.684 0.034 -0.858 0.468 -0.043 0.5717470681 349 0.020 -2.684 0.034 -0.858 0.468 -0.043 0.5717470042 powell nthiter 4: fret = 0.571747 357 0.030 -2.684 0.034 -0.858 0.468 -0.043 0.5717324223 359 0.031 -2.684 0.034 -0.858 0.468 -0.043 0.5717322365 360 0.032 -2.684 0.034 -0.858 0.468 -0.043 0.5717321945 378 0.032 -2.683 0.034 -0.858 0.468 -0.043 0.5717318471 386 0.032 -2.683 0.034 -0.858 0.468 -0.051 0.5717185778 388 0.032 -2.683 0.034 -0.858 0.468 -0.070 0.5717185244 389 0.032 -2.683 0.034 -0.858 0.468 -0.061 0.5717148684 402 0.032 -2.683 0.034 -0.853 0.468 -0.059 0.5717072341 403 0.032 -2.683 0.034 -0.827 0.468 -0.059 0.5717027362 405 0.032 -2.683 0.034 -0.838 0.468 -0.059 0.5716946664 416 0.032 -2.683 0.034 -0.838 0.471 -0.059 0.5716933646 424 0.032 -2.676 0.055 -0.834 0.478 -0.049 0.5716911087 425 0.032 -2.679 0.045 -0.836 0.475 -0.053 0.5716845155 426 0.032 -2.679 0.045 -0.836 0.475 -0.053 0.5716844795 431 0.032 -2.679 0.045 -0.836 0.475 -0.053 0.5716843301 powell nthiter 5: fret = 0.571684 450 0.032 -2.735 0.045 -0.836 0.475 -0.053 0.5715867474 451 0.032 -2.737 0.045 -0.836 0.475 -0.053 0.5715754979 454 0.032 -2.776 0.045 -0.836 0.475 -0.053 0.5713889613 464 0.032 -2.776 0.045 -0.836 0.475 -0.074 0.5713809589 465 0.032 -2.776 0.045 -0.836 0.475 -0.073 0.5713808152 466 0.032 -2.776 0.045 -0.836 0.475 -0.070 0.5713805175 468 0.032 -2.776 0.045 -0.836 0.475 -0.068 0.5713804441 470 0.032 -2.776 0.045 -0.836 0.475 -0.069 0.5713803934 480 0.032 -2.776 0.045 -0.829 0.475 -0.069 0.5713762353 482 0.032 -2.776 0.045 -0.831 0.475 -0.069 0.5713751286 493 0.032 -2.776 0.045 -0.831 0.471 -0.069 0.5713734654 497 0.031 -2.757 0.100 -0.821 0.488 -0.044 0.5712939509 501 0.031 -2.764 0.079 -0.825 0.482 -0.054 0.5712501671 502 0.031 -2.764 0.081 -0.824 0.482 -0.053 0.5712499967 503 0.031 -2.764 0.080 -0.825 0.482 -0.053 0.5712496153 powell nthiter 6: fret = 0.571250 516 0.036 -2.764 0.080 -0.825 0.482 -0.053 0.5712459753 527 0.037 -2.767 0.080 -0.825 0.482 -0.053 0.5712446523 536 0.037 -2.767 0.080 -0.825 0.482 -0.067 0.5712251506 537 0.037 -2.767 0.080 -0.825 0.482 -0.100 0.5712199043 539 0.037 -2.767 0.080 -0.825 0.482 -0.086 0.5712176350 542 0.037 -2.767 0.080 -0.825 0.482 -0.083 0.5712171625 553 0.037 -2.767 0.080 -0.823 0.482 -0.082 0.5712107091 554 0.037 -2.767 0.080 -0.813 0.482 -0.082 0.5711920449 556 0.037 -2.767 0.080 -0.812 0.482 -0.082 0.5711919086 567 0.037 -2.767 0.080 -0.812 0.475 -0.082 0.5711832694 568 0.037 -2.767 0.080 -0.812 0.474 -0.082 0.5711832690 575 0.037 -2.760 0.102 -0.808 0.480 -0.073 0.5711599050 576 0.037 -2.762 0.096 -0.809 0.479 -0.075 0.5711567305 577 0.037 -2.762 0.096 -0.809 0.479 -0.075 0.5711566012 580 0.037 -2.762 0.096 -0.809 0.479 -0.075 0.5711563954 powell nthiter 7: fret = 0.571156 592 0.038 -2.762 0.096 -0.809 0.479 -0.075 0.5711562167 602 0.038 -2.757 0.096 -0.809 0.479 -0.075 0.5711431718 615 0.038 -2.757 0.096 -0.809 0.479 -0.088 0.5711342177 616 0.038 -2.757 0.096 -0.809 0.479 -0.090 0.5711337666 617 0.038 -2.757 0.096 -0.809 0.479 -0.091 0.5711334878 654 0.038 -2.757 0.096 -0.810 0.479 -0.091 0.5711334389 Powell done niters = 7 Computing relative cost 0 -25.0 -25.0 -25.0 1.034281 1 -25.0 -25.0 25.0 1.057439 2 -25.0 25.0 -25.0 1.057510 3 -25.0 25.0 25.0 1.073082 4 25.0 -25.0 -25.0 1.053232 5 25.0 -25.0 25.0 1.037625 6 25.0 25.0 -25.0 1.022211 7 25.0 25.0 25.0 1.039206 REL: 8 0.571133 8.374587 1.046823 rel = 0.545587 Number of iterations 7 Min cost was 0.571133 Number of FunctionCalls 656 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 1.258000 sec Parameters at optimum (transmm) 0.03761 -2.75652 0.09632 Parameters at optimum (rotdeg) -0.81049 0.47867 -0.09126 Final costs ---------------- Number of surface hits 3040 WM Intensity 820.0677 +/- 218.9777 Ctx Intensity 847.2858 +/- 251.0687 Pct Contrast 1.1995 +/- 21.7069 Cost 0.5711 RelCost 0.6972 Reg at min cost was 0.99982 -0.01869 -0.00276 -0.45147; -0.00192 -0.24576 0.96933 -41.17838; 0.01879 0.96915 0.24575 -1.62489; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/004/tmp.bbregister.10182/bbr.pass1.dat, type = 14 Original Reg 0.99963 -0.02639 -0.00635 -0.41348; -0.00071 -0.25947 0.96575 -38.39435; 0.02714 0.96539 0.25939 -2.26805; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00019 -0.00770 -0.00360 0.03799; 0.00121 -0.01371 -0.00358 2.78403; 0.00834 -0.00376 0.01364 -0.64316; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 2.930060 Computing change in rh position Surface-RMS-Diff-mm 2.933595 0.629779 4.253224 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.10182/template.nii --init-reg bold/004/tmp.bbregister.10182/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.10182/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.112 2014/02/25 19:06:37 greve Exp $ setenv SUBJECTS_DIR /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects cd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01 mri_segreg --mov bold/004/tmp.bbregister.10182/template.nii --init-reg bold/004/tmp.bbregister.10182/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.10182/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname transfer machine x86_64 user zkaufman movvol bold/004/tmp.bbregister.10182/template.nii regfile bold/004/tmp.bbregister.10182/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 1459741683 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99982 -0.01869 -0.00276 -0.45147; -0.00192 -0.24576 0.96933 -41.17838; 0.01879 0.96915 0.24575 -1.62489; 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 1.038415 1 -25.0 -25.0 25.0 1.047274 2 -25.0 25.0 -25.0 1.055964 3 -25.0 25.0 25.0 1.064075 4 25.0 -25.0 -25.0 1.039807 5 25.0 -25.0 25.0 1.030289 6 25.0 25.0 -25.0 1.021936 7 25.0 25.0 25.0 1.052059 REL: 8 0.578277 8.349818 1.043727 rel = 0.55405 Initial costs ---------------- Number of surface hits 304441 WM Intensity 821.2704 +/- 215.7741 Ctx Intensity 849.6532 +/- 247.2320 Pct Contrast 1.4959 +/- 21.7200 Cost 0.5783 RelCost 0.5540 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.5749 0.5749 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.5743 0.5743 0.0 2 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.5737 0.5737 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.5733 0.5733 0.0 5 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1000 0.5726 0.5726 0.0 41 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.1000 0.5723 0.5723 0.0 121 -0.1000 0.0000 0.0000 0.0000 0.0000 0.0000 0.5723 0.5723 0.0 122 -0.1000 0.0000 0.0000 0.0000 0.0000 0.1000 0.5720 0.5720 0.0 275 0.0000 -0.1000 0.0000 -0.1000 0.0000 0.1000 0.5720 0.5720 0.0 283 0.0000 -0.1000 0.0000 0.0000 0.0000 0.0000 0.5719 0.5719 0.0 337 0.0000 0.0000 -0.1000 0.0000 0.0000 0.0000 0.5718 0.5718 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.5711 0.5711 0.0 Brute Force -------------------------- Min cost was 0.571133 Number of iterations 729 Search time 1.396000 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 = 0.578277 7 -0.044 0.000 0.000 0.000 0.000 0.000 0.5782480469 8 -0.035 0.000 0.000 0.000 0.000 0.000 0.5782477520 9 -0.039 0.000 0.000 0.000 0.000 0.000 0.5782475547 18 -0.038 0.030 0.000 0.000 0.000 0.000 0.5782171926 19 -0.038 0.036 0.000 0.000 0.000 0.000 0.5782161619 28 -0.038 0.036 -0.181 0.000 0.000 0.000 0.5776288190 29 -0.038 0.036 -0.160 0.000 0.000 0.000 0.5776168771 30 -0.038 0.036 -0.158 0.000 0.000 0.000 0.5776167419 31 -0.038 0.036 -0.157 0.000 0.000 0.000 0.5776167275 44 -0.038 0.036 -0.156 0.040 0.000 0.000 0.5776104255 45 -0.038 0.036 -0.156 0.024 0.000 0.000 0.5776044712 46 -0.038 0.036 -0.156 0.023 0.000 0.000 0.5776044696 47 -0.038 0.036 -0.156 0.022 0.000 0.000 0.5776044167 50 -0.038 0.036 -0.156 0.021 0.000 0.000 0.5776043792 58 -0.038 0.036 -0.156 0.021 -0.304 0.000 0.5750878117 60 -0.038 0.036 -0.156 0.021 -0.293 0.000 0.5750847283 62 -0.038 0.036 -0.156 0.021 -0.294 0.000 0.5750844900 70 -0.038 0.036 -0.156 0.021 -0.294 0.030 0.5750692878 72 -0.038 0.036 -0.156 0.021 -0.294 0.028 0.5750691256 84 -0.043 0.042 -0.180 0.025 -0.340 0.031 0.5750197323 88 -0.042 0.041 -0.176 0.024 -0.332 0.031 0.5750192016 powell nthiter 1: fret = 0.575019 102 -0.114 0.041 -0.176 0.024 -0.332 0.031 0.5749034338 104 -0.119 0.041 -0.176 0.024 -0.332 0.031 0.5749032087 106 -0.117 0.041 -0.176 0.024 -0.332 0.031 0.5749031321 115 -0.118 0.056 -0.176 0.024 -0.332 0.031 0.5748899353 116 -0.118 0.067 -0.176 0.024 -0.332 0.031 0.5748880823 117 -0.118 0.065 -0.176 0.024 -0.332 0.031 0.5748878791 126 -0.118 0.064 -0.233 0.024 -0.332 0.031 0.5747596485 128 -0.118 0.064 -0.241 0.024 -0.332 0.031 0.5747577854 137 -0.118 0.064 -0.240 0.061 -0.332 0.031 0.5747344773 138 -0.118 0.064 -0.240 0.059 -0.332 0.031 0.5747335385 139 -0.118 0.064 -0.240 0.054 -0.332 0.031 0.5747327330 141 -0.118 0.064 -0.240 0.052 -0.332 0.031 0.5747326147 142 -0.118 0.064 -0.240 0.051 -0.332 0.031 0.5747326015 150 -0.118 0.064 -0.240 0.051 -0.332 0.013 0.5747301302 151 -0.118 0.064 -0.240 0.051 -0.332 0.016 0.5747297250 160 -0.118 0.064 -0.238 0.051 -0.329 0.016 0.5747291870 161 -0.118 0.063 -0.238 0.051 -0.328 0.016 0.5747291649 162 -0.118 0.063 -0.237 0.051 -0.327 0.016 0.5747290501 powell nthiter 2: fret = 0.574729 178 -0.117 0.063 -0.237 0.051 -0.326 0.016 0.5747290128 186 -0.116 0.064 -0.237 0.051 -0.326 0.016 0.5747283348 187 -0.116 0.077 -0.237 0.051 -0.326 0.016 0.5747263951 189 -0.116 0.073 -0.237 0.051 -0.326 0.016 0.5747257822 218 -0.116 0.072 -0.237 0.050 -0.326 0.019 0.5747257072 219 -0.116 0.072 -0.237 0.050 -0.326 0.020 0.5747256676 220 -0.116 0.072 -0.237 0.050 -0.326 0.021 0.5747256344 228 -0.116 0.072 -0.237 0.050 -0.326 0.021 0.5747255741 239 -0.115 0.074 -0.237 0.049 -0.326 0.022 0.5747255734 240 -0.115 0.073 -0.237 0.049 -0.326 0.022 0.5747255066 242 -0.115 0.073 -0.237 0.049 -0.326 0.022 0.5747254610 243 -0.115 0.073 -0.237 0.049 -0.326 0.022 0.5747254576 powell nthiter 3: fret = 0.574725 254 -0.114 0.073 -0.237 0.049 -0.326 0.022 0.5747253918 299 -0.113 0.073 -0.237 0.049 -0.326 0.022 0.5747253865 301 -0.114 0.073 -0.237 0.049 -0.326 0.022 0.5747253560 303 -0.114 0.073 -0.237 0.049 -0.326 0.022 0.5747253507 304 -0.114 0.073 -0.237 0.049 -0.326 0.022 0.5747253429 powell nthiter 4: fret = 0.574725 364 -0.114 0.073 -0.237 0.049 -0.326 0.022 0.5747253409 Powell done niters = 4 Computing relative cost 0 -25.0 -25.0 -25.0 1.037200 1 -25.0 -25.0 25.0 1.048312 2 -25.0 25.0 -25.0 1.056333 3 -25.0 25.0 25.0 1.062960 4 25.0 -25.0 -25.0 1.038868 5 25.0 -25.0 25.0 1.030404 6 25.0 25.0 -25.0 1.020610 7 25.0 25.0 25.0 1.050881 REL: 8 0.574725 8.345568 1.043196 rel = 0.550927 Number of iterations 4 Min cost was 0.574725 Number of FunctionCalls 366 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 43.835000 sec Parameters at optimum (transmm) -0.11351 0.07276 -0.23699 Parameters at optimum (rotdeg) 0.04937 -0.32609 0.02157 Final costs ---------------- Number of surface hits 304441 WM Intensity 821.6777 +/- 215.1433 Ctx Intensity 850.2660 +/- 246.7861 Pct Contrast 1.5261 +/- 21.7303 Cost 0.5747 RelCost 0.5540 Reg at min cost was 0.99970 -0.02411 -0.00452 -0.54002; -0.00156 -0.24660 0.96912 -41.10437; 0.02448 0.96882 0.24656 -1.89991; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to bold/004/register.dof6.dat, type = 14 Original Reg 0.99982 -0.01869 -0.00276 -0.45147; -0.00192 -0.24576 0.96933 -41.17838; 0.01879 0.96915 0.24575 -1.62489; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00012 0.00542 0.00177 0.08854; -0.00036 0.00084 0.00021 -0.07401; -0.00569 0.00033 -0.00082 0.27502; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.477579 Computing change in rh position Surface-RMS-Diff-mm 0.381635 0.150952 0.700126 mri_segreg done MinCost: 0.574725 821.677711 850.265989 1.526104 tkregister2_cmdl --mov bold/004/template.nii.gz --reg bold/004/register.dof6.dat --noedit --ltaout bold/004/register.dof6.lta tkregister_tcl /usr/local/freesurfer/dev/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume bold/004/template.nii.gz reg file bold/004/register.dof6.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.131 2016/03/24 17:39:56 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- 0.99970 -0.02411 -0.00452 -0.54002; -0.00156 -0.24660 0.96912 -41.10437; 0.02448 0.96882 0.24656 -1.89991; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: loading target /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/orig.mgz Ttarg: -------------------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading movable bold/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 -------- 0.99970 -0.02411 -0.00452 -0.54002; -0.00156 -0.24660 0.96912 -41.10437; 0.02448 0.96882 0.24656 -1.89991; 0.00000 0.00000 0.00000 1.00000; Determinant -1 subject = fsf01anat RegMat --------------------------- 0.99970 -0.02411 -0.00452 -0.54002; -0.00156 -0.24660 0.96912 -41.10437; 0.02448 0.96882 0.24656 -1.89991; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Sun Mar 27 21:50:11 EDT 2016 Ended at Sun Mar 27 21:53:09 EDT 2016 BBR-Run-Time-Sec 178 bbregister Done To check results, run: tkregister2 --mov bold/004/template.nii.gz --reg bold/004/register.dof6.dat --surf Sun Mar 27 21:53:09 EDT 2016 register-sess completed sess01 Mask ------------------------ mkbrainmask-sess -maskstem brain -fsd bold -s sess01 -d /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional -per-run -nolog -update ------------------------------------------------ /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01 Sun Mar 27 21:53:09 EDT 2016 mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -reg /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/register.dof6.lta -ndil 1 -nerode 0 Sun Mar 27 21:53:09 EDT 2016 setenv SUBJECTS_DIR /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects cd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold /usr/local/freesurfer/dev/fsfast/bin/mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -reg /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/register.dof6.lta -ndil 1 -nerode 0 freesurfer-Linux-centos6_x86_64-dev-20160325 $Id: mkbrainmask,v 1.17 2015/12/10 22:51:30 zkaufman Exp $ Linux transfer 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux mri_vol2vol --mov template.nii.gz --reg /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/register.dof6.lta --inv --interp nearest --o masks/brain.nii.gz --targ /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/aparc+aseg.mgz regio_read_register: loading lta Matrix from regfile: 0.99999 0.00272 -0.00381 0.80641; 0.00432 -0.22201 0.97504 -40.37724; -0.00180 0.97504 0.22201 -1.16013; 0.00000 0.00000 0.00000 1.00000; freadFloat: fread failed movvol template.nii.gz targvol /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/aparc+aseg.mgz outvol masks/brain.nii.gz regfile /autofs/cluster/pubftp/data/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 1459197934 Invert! Inverting registration Final tkRAS-to-tkRAS Matrix is: 0.99999 0.00432 -0.00180 -0.63416; 0.00272 -0.22201 0.97504 -7.83497; -0.00381 0.97504 0.22201 39.62988; -0.00000 -0.00000 -0.00000 1.00000; Vox2Vox Matrix is: 3.43746 -0.00620 -0.02159 19.15771; -0.01309 0.76317 -4.87518 137.49524; -0.00934 -3.35171 -1.11003 244.36896; 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 1.42 2016/01/07 22:23:57 greve Exp $ cwd /autofs/cluster/pubftp/data/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 transfer machine x86_64 user zkaufman 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 24226 values in range Counting number of voxels in first frame Found 24226 voxels in final mask Count: 24226 1431321.196648 122880 19.715169 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 1.42 2016/01/07 22:23:57 greve Exp $ cwd /autofs/cluster/pubftp/data/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 transfer machine x86_64 user zkaufman 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 24226 values in range Dilating 1 voxels in 3d Counting number of voxels in first frame Found 34981 voxels in final mask Count: 34981 2066748.401714 122880 28.467611 mri_binarize done Started at Sun Mar 27 21:53:09 EDT 2016 Ended at Sun Mar 27 21:53:12 EDT 2016 Mkbrainmask-Run-Time-Sec 3 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 1.42 2016/01/07 22:23:57 greve Exp $ cwd /autofs/cluster/pubftp/data/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 transfer machine x86_64 user zkaufman 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 34318 values in range Eroding 3 voxels in 3d Counting number of voxels in first frame Found 13938 voxels in final mask Count: 13938 823485.298393 122880 11.342773 mri_binarize done mkbrainmask -i 001/template.nii.gz -o 001/masks/brain.nii.gz -reg /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/register.dof6.lta -ndil 1 -nerode 0 Sun Mar 27 21:53:12 EDT 2016 setenv SUBJECTS_DIR /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects cd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold /usr/local/freesurfer/dev/fsfast/bin/mkbrainmask -i 001/template.nii.gz -o 001/masks/brain.nii.gz -reg /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/register.dof6.lta -ndil 1 -nerode 0 freesurfer-Linux-centos6_x86_64-dev-20160325 $Id: mkbrainmask,v 1.17 2015/12/10 22:51:30 zkaufman Exp $ Linux transfer 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux mri_vol2vol --mov 001/template.nii.gz --reg /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/register.dof6.lta --inv --interp nearest --o 001/masks/brain.nii.gz --targ /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/aparc+aseg.mgz regio_read_register: loading lta Matrix from regfile: 1.00000 -0.00030 -0.00116 0.63847; 0.00106 -0.23893 0.97104 -40.48508; 0.00057 0.97104 0.23893 -1.35980; 0.00000 0.00000 0.00000 1.00000; freadFloat: fread failed movvol 001/template.nii.gz targvol /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/aparc+aseg.mgz outvol 001/masks/brain.nii.gz regfile /autofs/cluster/pubftp/data/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 1459451216 Invert! Inverting registration Final tkRAS-to-tkRAS Matrix is: 1.00000 0.00106 0.00057 -0.59493; -0.00030 -0.23893 0.97104 -8.35248; -0.00116 0.97104 0.23893 39.63811; -0.00000 -0.00000 -0.00000 1.00000; Vox2Vox Matrix is: 3.43750 0.00195 -0.00528 18.61178; -0.00399 0.82132 -4.85518 135.03517; 0.00103 -3.33794 -1.19465 244.34839; 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 1.42 2016/01/07 22:23:57 greve Exp $ cwd /autofs/cluster/pubftp/data/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 transfer machine x86_64 user zkaufman 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 24269 values in range Counting number of voxels in first frame Found 24269 voxels in final mask Count: 24269 1433861.723827 122880 19.750163 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 1.42 2016/01/07 22:23:57 greve Exp $ cwd /autofs/cluster/pubftp/data/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 transfer machine x86_64 user zkaufman 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 24269 values in range Dilating 1 voxels in 3d Counting number of voxels in first frame Found 35034 voxels in final mask Count: 35034 2069879.749168 122880 28.510742 mri_binarize done Started at Sun Mar 27 21:53:12 EDT 2016 Ended at Sun Mar 27 21:53:13 EDT 2016 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 1.42 2016/01/07 22:23:57 greve Exp $ cwd /autofs/cluster/pubftp/data/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 transfer machine x86_64 user zkaufman 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 34355 values in range Eroding 3 voxels in 3d Counting number of voxels in first frame Found 13918 voxels in final mask Count: 13918 822303.657845 122880 11.326497 mri_binarize done mkbrainmask -i 002/template.nii.gz -o 002/masks/brain.nii.gz -reg /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/register.dof6.lta -ndil 1 -nerode 0 Sun Mar 27 21:53:14 EDT 2016 setenv SUBJECTS_DIR /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects cd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold /usr/local/freesurfer/dev/fsfast/bin/mkbrainmask -i 002/template.nii.gz -o 002/masks/brain.nii.gz -reg /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/register.dof6.lta -ndil 1 -nerode 0 freesurfer-Linux-centos6_x86_64-dev-20160325 $Id: mkbrainmask,v 1.17 2015/12/10 22:51:30 zkaufman Exp $ Linux transfer 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux mri_vol2vol --mov 002/template.nii.gz --reg /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/register.dof6.lta --inv --interp nearest --o 002/masks/brain.nii.gz --targ /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/aparc+aseg.mgz regio_read_register: loading lta Matrix from regfile: 0.99997 -0.00328 0.00685 0.17505; -0.00746 -0.25525 0.96685 -40.60712; 0.00143 0.96687 0.25527 -1.84499; 0.00000 0.00000 0.00000 1.00000; freadFloat: fread failed movvol 002/template.nii.gz targvol /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/aparc+aseg.mgz outvol 002/masks/brain.nii.gz regfile /autofs/cluster/pubftp/data/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 1459224035 Invert! Inverting registration Final tkRAS-to-tkRAS Matrix is: 0.99997 -0.00746 0.00143 -0.47552; -0.00328 -0.25525 0.96687 -8.58071; 0.00685 0.96684 0.25527 39.73056; -0.00000 -0.00000 -0.00000 1.00000; Vox2Vox Matrix is: 3.43740 0.00490 0.03732 17.76211; 0.02356 0.87750 -4.83422 131.94907; 0.01129 -3.32361 -1.27627 244.55766; 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 1.42 2016/01/07 22:23:57 greve Exp $ cwd /autofs/cluster/pubftp/data/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 transfer machine x86_64 user zkaufman 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 24289 values in range Counting number of voxels in first frame Found 24289 voxels in final mask Count: 24289 1435043.364376 122880 19.766439 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 1.42 2016/01/07 22:23:57 greve Exp $ cwd /autofs/cluster/pubftp/data/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 transfer machine x86_64 user zkaufman 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 24289 values in range Dilating 1 voxels in 3d Counting number of voxels in first frame Found 35028 voxels in final mask Count: 35028 2069525.257004 122880 28.505859 mri_binarize done Started at Sun Mar 27 21:53:14 EDT 2016 Ended at Sun Mar 27 21:53:15 EDT 2016 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 1.42 2016/01/07 22:23:57 greve Exp $ cwd /autofs/cluster/pubftp/data/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 transfer machine x86_64 user zkaufman 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 34364 values in range Eroding 3 voxels in 3d Counting number of voxels in first frame Found 13893 voxels in final mask Count: 13893 820826.607159 122880 11.306152 mri_binarize done mkbrainmask -i 003/template.nii.gz -o 003/masks/brain.nii.gz -reg /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/register.dof6.lta -ndil 1 -nerode 0 Sun Mar 27 21:53:15 EDT 2016 setenv SUBJECTS_DIR /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects cd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold /usr/local/freesurfer/dev/fsfast/bin/mkbrainmask -i 003/template.nii.gz -o 003/masks/brain.nii.gz -reg /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/register.dof6.lta -ndil 1 -nerode 0 freesurfer-Linux-centos6_x86_64-dev-20160325 $Id: mkbrainmask,v 1.17 2015/12/10 22:51:30 zkaufman Exp $ Linux transfer 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux mri_vol2vol --mov 003/template.nii.gz --reg /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/register.dof6.lta --inv --interp nearest --o 003/masks/brain.nii.gz --targ /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/aparc+aseg.mgz regio_read_register: loading lta Matrix from regfile: 0.99985 -0.01758 -0.00046 -0.36206; -0.00410 -0.25832 0.96605 -41.03094; 0.01710 0.96590 0.25835 -2.00327; 0.00000 0.00000 0.00000 1.00000; freadFloat: fread failed movvol 003/template.nii.gz targvol /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/aparc+aseg.mgz outvol 003/masks/brain.nii.gz regfile /autofs/cluster/pubftp/data/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 1459992271 Invert! Inverting registration Final tkRAS-to-tkRAS Matrix is: 0.99985 -0.00410 0.01710 0.22805; -0.01758 -0.25832 0.96590 -8.67047; -0.00046 0.96605 0.25835 40.15536; -0.00000 -0.00000 -0.00000 1.00000; Vox2Vox Matrix is: 3.43697 0.05880 0.02050 15.60001; -0.00158 0.88808 -4.83025 131.93027; 0.06044 -3.32028 -1.29159 243.01820; 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 1.42 2016/01/07 22:23:57 greve Exp $ cwd /autofs/cluster/pubftp/data/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 transfer machine x86_64 user zkaufman 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 24335 values in range Counting number of voxels in first frame Found 24335 voxels in final mask Count: 24335 1437761.137638 122880 19.803874 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 1.42 2016/01/07 22:23:57 greve Exp $ cwd /autofs/cluster/pubftp/data/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 transfer machine x86_64 user zkaufman 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 24335 values in range Dilating 1 voxels in 3d Counting number of voxels in first frame Found 35044 voxels in final mask Count: 35044 2070470.569443 122880 28.518880 mri_binarize done Started at Sun Mar 27 21:53:15 EDT 2016 Ended at Sun Mar 27 21:53:17 EDT 2016 Mkbrainmask-Run-Time-Sec 2 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 1.42 2016/01/07 22:23:57 greve Exp $ cwd /autofs/cluster/pubftp/data/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 transfer machine x86_64 user zkaufman 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 34366 values in range Eroding 3 voxels in 3d Counting number of voxels in first frame Found 13948 voxels in final mask Count: 13948 824076.118668 122880 11.350911 mri_binarize done mkbrainmask -i 004/template.nii.gz -o 004/masks/brain.nii.gz -reg /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/register.dof6.lta -ndil 1 -nerode 0 Sun Mar 27 21:53:17 EDT 2016 setenv SUBJECTS_DIR /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects cd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold /usr/local/freesurfer/dev/fsfast/bin/mkbrainmask -i 004/template.nii.gz -o 004/masks/brain.nii.gz -reg /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/register.dof6.lta -ndil 1 -nerode 0 freesurfer-Linux-centos6_x86_64-dev-20160325 $Id: mkbrainmask,v 1.17 2015/12/10 22:51:30 zkaufman Exp $ Linux transfer 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux mri_vol2vol --mov 004/template.nii.gz --reg /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/register.dof6.lta --inv --interp nearest --o 004/masks/brain.nii.gz --targ /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/aparc+aseg.mgz regio_read_register: loading lta Matrix from regfile: 0.99970 -0.02411 -0.00452 -0.54004; -0.00156 -0.24660 0.96912 -41.10435; 0.02448 0.96882 0.24656 -1.89989; 0.00000 0.00000 0.00000 1.00000; freadFloat: fread failed movvol 004/template.nii.gz targvol /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/mri/aparc+aseg.mgz outvol 004/masks/brain.nii.gz regfile /autofs/cluster/pubftp/data/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 1459769660 Invert! Inverting registration Final tkRAS-to-tkRAS Matrix is: 0.99970 -0.00156 0.02448 0.52223; -0.02411 -0.24660 0.96882 -8.30875; -0.00452 0.96912 0.24656 40.30089; -0.00000 -0.00000 -0.00000 1.00000; Vox2Vox Matrix is: 3.43647 0.08415 0.00780 14.70116; -0.01555 0.84757 -4.84558 133.75839; 0.08287 -3.33031 -1.23301 242.10437; 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 1.42 2016/01/07 22:23:57 greve Exp $ cwd /autofs/cluster/pubftp/data/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 transfer machine x86_64 user zkaufman 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 24196 values in range Counting number of voxels in first frame Found 24196 voxels in final mask Count: 24196 1429548.735825 122880 19.690755 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 1.42 2016/01/07 22:23:57 greve Exp $ cwd /autofs/cluster/pubftp/data/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 transfer machine x86_64 user zkaufman 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 24196 values in range Dilating 1 voxels in 3d Counting number of voxels in first frame Found 34960 voxels in final mask Count: 34960 2065507.679138 122880 28.450521 mri_binarize done Started at Sun Mar 27 21:53:17 EDT 2016 Ended at Sun Mar 27 21:53:19 EDT 2016 Mkbrainmask-Run-Time-Sec 2 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 1.42 2016/01/07 22:23:57 greve Exp $ cwd /autofs/cluster/pubftp/data/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 transfer machine x86_64 user zkaufman 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 34277 values in range Eroding 3 voxels in 3d Counting number of voxels in first frame Found 13879 voxels in final mask Count: 13879 819999.458775 122880 11.294759 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 Mar 27 21:53:19 EDT 2016 setenv SUBJECTS_DIR /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects cd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold /usr/local/freesurfer/dev/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-dev-20160325 Linux transfer 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux mri_segstats --seg 001/masks/brain.e3.nii.gz --id 1 --sum /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/tmpdir.meanval.11809/blah.11809 --in 001/f.nii.gz --sfavg 001/global.meanval.dat --avgwf 001/global.waveform.dat $Id: mri_segstats.c,v 1.120 2016/03/02 22:30:05 greve Exp $ cwd cmdline mri_segstats --seg 001/masks/brain.e3.nii.gz --id 1 --sum /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/tmpdir.meanval.11809/blah.11809 --in 001/f.nii.gz --sfavg 001/global.meanval.dat --avgwf 001/global.waveform.dat sysname Linux hostname transfer machine x86_64 user zkaufman 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 0 866.314 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 Mar 27 21:53:21 EDT 2016 setenv SUBJECTS_DIR /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects cd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold /usr/local/freesurfer/dev/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-dev-20160325 Linux transfer 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux mri_segstats --seg 002/masks/brain.e3.nii.gz --id 1 --sum /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/tmpdir.meanval.11873/blah.11873 --in 002/f.nii.gz --sfavg 002/global.meanval.dat --avgwf 002/global.waveform.dat $Id: mri_segstats.c,v 1.120 2016/03/02 22:30:05 greve Exp $ cwd cmdline mri_segstats --seg 002/masks/brain.e3.nii.gz --id 1 --sum /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/tmpdir.meanval.11873/blah.11873 --in 002/f.nii.gz --sfavg 002/global.meanval.dat --avgwf 002/global.waveform.dat sysname Linux hostname transfer machine x86_64 user zkaufman 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 0 864.736 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 Mar 27 21:53:23 EDT 2016 setenv SUBJECTS_DIR /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects cd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold /usr/local/freesurfer/dev/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-dev-20160325 Linux transfer 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux mri_segstats --seg 003/masks/brain.e3.nii.gz --id 1 --sum /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/tmpdir.meanval.11924/blah.11924 --in 003/f.nii.gz --sfavg 003/global.meanval.dat --avgwf 003/global.waveform.dat $Id: mri_segstats.c,v 1.120 2016/03/02 22:30:05 greve Exp $ cwd cmdline mri_segstats --seg 003/masks/brain.e3.nii.gz --id 1 --sum /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/tmpdir.meanval.11924/blah.11924 --in 003/f.nii.gz --sfavg 003/global.meanval.dat --avgwf 003/global.waveform.dat sysname Linux hostname transfer machine x86_64 user zkaufman 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 0 862.917 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 Mar 27 21:53:25 EDT 2016 setenv SUBJECTS_DIR /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects cd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold /usr/local/freesurfer/dev/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-dev-20160325 Linux transfer 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux mri_segstats --seg 004/masks/brain.e3.nii.gz --id 1 --sum /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/tmpdir.meanval.11980/blah.11980 --in 004/f.nii.gz --sfavg 004/global.meanval.dat --avgwf 004/global.waveform.dat $Id: mri_segstats.c,v 1.120 2016/03/02 22:30:05 greve Exp $ cwd cmdline mri_segstats --seg 004/masks/brain.e3.nii.gz --id 1 --sum /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/tmpdir.meanval.11980/blah.11980 --in 004/f.nii.gz --sfavg 004/global.meanval.dat --avgwf 004/global.waveform.dat sysname Linux hostname transfer machine x86_64 user zkaufman 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 0 864.107 Writing to 004/global.waveform.dat mri_segstats done Sun Mar 27 21:53:27 EDT 2016 mkbrainmask-sess done sess01 MC ----------------------------- mc-sess -fstem f -fmcstem fmcpr -s sess01 -d /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional -fsd bold -per-run -nolog -update Logfile is /dev/null ------------------------------------------- /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01 RunList: 001 002 003 004 ------- ************************** ----------- ------- Motion Correcting Run 001 ----------- ------- ************************** ----------- sess = sess01 Sun Mar 27 21:53:27 EDT 2016 mc-afni2 --i 001/f.nii.gz --t 001/template.nii.gz --o 001/fmcpr.nii.gz --mcdat 001/fmcpr.mcdat /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold mri_info --nframes --o /tmp/mriinfo.12098 001/template.nii.gz log file is 001/fmcpr.nii.gz.mclog mcdat file is 001/fmcpr.mcdat tmp dir is 001/tmp.mc-afni2.12098 #@# -------------------------------- /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold mri_convert 001/template.nii.gz 001/tmp.mc-afni2.12098/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float mri_convert.bin 001/template.nii.gz 001/tmp.mc-afni2.12098/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float nskip = 0 ndrop = 0 $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from 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) changing data type from short to float (noscale = 0)... writing to 001/tmp.mc-afni2.12098/tempvol.nii.gz... #@# -------------------------------- /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold mri_convert 001/f.nii.gz 001/tmp.mc-afni2.12098/invol.nii.gz -odt float mri_convert.bin 001/f.nii.gz 001/tmp.mc-afni2.12098/invol.nii.gz -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from 001/f.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) changing data type from short to float (noscale = 0)... writing to 001/tmp.mc-afni2.12098/invol.nii.gz... #@# -------------------------------- /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold 3dvolreg.afni -verbose -dfile 001/fmcpr.mcdat -1Dmatrix_save 001/fmcpr.mat -base 001/tmp.mc-afni2.12098/tempvol.nii.gz -prefix 001/tmp.mc-afni2.12098/outvol.nii.gz 001/tmp.mc-afni2.12098/invol.nii.gz ++ 3dvolreg: AFNI version=AFNI_2011_12_21_1014 (Aug 29 2012) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as 001/tmp.mc-afni2.12098/tempvol.nii.gz, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:001/tmp.mc-afni2.12098/tempvol.nii.gz is 13.100002 degrees from plumb. ++ Reading in base dataset 001/tmp.mc-afni2.12098/tempvol.nii.gz ++ Oblique dataset:001/tmp.mc-afni2.12098/invol.nii.gz is 13.100002 degrees from plumb. ++ Reading input dataset 001/tmp.mc-afni2.12098/invol.nii.gz ++ Edging: x=3 y=3 z=2 ++ Creating mask for -maxdisp + Automask has 27062 voxels + 4509 voxels left in -maxdisp mask after erosion ++ Initializing alignment base ++ Starting final pass on 142 sub-bricks: 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141.. ++ CPU time for realignment=0 s [=0 s/sub-brick] ++ Min : roll=-0.022 pitch=-0.663 yaw=-0.165 dS=-0.157 dL=-0.038 dP=-0.344 ++ Mean: roll=+0.012 pitch=-0.019 yaw=+0.021 dS=+0.041 dL=-0.008 dP=+0.002 ++ Max : roll=+0.137 pitch=+0.722 yaw=+0.201 dS=+0.302 dL=+0.058 dP=+0.294 ++ Max displacements (mm) for each sub-brick: 1.37 1.30 1.41 1.43 1.20 0.95 0.96 0.97 0.97 1.14 1.05 1.12 1.01 1.03 0.79 0.77 0.89 0.81 0.90 0.87 0.90 0.83 0.86 0.91 0.85 0.80 0.86 0.83 0.80 0.70 0.77 0.73 0.70 0.73 0.67 0.63 0.70 0.63 0.56 0.63 0.59 0.53 0.58 0.49 0.55 0.50 0.48 0.41 0.39 0.42 0.35 0.36 0.29 0.34 0.28 0.23 0.20 0.20 0.17 0.18 0.19 0.17 0.11 0.16 0.11 0.13 0.08 0.05 0.11 0.15 0.32 0.00 0.06 0.13 0.07 0.12 0.18 0.17 0.17 0.18 0.22 0.36 0.39 0.40 0.45 0.46 0.42 0.44 0.52 0.49 0.49 0.55 0.54 0.48 0.49 0.55 0.57 0.57 0.65 0.67 0.65 0.74 0.75 0.73 0.71 0.79 0.73 0.72 0.68 0.78 0.80 0.86 0.91 0.98 1.03 1.02 1.07 1.17 1.17 1.17 1.12 1.11 1.18 1.15 1.17 1.14 1.17 1.20 1.17 1.25 1.27 1.20 1.23 1.31 1.31 1.32 1.40 1.34 1.43 1.39 1.41 1.38 ++ Max displacement in automask = 1.43 (mm) at sub-brick 3 ++ Wrote dataset to disk in 001/tmp.mc-afni2.12098/outvol.nii.gz ** Warning: overwriting file 001/fmcpr.mcdat #@# -------------------------------- /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold mri_convert 001/tmp.mc-afni2.12098/outvol.nii.gz 001/fmcpr.nii.gz --in_like 001/template.nii.gz mri_convert.bin 001/tmp.mc-afni2.12098/outvol.nii.gz 001/fmcpr.nii.gz --in_like 001/template.nii.gz reading info from 001/template.nii.gz... $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from 001/tmp.mc-afni2.12098/outvol.nii.gz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 INFO: frames are not the same i_ras = (-1, -0, 0) j_ras = (-0, -0.973976, -0.226651) k_ras = (-2.36491e-18, -0.226651, 0.973976) writing to 001/fmcpr.nii.gz... ... cleaning up .... Sun Mar 27 21:53:57 EDT 2016 mc-afni2 done INFO: Making external regressor from mc params mcdat2mcextreg --i 001/fmcpr.mcdat --o 001/mcprextreg Sun Mar 27 21:53:57 EDT 2016 setenv SUBJECTS_DIR /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects cd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold /usr/local/freesurfer/dev/fsfast/bin/mcdat2mcextreg --i 001/fmcpr.mcdat --o 001/mcprextreg freesurfer-Linux-centos6_x86_64-dev-20160325 Linux transfer 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux mri_glmfit --table /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/tmpdir.mcdat2extreg.12326/table.dat --glmdir /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/tmpdir.mcdat2extreg.12326/glm --osgm --y-out /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/tmpdir.mcdat2extreg.12326/y.out.nii --pca $Id: mri_glmfit.c,v 1.241 2015/08/12 21:03:09 greve Exp $ cwd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold cmdline mri_glmfit.bin --table /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/tmpdir.mcdat2extreg.12326/table.dat --glmdir /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/tmpdir.mcdat2extreg.12326/glm --osgm --y-out /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/tmpdir.mcdat2extreg.12326/y.out.nii --pca sysname Linux hostname transfer machine x86_64 user zkaufman FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 1 y /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/tmpdir.mcdat2extreg.12326/table.dat logyflag 0 usedti 0 glmdir /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/tmpdir.mcdat2extreg.12326/glm IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/tmpdir.mcdat2extreg.12326/glm Loading y from /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/tmpdir.mcdat2extreg.12326/table.dat Found 6 data colums Found 142 data rows Saving design matrix to /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/tmpdir.mcdat2extreg.12326/glm/Xg.dat Computing normalized matrix Normalized matrix condition is 1 Matrix condition is 1 search space = 6.000000 DOF = 141 Starting fit and test Fit completed in 0 minutes Writing results osgm maxvox sig=7.0729 F=31.9512 at index 0 0 0 seed=1459635984 Measure:MC osgm Tx 7.073 Ty -0.255 Tz 1.363 Rx 5.389 Ry -6.684 Rz 0.064 Computing PCA (142) mri_glmfit done ninputs = 1 Checking inputs nframestot = 142 Allocing output Done allocing nframes = 142 Computing PCA Writing to /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/tmpdir.mcdat2extreg.12326/pca.nii mcdat2mcextreg done ------- ************************** ----------- ------- Motion Correcting Run 002 ----------- ------- ************************** ----------- sess = sess01 Sun Mar 27 21:53:58 EDT 2016 mc-afni2 --i 002/f.nii.gz --t 002/template.nii.gz --o 002/fmcpr.nii.gz --mcdat 002/fmcpr.mcdat /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold mri_info --nframes --o /tmp/mriinfo.12400 002/template.nii.gz log file is 002/fmcpr.nii.gz.mclog mcdat file is 002/fmcpr.mcdat tmp dir is 002/tmp.mc-afni2.12400 #@# -------------------------------- /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold mri_convert 002/template.nii.gz 002/tmp.mc-afni2.12400/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float mri_convert.bin 002/template.nii.gz 002/tmp.mc-afni2.12400/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float nskip = 0 ndrop = 0 $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from 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) changing data type from short to float (noscale = 0)... writing to 002/tmp.mc-afni2.12400/tempvol.nii.gz... #@# -------------------------------- /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold mri_convert 002/f.nii.gz 002/tmp.mc-afni2.12400/invol.nii.gz -odt float mri_convert.bin 002/f.nii.gz 002/tmp.mc-afni2.12400/invol.nii.gz -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from 002/f.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) changing data type from short to float (noscale = 0)... writing to 002/tmp.mc-afni2.12400/invol.nii.gz... #@# -------------------------------- /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold 3dvolreg.afni -verbose -dfile 002/fmcpr.mcdat -1Dmatrix_save 002/fmcpr.mat -base 002/tmp.mc-afni2.12400/tempvol.nii.gz -prefix 002/tmp.mc-afni2.12400/outvol.nii.gz 002/tmp.mc-afni2.12400/invol.nii.gz ++ 3dvolreg: AFNI version=AFNI_2011_12_21_1014 (Aug 29 2012) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as 002/tmp.mc-afni2.12400/tempvol.nii.gz, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:002/tmp.mc-afni2.12400/tempvol.nii.gz is 13.100002 degrees from plumb. ++ Reading in base dataset 002/tmp.mc-afni2.12400/tempvol.nii.gz ++ Oblique dataset:002/tmp.mc-afni2.12400/invol.nii.gz is 13.100002 degrees from plumb. ++ Reading input dataset 002/tmp.mc-afni2.12400/invol.nii.gz ++ Edging: x=3 y=3 z=2 ++ Creating mask for -maxdisp + Automask has 27116 voxels + 4503 voxels left in -maxdisp mask after erosion ++ Initializing alignment base ++ Starting final pass on 142 sub-bricks: 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141.. ++ CPU time for realignment=0 s [=0 s/sub-brick] ++ Min : roll=-0.407 pitch=-0.158 yaw=-0.139 dS=-0.153 dL=-0.355 dP=-0.137 ++ Mean: roll=-0.093 pitch=-0.014 yaw=-0.021 dS=+0.013 dL=-0.066 dP=-0.003 ++ Max : roll=+0.040 pitch=+0.134 yaw=+0.060 dS=+0.246 dL=+0.062 dP=+0.147 ++ Max displacements (mm) for each sub-brick: 0.40 0.34 0.35 0.33 0.34 0.31 0.33 0.29 0.32 0.30 0.27 0.22 0.27 0.28 0.38 0.31 0.28 0.25 0.26 0.25 0.24 0.25 0.28 0.29 0.29 0.33 0.26 0.33 0.31 0.33 0.32 0.36 0.34 0.31 0.31 0.29 0.36 0.28 0.30 0.27 0.26 0.31 0.29 0.18 0.21 0.18 0.21 0.18 0.18 0.14 0.14 0.14 0.14 0.18 0.15 0.14 0.16 0.16 0.14 0.16 0.16 0.17 0.15 0.13 0.14 0.11 0.07 0.05 0.07 0.07 0.08 0.00 0.09 0.05 0.06 0.12 0.18 0.19 0.21 0.21 0.23 0.25 0.31 0.31 0.32 0.35 0.34 0.37 0.36 0.34 0.38 0.29 0.30 0.32 0.27 0.31 0.29 0.31 0.30 0.36 0.31 0.34 0.37 0.37 0.41 0.40 0.53 0.54 0.64 0.70 0.76 0.79 0.85 0.76 0.82 0.84 0.89 0.70 0.68 0.79 0.88 0.89 0.93 0.95 0.97 1.02 1.01 1.03 1.00 1.04 1.02 1.01 0.95 0.93 1.06 1.06 1.08 1.08 1.12 1.15 1.17 1.17 ++ Max displacement in automask = 1.17 (mm) at sub-brick 141 ++ Wrote dataset to disk in 002/tmp.mc-afni2.12400/outvol.nii.gz ** Warning: overwriting file 002/fmcpr.mcdat #@# -------------------------------- /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold mri_convert 002/tmp.mc-afni2.12400/outvol.nii.gz 002/fmcpr.nii.gz --in_like 002/template.nii.gz mri_convert.bin 002/tmp.mc-afni2.12400/outvol.nii.gz 002/fmcpr.nii.gz --in_like 002/template.nii.gz reading info from 002/template.nii.gz... $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from 002/tmp.mc-afni2.12400/outvol.nii.gz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 INFO: frames are not the same i_ras = (-1, -0, 0) j_ras = (-0, -0.973976, -0.226651) k_ras = (-2.36491e-18, -0.226651, 0.973976) writing to 002/fmcpr.nii.gz... ... cleaning up .... Sun Mar 27 21:54:26 EDT 2016 mc-afni2 done INFO: Making external regressor from mc params mcdat2mcextreg --i 002/fmcpr.mcdat --o 002/mcprextreg Sun Mar 27 21:54:26 EDT 2016 setenv SUBJECTS_DIR /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects cd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold /usr/local/freesurfer/dev/fsfast/bin/mcdat2mcextreg --i 002/fmcpr.mcdat --o 002/mcprextreg freesurfer-Linux-centos6_x86_64-dev-20160325 Linux transfer 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux mri_glmfit --table /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/tmpdir.mcdat2extreg.12613/table.dat --glmdir /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/tmpdir.mcdat2extreg.12613/glm --osgm --y-out /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/tmpdir.mcdat2extreg.12613/y.out.nii --pca $Id: mri_glmfit.c,v 1.241 2015/08/12 21:03:09 greve Exp $ cwd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold cmdline mri_glmfit.bin --table /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/tmpdir.mcdat2extreg.12613/table.dat --glmdir /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/tmpdir.mcdat2extreg.12613/glm --osgm --y-out /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/tmpdir.mcdat2extreg.12613/y.out.nii --pca sysname Linux hostname transfer machine x86_64 user zkaufman FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 1 y /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/tmpdir.mcdat2extreg.12613/table.dat logyflag 0 usedti 0 glmdir /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/tmpdir.mcdat2extreg.12613/glm IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/tmpdir.mcdat2extreg.12613/glm Loading y from /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/tmpdir.mcdat2extreg.12613/table.dat Found 6 data colums Found 142 data rows Saving design matrix to /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/tmpdir.mcdat2extreg.12613/glm/Xg.dat Computing normalized matrix Normalized matrix condition is 1 Matrix condition is 1 search space = 6.000000 DOF = 141 Starting fit and test Fit completed in 0 minutes Writing results osgm maxvox sig=-11.6183 F=59.0017 at index 0 0 0 seed=1459548810 Measure:MC osgm Tx -11.618 Ty -1.294 Tz -5.836 Rx 0.890 Ry -8.134 Rz -0.265 Computing PCA (142) mri_glmfit done ninputs = 1 Checking inputs nframestot = 142 Allocing output Done allocing nframes = 142 Computing PCA Writing to /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/tmpdir.mcdat2extreg.12613/pca.nii mcdat2mcextreg done ------- ************************** ----------- ------- Motion Correcting Run 003 ----------- ------- ************************** ----------- sess = sess01 Sun Mar 27 21:54:26 EDT 2016 mc-afni2 --i 003/f.nii.gz --t 003/template.nii.gz --o 003/fmcpr.nii.gz --mcdat 003/fmcpr.mcdat /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold mri_info --nframes --o /tmp/mriinfo.12678 003/template.nii.gz log file is 003/fmcpr.nii.gz.mclog mcdat file is 003/fmcpr.mcdat tmp dir is 003/tmp.mc-afni2.12678 #@# -------------------------------- /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold mri_convert 003/template.nii.gz 003/tmp.mc-afni2.12678/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float mri_convert.bin 003/template.nii.gz 003/tmp.mc-afni2.12678/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float nskip = 0 ndrop = 0 $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from 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) changing data type from short to float (noscale = 0)... writing to 003/tmp.mc-afni2.12678/tempvol.nii.gz... #@# -------------------------------- /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold mri_convert 003/f.nii.gz 003/tmp.mc-afni2.12678/invol.nii.gz -odt float mri_convert.bin 003/f.nii.gz 003/tmp.mc-afni2.12678/invol.nii.gz -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from 003/f.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) changing data type from short to float (noscale = 0)... writing to 003/tmp.mc-afni2.12678/invol.nii.gz... #@# -------------------------------- /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold 3dvolreg.afni -verbose -dfile 003/fmcpr.mcdat -1Dmatrix_save 003/fmcpr.mat -base 003/tmp.mc-afni2.12678/tempvol.nii.gz -prefix 003/tmp.mc-afni2.12678/outvol.nii.gz 003/tmp.mc-afni2.12678/invol.nii.gz ++ 3dvolreg: AFNI version=AFNI_2011_12_21_1014 (Aug 29 2012) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as 003/tmp.mc-afni2.12678/tempvol.nii.gz, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:003/tmp.mc-afni2.12678/tempvol.nii.gz is 13.100002 degrees from plumb. ++ Reading in base dataset 003/tmp.mc-afni2.12678/tempvol.nii.gz ++ Oblique dataset:003/tmp.mc-afni2.12678/invol.nii.gz is 13.100002 degrees from plumb. ++ Reading input dataset 003/tmp.mc-afni2.12678/invol.nii.gz ++ Edging: x=3 y=3 z=2 ++ Creating mask for -maxdisp + Automask has 27245 voxels + 4519 voxels left in -maxdisp mask after erosion ++ Initializing alignment base ++ Starting final pass on 142 sub-bricks: 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141.. ++ CPU time for realignment=0 s [=0 s/sub-brick] ++ Min : roll=-0.217 pitch=-0.054 yaw=-0.066 dS=-0.274 dL=-0.203 dP=-0.126 ++ Mean: roll=+0.031 pitch=+0.042 yaw=+0.025 dS=-0.032 dL=+0.027 dP=-0.035 ++ Max : roll=+0.350 pitch=+0.148 yaw=+0.186 dS=+0.064 dL=+0.331 dP=+0.046 ++ Max displacements (mm) for each sub-brick: 0.87 0.87 0.86 0.84 0.81 1.04 0.91 0.87 0.80 0.75 0.80 0.82 0.83 0.68 0.65 0.72 0.71 0.66 0.66 0.68 0.77 0.71 0.63 0.60 0.54 0.51 0.51 0.50 0.50 0.47 0.49 0.47 0.45 0.51 0.45 0.46 0.42 0.43 0.44 0.47 0.41 0.43 0.42 0.37 0.35 0.33 0.23 0.20 0.24 0.21 0.16 0.19 0.14 0.11 0.13 0.09 0.13 0.10 0.11 0.09 0.07 0.11 0.07 0.09 0.11 0.15 0.11 0.12 0.08 0.10 0.07 0.00 0.08 0.08 0.09 0.09 0.07 0.12 0.07 0.13 0.12 0.06 0.10 0.10 0.24 0.24 0.24 0.16 0.07 0.16 0.14 0.12 0.16 0.17 0.12 0.10 0.11 0.11 0.13 0.12 0.14 0.23 0.22 0.30 0.37 0.37 0.41 0.44 0.46 0.46 0.44 0.34 0.39 0.38 0.35 0.43 0.42 0.39 0.43 0.43 0.43 0.46 0.48 0.48 0.51 0.48 0.49 0.48 0.50 0.51 0.53 0.54 0.56 0.57 0.54 0.54 0.55 0.57 0.59 0.59 0.59 0.61 ++ Max displacement in automask = 1.04 (mm) at sub-brick 5 ++ Wrote dataset to disk in 003/tmp.mc-afni2.12678/outvol.nii.gz ** Warning: overwriting file 003/fmcpr.mcdat #@# -------------------------------- /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold mri_convert 003/tmp.mc-afni2.12678/outvol.nii.gz 003/fmcpr.nii.gz --in_like 003/template.nii.gz mri_convert.bin 003/tmp.mc-afni2.12678/outvol.nii.gz 003/fmcpr.nii.gz --in_like 003/template.nii.gz reading info from 003/template.nii.gz... $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from 003/tmp.mc-afni2.12678/outvol.nii.gz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 INFO: frames are not the same i_ras = (-1, -0, 0) j_ras = (-0, -0.973976, -0.226651) k_ras = (-2.36491e-18, -0.226651, 0.973976) writing to 003/fmcpr.nii.gz... ... cleaning up .... Sun Mar 27 21:54:54 EDT 2016 mc-afni2 done INFO: Making external regressor from mc params mcdat2mcextreg --i 003/fmcpr.mcdat --o 003/mcprextreg Sun Mar 27 21:54:54 EDT 2016 setenv SUBJECTS_DIR /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects cd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold /usr/local/freesurfer/dev/fsfast/bin/mcdat2mcextreg --i 003/fmcpr.mcdat --o 003/mcprextreg freesurfer-Linux-centos6_x86_64-dev-20160325 Linux transfer 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux mri_glmfit --table /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/tmpdir.mcdat2extreg.12897/table.dat --glmdir /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/tmpdir.mcdat2extreg.12897/glm --osgm --y-out /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/tmpdir.mcdat2extreg.12897/y.out.nii --pca $Id: mri_glmfit.c,v 1.241 2015/08/12 21:03:09 greve Exp $ cwd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold cmdline mri_glmfit.bin --table /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/tmpdir.mcdat2extreg.12897/table.dat --glmdir /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/tmpdir.mcdat2extreg.12897/glm --osgm --y-out /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/tmpdir.mcdat2extreg.12897/y.out.nii --pca sysname Linux hostname transfer machine x86_64 user zkaufman FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 1 y /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/tmpdir.mcdat2extreg.12897/table.dat logyflag 0 usedti 0 glmdir /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/tmpdir.mcdat2extreg.12897/glm IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/tmpdir.mcdat2extreg.12897/glm Loading y from /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/tmpdir.mcdat2extreg.12897/table.dat Found 6 data colums Found 142 data rows Saving design matrix to /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/tmpdir.mcdat2extreg.12897/glm/Xg.dat Computing normalized matrix Normalized matrix condition is 1 Matrix condition is 1 search space = 6.000000 DOF = 141 Starting fit and test Fit completed in 0 minutes Writing results osgm maxvox sig=-19.7732 F=119.255 at index 5 0 0 seed=1459732456 Measure:MC osgm Tx 1.634 Ty 16.959 Tz 7.762 Rx -6.242 Ry 1.550 Rz -19.773 Computing PCA (142) mri_glmfit done ninputs = 1 Checking inputs nframestot = 142 Allocing output Done allocing nframes = 142 Computing PCA Writing to /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/tmpdir.mcdat2extreg.12897/pca.nii mcdat2mcextreg done ------- ************************** ----------- ------- Motion Correcting Run 004 ----------- ------- ************************** ----------- sess = sess01 Sun Mar 27 21:54:54 EDT 2016 mc-afni2 --i 004/f.nii.gz --t 004/template.nii.gz --o 004/fmcpr.nii.gz --mcdat 004/fmcpr.mcdat /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold mri_info --nframes --o /tmp/mriinfo.12962 004/template.nii.gz log file is 004/fmcpr.nii.gz.mclog mcdat file is 004/fmcpr.mcdat tmp dir is 004/tmp.mc-afni2.12962 #@# -------------------------------- /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold mri_convert 004/template.nii.gz 004/tmp.mc-afni2.12962/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float mri_convert.bin 004/template.nii.gz 004/tmp.mc-afni2.12962/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float nskip = 0 ndrop = 0 $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from 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) changing data type from short to float (noscale = 0)... writing to 004/tmp.mc-afni2.12962/tempvol.nii.gz... #@# -------------------------------- /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold mri_convert 004/f.nii.gz 004/tmp.mc-afni2.12962/invol.nii.gz -odt float mri_convert.bin 004/f.nii.gz 004/tmp.mc-afni2.12962/invol.nii.gz -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from 004/f.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) changing data type from short to float (noscale = 0)... writing to 004/tmp.mc-afni2.12962/invol.nii.gz... #@# -------------------------------- /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold 3dvolreg.afni -verbose -dfile 004/fmcpr.mcdat -1Dmatrix_save 004/fmcpr.mat -base 004/tmp.mc-afni2.12962/tempvol.nii.gz -prefix 004/tmp.mc-afni2.12962/outvol.nii.gz 004/tmp.mc-afni2.12962/invol.nii.gz ++ 3dvolreg: AFNI version=AFNI_2011_12_21_1014 (Aug 29 2012) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as 004/tmp.mc-afni2.12962/tempvol.nii.gz, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:004/tmp.mc-afni2.12962/tempvol.nii.gz is 13.100002 degrees from plumb. ++ Reading in base dataset 004/tmp.mc-afni2.12962/tempvol.nii.gz ++ Oblique dataset:004/tmp.mc-afni2.12962/invol.nii.gz is 13.100002 degrees from plumb. ++ Reading input dataset 004/tmp.mc-afni2.12962/invol.nii.gz ++ Edging: x=3 y=3 z=2 ++ Creating mask for -maxdisp + Automask has 27184 voxels + 4492 voxels left in -maxdisp mask after erosion ++ Initializing alignment base ++ Starting final pass on 142 sub-bricks: 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141.. ++ CPU time for realignment=0 s [=0 s/sub-brick] ++ Min : roll=-0.066 pitch=-0.160 yaw=-0.028 dS=-0.307 dL=-0.037 dP=-0.074 ++ Mean: roll=+0.014 pitch=+0.014 yaw=+0.036 dS=-0.062 dL=+0.046 dP=+0.025 ++ Max : roll=+0.098 pitch=+0.156 yaw=+0.129 dS=+0.032 dL=+0.160 dP=+0.139 ++ Max displacements (mm) for each sub-brick: 0.36 0.35 0.36 0.45 0.39 0.47 0.37 0.41 0.43 0.35 0.40 0.42 0.35 0.34 0.31 0.27 0.29 0.34 0.25 0.27 0.31 0.24 0.19 0.24 0.25 0.20 0.21 0.20 0.23 0.14 0.19 0.23 0.19 0.19 0.21 0.17 0.26 0.18 0.21 0.14 0.09 0.21 0.11 0.26 0.40 0.50 0.43 0.29 0.24 0.17 0.14 0.09 0.11 0.21 0.21 0.26 0.24 0.15 0.19 0.20 0.13 0.15 0.19 0.11 0.10 0.09 0.13 0.10 0.13 0.15 0.12 0.00 0.12 0.10 0.09 0.09 0.09 0.05 0.09 0.10 0.11 0.08 0.10 0.14 0.12 0.10 0.14 0.12 0.10 0.10 0.23 0.19 0.13 0.16 0.09 0.15 0.17 0.10 0.15 0.20 0.11 0.18 0.16 0.16 0.16 0.16 0.15 0.14 0.17 0.18 0.21 0.20 0.20 0.20 0.20 0.22 0.23 0.28 0.23 0.26 0.24 0.26 0.22 0.27 0.28 0.31 0.28 0.30 0.26 0.29 0.30 0.29 0.32 0.34 0.34 0.32 0.33 0.31 0.36 0.37 0.34 0.39 ++ Max displacement in automask = 0.50 (mm) at sub-brick 45 ++ Wrote dataset to disk in 004/tmp.mc-afni2.12962/outvol.nii.gz ** Warning: overwriting file 004/fmcpr.mcdat #@# -------------------------------- /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold mri_convert 004/tmp.mc-afni2.12962/outvol.nii.gz 004/fmcpr.nii.gz --in_like 004/template.nii.gz mri_convert.bin 004/tmp.mc-afni2.12962/outvol.nii.gz 004/fmcpr.nii.gz --in_like 004/template.nii.gz reading info from 004/template.nii.gz... $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from 004/tmp.mc-afni2.12962/outvol.nii.gz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 INFO: frames are not the same i_ras = (-1, -0, 0) j_ras = (-0, -0.973976, -0.226651) k_ras = (-2.36491e-18, -0.226651, 0.973976) writing to 004/fmcpr.nii.gz... ... cleaning up .... Sun Mar 27 21:55:23 EDT 2016 mc-afni2 done INFO: Making external regressor from mc params mcdat2mcextreg --i 004/fmcpr.mcdat --o 004/mcprextreg Sun Mar 27 21:55:23 EDT 2016 setenv SUBJECTS_DIR /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects cd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold /usr/local/freesurfer/dev/fsfast/bin/mcdat2mcextreg --i 004/fmcpr.mcdat --o 004/mcprextreg freesurfer-Linux-centos6_x86_64-dev-20160325 Linux transfer 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux mri_glmfit --table /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/tmpdir.mcdat2extreg.13180/table.dat --glmdir /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/tmpdir.mcdat2extreg.13180/glm --osgm --y-out /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/tmpdir.mcdat2extreg.13180/y.out.nii --pca $Id: mri_glmfit.c,v 1.241 2015/08/12 21:03:09 greve Exp $ cwd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold cmdline mri_glmfit.bin --table /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/tmpdir.mcdat2extreg.13180/table.dat --glmdir /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/tmpdir.mcdat2extreg.13180/glm --osgm --y-out /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/tmpdir.mcdat2extreg.13180/y.out.nii --pca sysname Linux hostname transfer machine x86_64 user zkaufman FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 1 y /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/tmpdir.mcdat2extreg.13180/table.dat logyflag 0 usedti 0 glmdir /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/tmpdir.mcdat2extreg.13180/glm IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/tmpdir.mcdat2extreg.13180/glm Loading y from /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/tmpdir.mcdat2extreg.13180/table.dat Found 6 data colums Found 142 data rows Saving design matrix to /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/tmpdir.mcdat2extreg.13180/glm/Xg.dat Computing normalized matrix Normalized matrix condition is 1 Matrix condition is 1 search space = 6.000000 DOF = 141 Starting fit and test Fit completed in 0 minutes Writing results osgm maxvox sig=23.7337 F=154.923 at index 2 0 0 seed=1459249441 Measure:MC osgm Tx 4.076 Ty 1.819 Tz 23.734 Rx -21.844 Ry 19.528 Rz 13.094 Computing PCA (142) mri_glmfit done ninputs = 1 Checking inputs nframestot = 142 Allocing output Done allocing nframes = 142 Computing PCA Writing to /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/tmpdir.mcdat2extreg.13180/pca.nii mcdat2mcextreg done Sun Mar 27 21:55:23 EDT 2016 mc-sess completed SUCCESSFULLY sess01 STC ----------------------------- stc-sess -i fmcpr -o fmcpr.up -ngroups 1 -so up -s sess01 -d /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional -fsd bold -nolog -update Sun Mar 27 21:55:23 EDT 2016 /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional /usr/local/freesurfer/dev/fsfast/bin/stc-sess -i fmcpr -o fmcpr.up -ngroups 1 -so up -s sess01 -d /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional -fsd bold -nolog -update $Id: stc-sess,v 1.13 2015/12/10 22:51:31 zkaufman Exp $ transfer sess01 ----------------- Sun Mar 27 21:55:23 EDT 2016 --------------------------------------------- /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional stc.fsl --i /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/fmcpr.nii.gz --o /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/fmcpr.up.nii.gz --ngroups 1 --up Sun Mar 27 21:55:23 EDT 2016 /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional /usr/local/freesurfer/dev/fsfast/bin/stc.fsl --i /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/fmcpr.nii.gz --o /autofs/cluster/pubftp/data/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 $ transfer /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional mri_info --nslices --o /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/tmp.13293/nslices.dat /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/fmcpr.nii.gz nslices = 30 slicedelay --nslices 30 --up --o /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/tmp.13293/sdf.txt --ngroups 1 sdf /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/tmp.13293/sdf.txt nslices 30 order up ngroups 1 nslicespg 30 [0.48333333333333334, 0.45000000000000001, 0.41666666666666669, 0.38333333333333336, 0.34999999999999998, 0.31666666666666665, 0.28333333333333333, 0.25, 0.21666666666666667, 0.18333333333333332, 0.14999999999999999, 0.11666666666666667, 0.083333333333333329, 0.050000000000000003, 0.016666666666666666, -0.016666666666666666, -0.050000000000000003, -0.083333333333333329, -0.11666666666666667, -0.14999999999999999, -0.18333333333333332, -0.21666666666666667, -0.25, -0.28333333333333333, -0.31666666666666665, -0.34999999999999998, -0.38333333333333336, -0.41666666666666669, -0.45000000000000001, -0.48333333333333334] sg 1 ---------- Slice Delay (fraction of TR) --------------- 0.4833333333333 0.4500000000000 0.4166666666667 0.3833333333333 0.3500000000000 0.3166666666667 0.2833333333333 0.2500000000000 0.2166666666667 0.1833333333333 0.1500000000000 0.1166666666667 0.0833333333333 0.0500000000000 0.0166666666667 -0.0166666666667 -0.0500000000000 -0.0833333333333 -0.1166666666667 -0.1500000000000 -0.1833333333333 -0.2166666666667 -0.2500000000000 -0.2833333333333 -0.3166666666667 -0.3500000000000 -0.3833333333333 -0.4166666666667 -0.4500000000000 -0.4833333333333 ----------------------------------------- /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional mri_convert /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/fmcpr.nii.gz /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/tmp.13293/in.nii mri_convert.bin /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/fmcpr.nii.gz /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/tmp.13293/in.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/fmcpr.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 /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/tmp.13293/in.nii... /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional slicetimer.fsl -i /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/tmp.13293/in.nii -o /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/tmp.13293/out.nii --tcustom=/autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/tmp.13293/sdf.txt /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional mri_convert /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/tmp.13293/out.nii /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/fmcpr.up.nii.gz mri_convert.bin /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/tmp.13293/out.nii /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/fmcpr.up.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/tmp.13293/out.nii... 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 /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/fmcpr.up.nii.gz... stc.fsl Done --------------------------------------------- /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional stc.fsl --i /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/fmcpr.nii.gz --o /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/fmcpr.up.nii.gz --ngroups 1 --up Sun Mar 27 21:55:39 EDT 2016 /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional /usr/local/freesurfer/dev/fsfast/bin/stc.fsl --i /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/fmcpr.nii.gz --o /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/fmcpr.up.nii.gz --ngroups 1 --up $Id: stc.fsl,v 1.11 2015/12/10 22:51:31 zkaufman Exp $ transfer /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional mri_info --nslices --o /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/tmp.13437/nslices.dat /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/fmcpr.nii.gz nslices = 30 slicedelay --nslices 30 --up --o /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/tmp.13437/sdf.txt --ngroups 1 sdf /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/tmp.13437/sdf.txt nslices 30 order up ngroups 1 nslicespg 30 [0.48333333333333334, 0.45000000000000001, 0.41666666666666669, 0.38333333333333336, 0.34999999999999998, 0.31666666666666665, 0.28333333333333333, 0.25, 0.21666666666666667, 0.18333333333333332, 0.14999999999999999, 0.11666666666666667, 0.083333333333333329, 0.050000000000000003, 0.016666666666666666, -0.016666666666666666, -0.050000000000000003, -0.083333333333333329, -0.11666666666666667, -0.14999999999999999, -0.18333333333333332, -0.21666666666666667, -0.25, -0.28333333333333333, -0.31666666666666665, -0.34999999999999998, -0.38333333333333336, -0.41666666666666669, -0.45000000000000001, -0.48333333333333334] sg 1 ---------- Slice Delay (fraction of TR) --------------- 0.4833333333333 0.4500000000000 0.4166666666667 0.3833333333333 0.3500000000000 0.3166666666667 0.2833333333333 0.2500000000000 0.2166666666667 0.1833333333333 0.1500000000000 0.1166666666667 0.0833333333333 0.0500000000000 0.0166666666667 -0.0166666666667 -0.0500000000000 -0.0833333333333 -0.1166666666667 -0.1500000000000 -0.1833333333333 -0.2166666666667 -0.2500000000000 -0.2833333333333 -0.3166666666667 -0.3500000000000 -0.3833333333333 -0.4166666666667 -0.4500000000000 -0.4833333333333 ----------------------------------------- /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional mri_convert /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/fmcpr.nii.gz /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/tmp.13437/in.nii mri_convert.bin /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/fmcpr.nii.gz /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/tmp.13437/in.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/fmcpr.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 /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/tmp.13437/in.nii... /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional slicetimer.fsl -i /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/tmp.13437/in.nii -o /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/tmp.13437/out.nii --tcustom=/autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/tmp.13437/sdf.txt /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional mri_convert /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/tmp.13437/out.nii /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/fmcpr.up.nii.gz mri_convert.bin /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/tmp.13437/out.nii /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/fmcpr.up.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/tmp.13437/out.nii... 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 /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/fmcpr.up.nii.gz... stc.fsl Done --------------------------------------------- /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional stc.fsl --i /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/fmcpr.nii.gz --o /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/fmcpr.up.nii.gz --ngroups 1 --up Sun Mar 27 21:55:54 EDT 2016 /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional /usr/local/freesurfer/dev/fsfast/bin/stc.fsl --i /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/fmcpr.nii.gz --o /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/fmcpr.up.nii.gz --ngroups 1 --up $Id: stc.fsl,v 1.11 2015/12/10 22:51:31 zkaufman Exp $ transfer /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional mri_info --nslices --o /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/tmp.13598/nslices.dat /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/fmcpr.nii.gz nslices = 30 slicedelay --nslices 30 --up --o /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/tmp.13598/sdf.txt --ngroups 1 sdf /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/tmp.13598/sdf.txt nslices 30 order up ngroups 1 nslicespg 30 [0.48333333333333334, 0.45000000000000001, 0.41666666666666669, 0.38333333333333336, 0.34999999999999998, 0.31666666666666665, 0.28333333333333333, 0.25, 0.21666666666666667, 0.18333333333333332, 0.14999999999999999, 0.11666666666666667, 0.083333333333333329, 0.050000000000000003, 0.016666666666666666, -0.016666666666666666, -0.050000000000000003, -0.083333333333333329, -0.11666666666666667, -0.14999999999999999, -0.18333333333333332, -0.21666666666666667, -0.25, -0.28333333333333333, -0.31666666666666665, -0.34999999999999998, -0.38333333333333336, -0.41666666666666669, -0.45000000000000001, -0.48333333333333334] sg 1 ---------- Slice Delay (fraction of TR) --------------- 0.4833333333333 0.4500000000000 0.4166666666667 0.3833333333333 0.3500000000000 0.3166666666667 0.2833333333333 0.2500000000000 0.2166666666667 0.1833333333333 0.1500000000000 0.1166666666667 0.0833333333333 0.0500000000000 0.0166666666667 -0.0166666666667 -0.0500000000000 -0.0833333333333 -0.1166666666667 -0.1500000000000 -0.1833333333333 -0.2166666666667 -0.2500000000000 -0.2833333333333 -0.3166666666667 -0.3500000000000 -0.3833333333333 -0.4166666666667 -0.4500000000000 -0.4833333333333 ----------------------------------------- /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional mri_convert /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/fmcpr.nii.gz /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/tmp.13598/in.nii mri_convert.bin /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/fmcpr.nii.gz /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/tmp.13598/in.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/fmcpr.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 /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/tmp.13598/in.nii... /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional slicetimer.fsl -i /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/tmp.13598/in.nii -o /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/tmp.13598/out.nii --tcustom=/autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/tmp.13598/sdf.txt /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional mri_convert /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/tmp.13598/out.nii /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/fmcpr.up.nii.gz mri_convert.bin /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/tmp.13598/out.nii /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/fmcpr.up.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/tmp.13598/out.nii... 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 /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/fmcpr.up.nii.gz... stc.fsl Done --------------------------------------------- /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional stc.fsl --i /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/fmcpr.nii.gz --o /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/fmcpr.up.nii.gz --ngroups 1 --up Sun Mar 27 21:56:09 EDT 2016 /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional /usr/local/freesurfer/dev/fsfast/bin/stc.fsl --i /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/fmcpr.nii.gz --o /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/fmcpr.up.nii.gz --ngroups 1 --up $Id: stc.fsl,v 1.11 2015/12/10 22:51:31 zkaufman Exp $ transfer /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional mri_info --nslices --o /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/tmp.13749/nslices.dat /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/fmcpr.nii.gz nslices = 30 slicedelay --nslices 30 --up --o /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/tmp.13749/sdf.txt --ngroups 1 sdf /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/tmp.13749/sdf.txt nslices 30 order up ngroups 1 nslicespg 30 [0.48333333333333334, 0.45000000000000001, 0.41666666666666669, 0.38333333333333336, 0.34999999999999998, 0.31666666666666665, 0.28333333333333333, 0.25, 0.21666666666666667, 0.18333333333333332, 0.14999999999999999, 0.11666666666666667, 0.083333333333333329, 0.050000000000000003, 0.016666666666666666, -0.016666666666666666, -0.050000000000000003, -0.083333333333333329, -0.11666666666666667, -0.14999999999999999, -0.18333333333333332, -0.21666666666666667, -0.25, -0.28333333333333333, -0.31666666666666665, -0.34999999999999998, -0.38333333333333336, -0.41666666666666669, -0.45000000000000001, -0.48333333333333334] sg 1 ---------- Slice Delay (fraction of TR) --------------- 0.4833333333333 0.4500000000000 0.4166666666667 0.3833333333333 0.3500000000000 0.3166666666667 0.2833333333333 0.2500000000000 0.2166666666667 0.1833333333333 0.1500000000000 0.1166666666667 0.0833333333333 0.0500000000000 0.0166666666667 -0.0166666666667 -0.0500000000000 -0.0833333333333 -0.1166666666667 -0.1500000000000 -0.1833333333333 -0.2166666666667 -0.2500000000000 -0.2833333333333 -0.3166666666667 -0.3500000000000 -0.3833333333333 -0.4166666666667 -0.4500000000000 -0.4833333333333 ----------------------------------------- /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional mri_convert /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/fmcpr.nii.gz /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/tmp.13749/in.nii mri_convert.bin /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/fmcpr.nii.gz /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/tmp.13749/in.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/fmcpr.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 /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/tmp.13749/in.nii... /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional slicetimer.fsl -i /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/tmp.13749/in.nii -o /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/tmp.13749/out.nii --tcustom=/autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/tmp.13749/sdf.txt /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional mri_convert /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/tmp.13749/out.nii /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/fmcpr.up.nii.gz mri_convert.bin /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/tmp.13749/out.nii /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/fmcpr.up.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/tmp.13749/out.nii... 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 /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/fmcpr.up.nii.gz... stc.fsl Done Started at Sun Mar 27 21:55:23 EDT 2016 Ended at Sun Mar 27 21:56:24 EDT 2016 stc-sess Done sess01 To Surface ----------------------------- rawfunc2surf-sess -fwhm 5 -s sess01 -d /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional -fsd bold -hemi lh -trgsubject fsaverage -stc up -nolog -update -per-run instem fmcpr.up outstem fmcpr.up.sm5.fsaverage.hemi ------------------------------ 1/1 sess01 1/1 sess01 001 lh --------- Sun Mar 27 21:56:24 EDT 2016 mri_vol2surf --mov /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/masks/brain.nii.gz --reg /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/register.dof6.lta --trgsubject fsaverage --interp nearest --projfrac 0.5 --hemi lh --o /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/masks/brain.fsaverage.lh.pr.nii.gz --noreshape --cortex --surfreg sphere.reg srcvol = /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/masks/brain.nii.gz srcreg = /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/register.dof6.lta srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Input reg is LTA -------- original matrix ----------- 1.00000 -0.00030 -0.00116 0.63848; 0.00106 -0.23893 0.97104 -40.48508; 0.00057 0.97104 0.23893 -1.35978; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsaverage/label/lh.cortex.label Reading surface /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/surf/lh.white Done reading source surface Reading thickness /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 9104 Reading source surface registration /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/surf/lh.sphere.reg Done loading source registration surface Reading target registration /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsaverage/surf/lh.sphere.reg Done loading target registration surface Mapping Surfaces (fsf01anat -> fsaverage) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (162145) Reverse Loop had 37317 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 Done mapping surfaces nSrc121 = 131442, nSrcLost = 0, nSrcMulti = 30703, MnSrcMultiHits = 2.27069 nTrg121 = 134928, nTrgMulti = 28914, MnTrgMultiHits = 2.29062 Masking with /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsaverage/label/lh.cortex.label Writing to /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/masks/brain.fsaverage.lh.pr.nii.gz Dim: 163842 1 1 mri_binarize --i /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/masks/brain.fsaverage.lh.pr.nii.gz --min .00001 --o /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/masks/brain.fsaverage.lh.pr.nii.gz $Id: mri_binarize.c,v 1.42 2016/01/07 22:23:57 greve Exp $ cwd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional cmdline mri_binarize.bin --i /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/masks/brain.fsaverage.lh.pr.nii.gz --min .00001 --o /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/masks/brain.fsaverage.lh.pr.nii.gz sysname Linux hostname transfer machine x86_64 user zkaufman input /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/masks/brain.fsaverage.lh.pr.nii.gz frame 0 nErode3d 0 nErode2d 0 output /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/masks/brain.fsaverage.lh.pr.nii.gz Binarizing based on threshold min 1e-05 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 149955 values in range Counting number of voxels in first frame Found 149955 voxels in final mask Count: 149955 149955.000000 163842 91.524151 mri_binarize done 1/1 sess01 002 lh --------- Sun Mar 27 21:56:36 EDT 2016 mri_vol2surf --mov /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/masks/brain.nii.gz --reg /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/register.dof6.lta --trgsubject fsaverage --interp nearest --projfrac 0.5 --hemi lh --o /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/masks/brain.fsaverage.lh.pr.nii.gz --noreshape --cortex --surfreg sphere.reg srcvol = /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/masks/brain.nii.gz srcreg = /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/register.dof6.lta srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Input reg is LTA -------- original matrix ----------- 0.99997 -0.00328 0.00685 0.17505; -0.00746 -0.25525 0.96685 -40.60712; 0.00143 0.96687 0.25527 -1.84501; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsaverage/label/lh.cortex.label Reading surface /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/surf/lh.white Done reading source surface Reading thickness /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 9086 Reading source surface registration /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/surf/lh.sphere.reg Done loading source registration surface Reading target registration /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsaverage/surf/lh.sphere.reg Done loading target registration surface Mapping Surfaces (fsf01anat -> fsaverage) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (162145) Reverse Loop had 37317 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 Done mapping surfaces nSrc121 = 131442, nSrcLost = 0, nSrcMulti = 30703, MnSrcMultiHits = 2.27069 nTrg121 = 134928, nTrgMulti = 28914, MnTrgMultiHits = 2.29062 Masking with /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsaverage/label/lh.cortex.label Writing to /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/masks/brain.fsaverage.lh.pr.nii.gz Dim: 163842 1 1 mri_binarize --i /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/masks/brain.fsaverage.lh.pr.nii.gz --min .00001 --o /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/masks/brain.fsaverage.lh.pr.nii.gz $Id: mri_binarize.c,v 1.42 2016/01/07 22:23:57 greve Exp $ cwd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional cmdline mri_binarize.bin --i /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/masks/brain.fsaverage.lh.pr.nii.gz --min .00001 --o /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/masks/brain.fsaverage.lh.pr.nii.gz sysname Linux hostname transfer machine x86_64 user zkaufman input /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/masks/brain.fsaverage.lh.pr.nii.gz frame 0 nErode3d 0 nErode2d 0 output /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/masks/brain.fsaverage.lh.pr.nii.gz Binarizing based on threshold min 1e-05 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 149955 values in range Counting number of voxels in first frame Found 149955 voxels in final mask Count: 149955 149955.000000 163842 91.524151 mri_binarize done 1/1 sess01 003 lh --------- Sun Mar 27 21:56:47 EDT 2016 mri_vol2surf --mov /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/masks/brain.nii.gz --reg /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/register.dof6.lta --trgsubject fsaverage --interp nearest --projfrac 0.5 --hemi lh --o /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/masks/brain.fsaverage.lh.pr.nii.gz --noreshape --cortex --surfreg sphere.reg srcvol = /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/masks/brain.nii.gz srcreg = /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/register.dof6.lta srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Input reg is LTA -------- original matrix ----------- 0.99985 -0.01758 -0.00046 -0.36206; -0.00410 -0.25832 0.96605 -41.03092; 0.01710 0.96590 0.25835 -2.00325; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsaverage/label/lh.cortex.label Reading surface /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/surf/lh.white Done reading source surface Reading thickness /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 9077 Reading source surface registration /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/surf/lh.sphere.reg Done loading source registration surface Reading target registration /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsaverage/surf/lh.sphere.reg Done loading target registration surface Mapping Surfaces (fsf01anat -> fsaverage) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (162145) Reverse Loop had 37317 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 Done mapping surfaces nSrc121 = 131442, nSrcLost = 0, nSrcMulti = 30703, MnSrcMultiHits = 2.27069 nTrg121 = 134928, nTrgMulti = 28914, MnTrgMultiHits = 2.29062 Masking with /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsaverage/label/lh.cortex.label Writing to /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/masks/brain.fsaverage.lh.pr.nii.gz Dim: 163842 1 1 mri_binarize --i /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/masks/brain.fsaverage.lh.pr.nii.gz --min .00001 --o /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/masks/brain.fsaverage.lh.pr.nii.gz $Id: mri_binarize.c,v 1.42 2016/01/07 22:23:57 greve Exp $ cwd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional cmdline mri_binarize.bin --i /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/masks/brain.fsaverage.lh.pr.nii.gz --min .00001 --o /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/masks/brain.fsaverage.lh.pr.nii.gz sysname Linux hostname transfer machine x86_64 user zkaufman input /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/masks/brain.fsaverage.lh.pr.nii.gz frame 0 nErode3d 0 nErode2d 0 output /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/masks/brain.fsaverage.lh.pr.nii.gz Binarizing based on threshold min 1e-05 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 149955 values in range Counting number of voxels in first frame Found 149955 voxels in final mask Count: 149955 149955.000000 163842 91.524151 mri_binarize done 1/1 sess01 004 lh --------- Sun Mar 27 21:56:59 EDT 2016 mri_vol2surf --mov /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/masks/brain.nii.gz --reg /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/register.dof6.lta --trgsubject fsaverage --interp nearest --projfrac 0.5 --hemi lh --o /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/masks/brain.fsaverage.lh.pr.nii.gz --noreshape --cortex --surfreg sphere.reg srcvol = /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/masks/brain.nii.gz srcreg = /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/register.dof6.lta srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Input reg is LTA -------- original matrix ----------- 0.99970 -0.02411 -0.00452 -0.54002; -0.00156 -0.24660 0.96912 -41.10436; 0.02448 0.96882 0.24656 -1.89992; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsaverage/label/lh.cortex.label Reading surface /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/surf/lh.white Done reading source surface Reading thickness /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 9087 Reading source surface registration /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/surf/lh.sphere.reg Done loading source registration surface Reading target registration /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsaverage/surf/lh.sphere.reg Done loading target registration surface Mapping Surfaces (fsf01anat -> fsaverage) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (162145) Reverse Loop had 37317 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 Done mapping surfaces nSrc121 = 131442, nSrcLost = 0, nSrcMulti = 30703, MnSrcMultiHits = 2.27069 nTrg121 = 134928, nTrgMulti = 28914, MnTrgMultiHits = 2.29062 Masking with /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsaverage/label/lh.cortex.label Writing to /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/masks/brain.fsaverage.lh.pr.nii.gz Dim: 163842 1 1 mri_binarize --i /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/masks/brain.fsaverage.lh.pr.nii.gz --min .00001 --o /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/masks/brain.fsaverage.lh.pr.nii.gz $Id: mri_binarize.c,v 1.42 2016/01/07 22:23:57 greve Exp $ cwd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional cmdline mri_binarize.bin --i /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/masks/brain.fsaverage.lh.pr.nii.gz --min .00001 --o /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/masks/brain.fsaverage.lh.pr.nii.gz sysname Linux hostname transfer machine x86_64 user zkaufman input /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/masks/brain.fsaverage.lh.pr.nii.gz frame 0 nErode3d 0 nErode2d 0 output /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/masks/brain.fsaverage.lh.pr.nii.gz Binarizing based on threshold min 1e-05 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 149955 values in range Counting number of voxels in first frame Found 149955 voxels in final mask Count: 149955 149955.000000 163842 91.524151 mri_binarize done mri_concat --o /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/masks/brain.fsaverage.lh.pr.nii.gz --mean /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/masks/brain.fsaverage.lh.pr.nii.gz /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/masks/brain.fsaverage.lh.pr.nii.gz /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/masks/brain.fsaverage.lh.pr.nii.gz /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/masks/brain.fsaverage.lh.pr.nii.gz ninputs = 4 Checking inputs nframestot = 4 Allocing output Done allocing nframes = 4 Computing mean across frames Writing to /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/masks/brain.fsaverage.lh.pr.nii.gz mri_binarize --i /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/masks/brain.fsaverage.lh.pr.nii.gz --min 10e-10 --o /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/masks/brain.fsaverage.lh.pr.nii.gz $Id: mri_binarize.c,v 1.42 2016/01/07 22:23:57 greve Exp $ cwd /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional cmdline mri_binarize.bin --i /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/masks/brain.fsaverage.lh.pr.nii.gz --min 10e-10 --o /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/masks/brain.fsaverage.lh.pr.nii.gz sysname Linux hostname transfer machine x86_64 user zkaufman input /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/masks/brain.fsaverage.lh.pr.nii.gz frame 0 nErode3d 0 nErode2d 0 output /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/masks/brain.fsaverage.lh.pr.nii.gz Binarizing based on threshold min 1e-09 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 149955 values in range Counting number of voxels in first frame Found 149955 voxels in final mask Count: 149955 149955.000000 163842 91.524151 mri_binarize done 1/1 sess01 001 lh --------- Sun Mar 27 21:57:10 EDT 2016 mri_vol2surf --mov /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/fmcpr.up.nii.gz --reg /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/register.dof6.lta --trgsubject fsaverage --interp trilin --projfrac 0.5 --hemi lh --o /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/fmcpr.up.sm5.fsaverage.lh.nii.gz --noreshape --cortex --surfreg sphere.reg srcvol = /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/fmcpr.up.nii.gz srcreg = /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/register.dof6.lta srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilin float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Input reg is LTA -------- original matrix ----------- 1.00000 -0.00030 -0.00116 0.63848; 0.00106 -0.23893 0.97104 -40.48508; 0.00057 0.97104 0.23893 -1.35978; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsaverage/label/lh.cortex.label Reading surface /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/surf/lh.white Done reading source surface Reading thickness /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 9104 Reading source surface registration /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/surf/lh.sphere.reg Done loading source registration surface Reading target registration /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsaverage/surf/lh.sphere.reg Done loading target registration surface Mapping Surfaces (fsf01anat -> fsaverage) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (162145) Reverse Loop had 37317 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 Done mapping surfaces nSrc121 = 131442, nSrcLost = 0, nSrcMulti = 30703, MnSrcMultiHits = 2.27069 nTrg121 = 134928, nTrgMulti = 28914, MnTrgMultiHits = 2.29062 Masking with /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsaverage/label/lh.cortex.label Writing to /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/fmcpr.up.sm5.fsaverage.lh.nii.gz Dim: 163842 1 1 mris_fwhm --s fsaverage --hemi lh --smooth-only --i /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/fmcpr.up.sm5.fsaverage.lh.nii.gz --fwhm 5 --o /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/fmcpr.up.sm5.fsaverage.lh.nii.gz --mask /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/masks/brain.fsaverage.lh.nii.gz --no-detrend fsaverage lh white Number of vertices 163842 Number of faces 327680 Total area 65416.984375 GroupSurface 82219.960938 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195470 Loading mask /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/001/masks/brain.fsaverage.lh.nii.gz Found 149955 voxels in mask Not Polynomial detrending Smoothing input by fwhm=5.000000, gstd=2.123305, niters=18 Only smoothing, so saving and exiting now 1/1 sess01 002 lh --------- Sun Mar 27 21:58:05 EDT 2016 mri_vol2surf --mov /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/fmcpr.up.nii.gz --reg /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/register.dof6.lta --trgsubject fsaverage --interp trilin --projfrac 0.5 --hemi lh --o /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/fmcpr.up.sm5.fsaverage.lh.nii.gz --noreshape --cortex --surfreg sphere.reg srcvol = /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/fmcpr.up.nii.gz srcreg = /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/register.dof6.lta srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilin float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Input reg is LTA -------- original matrix ----------- 0.99997 -0.00328 0.00685 0.17505; -0.00746 -0.25525 0.96685 -40.60712; 0.00143 0.96687 0.25527 -1.84501; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsaverage/label/lh.cortex.label Reading surface /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/surf/lh.white Done reading source surface Reading thickness /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 9086 Reading source surface registration /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/surf/lh.sphere.reg Done loading source registration surface Reading target registration /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsaverage/surf/lh.sphere.reg Done loading target registration surface Mapping Surfaces (fsf01anat -> fsaverage) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (162145) Reverse Loop had 37317 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 Done mapping surfaces nSrc121 = 131442, nSrcLost = 0, nSrcMulti = 30703, MnSrcMultiHits = 2.27069 nTrg121 = 134928, nTrgMulti = 28914, MnTrgMultiHits = 2.29062 Masking with /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsaverage/label/lh.cortex.label Writing to /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/fmcpr.up.sm5.fsaverage.lh.nii.gz Dim: 163842 1 1 mris_fwhm --s fsaverage --hemi lh --smooth-only --i /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/fmcpr.up.sm5.fsaverage.lh.nii.gz --fwhm 5 --o /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/fmcpr.up.sm5.fsaverage.lh.nii.gz --mask /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/masks/brain.fsaverage.lh.nii.gz --no-detrend fsaverage lh white Number of vertices 163842 Number of faces 327680 Total area 65416.984375 GroupSurface 82219.960938 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195470 Loading mask /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/002/masks/brain.fsaverage.lh.nii.gz Found 149955 voxels in mask Not Polynomial detrending Smoothing input by fwhm=5.000000, gstd=2.123305, niters=18 Only smoothing, so saving and exiting now 1/1 sess01 003 lh --------- Sun Mar 27 21:58:59 EDT 2016 mri_vol2surf --mov /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/fmcpr.up.nii.gz --reg /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/register.dof6.lta --trgsubject fsaverage --interp trilin --projfrac 0.5 --hemi lh --o /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/fmcpr.up.sm5.fsaverage.lh.nii.gz --noreshape --cortex --surfreg sphere.reg srcvol = /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/fmcpr.up.nii.gz srcreg = /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/register.dof6.lta srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilin float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Input reg is LTA -------- original matrix ----------- 0.99985 -0.01758 -0.00046 -0.36206; -0.00410 -0.25832 0.96605 -41.03092; 0.01710 0.96590 0.25835 -2.00325; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsaverage/label/lh.cortex.label Reading surface /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/surf/lh.white Done reading source surface Reading thickness /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 9077 Reading source surface registration /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/surf/lh.sphere.reg Done loading source registration surface Reading target registration /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsaverage/surf/lh.sphere.reg Done loading target registration surface Mapping Surfaces (fsf01anat -> fsaverage) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (162145) Reverse Loop had 37317 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 Done mapping surfaces nSrc121 = 131442, nSrcLost = 0, nSrcMulti = 30703, MnSrcMultiHits = 2.27069 nTrg121 = 134928, nTrgMulti = 28914, MnTrgMultiHits = 2.29062 Masking with /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsaverage/label/lh.cortex.label Writing to /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/fmcpr.up.sm5.fsaverage.lh.nii.gz Dim: 163842 1 1 mris_fwhm --s fsaverage --hemi lh --smooth-only --i /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/fmcpr.up.sm5.fsaverage.lh.nii.gz --fwhm 5 --o /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/fmcpr.up.sm5.fsaverage.lh.nii.gz --mask /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/masks/brain.fsaverage.lh.nii.gz --no-detrend fsaverage lh white Number of vertices 163842 Number of faces 327680 Total area 65416.984375 GroupSurface 82219.960938 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195470 Loading mask /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/003/masks/brain.fsaverage.lh.nii.gz Found 149955 voxels in mask Not Polynomial detrending Smoothing input by fwhm=5.000000, gstd=2.123305, niters=18 Only smoothing, so saving and exiting now 1/1 sess01 004 lh --------- Sun Mar 27 21:59:53 EDT 2016 mri_vol2surf --mov /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/fmcpr.up.nii.gz --reg /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/register.dof6.lta --trgsubject fsaverage --interp trilin --projfrac 0.5 --hemi lh --o /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/fmcpr.up.sm5.fsaverage.lh.nii.gz --noreshape --cortex --surfreg sphere.reg srcvol = /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/fmcpr.up.nii.gz srcreg = /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/register.dof6.lta srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilin float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Input reg is LTA -------- original matrix ----------- 0.99970 -0.02411 -0.00452 -0.54002; -0.00156 -0.24660 0.96912 -41.10436; 0.02448 0.96882 0.24656 -1.89992; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsaverage/label/lh.cortex.label Reading surface /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/surf/lh.white Done reading source surface Reading thickness /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 9087 Reading source surface registration /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsf01anat/surf/lh.sphere.reg Done loading source registration surface Reading target registration /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsaverage/surf/lh.sphere.reg Done loading target registration surface Mapping Surfaces (fsf01anat -> fsaverage) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (162145) Reverse Loop had 37317 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 Done mapping surfaces nSrc121 = 131442, nSrcLost = 0, nSrcMulti = 30703, MnSrcMultiHits = 2.27069 nTrg121 = 134928, nTrgMulti = 28914, MnTrgMultiHits = 2.29062 Masking with /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects/fsaverage/label/lh.cortex.label Writing to /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/fmcpr.up.sm5.fsaverage.lh.nii.gz Dim: 163842 1 1 mris_fwhm --s fsaverage --hemi lh --smooth-only --i /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/fmcpr.up.sm5.fsaverage.lh.nii.gz --fwhm 5 --o /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/fmcpr.up.sm5.fsaverage.lh.nii.gz --mask /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/masks/brain.fsaverage.lh.nii.gz --no-detrend fsaverage lh white Number of vertices 163842 Number of faces 327680 Total area 65416.984375 GroupSurface 82219.960938 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195470 Loading mask /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/004/masks/brain.fsaverage.lh.nii.gz Found 149955 voxels in mask Not Polynomial detrending Smoothing input by fwhm=5.000000, gstd=2.123305, niters=18 Only smoothing, so saving and exiting now Sun Mar 27 22:00:47 EDT 2016 rawfunc2surf-sess completed ---------------------------------------- Started at Sun Mar 27 21:37:16 EDT 2016 Ended at Sun Mar 27 22:00:47 EDT 2016 preproc-sess done ------------------------------------------- 1/1 /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01 Sun Mar 27 22:00:48 EDT 2016 anadir = /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/workmem.sm05.lh sess01 Update needed MLF is /tmp/selxavg3-sess-5698.m ------------------------------------------ % Sun Mar 27 22:00:47 EDT 2016 % /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional % workmem.sm05.lh which fast_selxavg3 which fast_ldanaflac which MRIread fast_selxavg3b('/autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/workmem.sm05.lh/sxa3.config.txt') if(~fast_fileexists('/tmp/selxavg3-sess-5698.ok')); quit; end %-------------------------------- quit; ------------------------------------------ ------------------------------------------ ------- matlab output -------------------- Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. Warning: No window system found. Java option 'MWT' ignored. < M A T L A B (R) > Copyright 1984-2013 The MathWorks, Inc. R2013b (8.2.0.701) 64-bit (glnxa64) August 13, 2013 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> /usr/local/freesurfer/dev/fsfast/toolbox/fast_selxavg3.m >> /usr/local/freesurfer/dev/fsfast/toolbox/fast_ldanaflac.m >> /usr/local/freesurfer/dev/matlab/MRIread.m >> >> >> starting fast_selxavg3b #@# sess01 ############################### /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01 ------------------------- $Id: fast_selxavg3b.m,v 1.3 2016/02/17 00:04:28 greve Exp $ ------------------------- outtop = /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional Extension format = nii.gz 1 distractor.avg-v-base.mat 2 emot.dist-v-base.mat 3 emot.dist-v-neut.dist.mat 4 encode-v-base.mat 5 probe.avg-v-base.mat Excluding 4 points nruns = 4 autostimdur = outanadir = /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/workmem.sm05.lh Excluding 4 points Excluding 4 points Excluding 4 points Excluding 4 points parfiles condition id list: 1 2 3 4 5 Found 149955/163842 (91.5) voxels in mask 1 Creating Design Matrix ... creation time = 0.006 sec DoMCFit = 1 ntptot = 568, nX = 33, DOF = 535 Saving X matrix to /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/workmem.sm05.lh/Xtmp.mat XCond = 11.8857 (normalized) Computing compensation for resdual AR1 bias 1 -0.5 -0.492866 (t=0.124818) 2 -0.25 -0.259072 (t=0.305866) 3 0 -0.0290439 (t=0.381512) 4 0.25 0.193784 (t=0.559751) 5 0.5 0.400223 (t=0.634269) AR1 Correction M: 0.0417295 1.11591 Computing contrast matrices OLS Beta Pass run 1 t= 0.0 reading data ... 1.59641 Global Mean 866.31 run 2 t= 2.8 reading data ... 1.5943 Global Mean 864.74 run 3 t= 2.8 reading data ... 1.58673 Global Mean 862.92 run 4 t= 2.8 reading data ... 1.58814 Global Mean 864.11 Global In-Mask Mean = 864.519 (873.353) Rescale Target = 100 RescaleFactor = 0.115671 OLS Residual Pass run 1 t= 0.0 reading data ... 1.5824 Saving rho1 run 2 t= 3.8 reading data ... 1.58872 Saving rho1 run 3 t= 3.9 reading data ... 1.59179 Saving rho1 run 4 t= 3.9 reading data ... 1.59108 Saving rho1 Smoothing ACF /usr/local/freesurfer/dev/bin/mris_fwhm --mask /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/workmem.sm05.lh/mask.nii.gz --i /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/workmem.sm05.lh/rho1mn.nii.gz --o /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/workmem.sm05.lh/rho1mn.sm.nii.gz --fwhm 20.000000 --smooth-only --s fsaverage --hemi lh --sd /cluster/pubftp/data/tutorial_data/fsfast-tutorial.subjects fsaverage lh white Number of vertices 163842 Number of faces 327680 Total area 65416.984375 GroupSurface 82219.960938 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195470 Loading mask /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/workmem.sm05.lh/mask.nii.gz Found 149955 voxels in mask Not Polynomial detrending Smoothing input by fwhm=20.000000, gstd=8.493218, niters=294 Only smoothing, so saving and exiting now Found 0 voxels with corrected AR1 > 0.90 Whitening Computing whitening matrices Alloc Sinv: 568 568 30 ... done t = 0.038571 sec seg 1 4999 nrho1 = 0.131 seg 2 4999 nrho1 = 0.245 seg 3 4999 nrho1 = 0.302 seg 4 4999 nrho1 = 0.345 seg 5 4999 nrho1 = 0.376 seg 6 4999 nrho1 = 0.399 seg 7 4999 nrho1 = 0.419 seg 8 4999 nrho1 = 0.436 seg 9 4999 nrho1 = 0.452 seg 10 4999 nrho1 = 0.467 seg 11 4998 nrho1 = 0.481 seg 12 5000 nrho1 = 0.493 seg 13 4999 nrho1 = 0.505 seg 14 4999 nrho1 = 0.516 seg 15 4998 nrho1 = 0.526 seg 16 5000 nrho1 = 0.535 seg 17 4999 nrho1 = 0.544 seg 18 4999 nrho1 = 0.551 seg 19 4999 nrho1 = 0.559 seg 20 4999 nrho1 = 0.566 seg 21 4999 nrho1 = 0.574 seg 22 4999 nrho1 = 0.582 seg 23 4999 nrho1 = 0.591 seg 24 4998 nrho1 = 0.600 seg 25 5000 nrho1 = 0.609 seg 26 4999 nrho1 = 0.620 seg 27 4999 nrho1 = 0.636 seg 28 4999 nrho1 = 0.652 seg 29 4999 nrho1 = 0.666 seg 30 4984 nrho1 = 0.695 GLS Beta Pass run 1 t= 0.0 run 2 t= 2.9 run 3 t= 5.8 run 4 t= 8.7 GLS Residual Pass run 1 t= 0.0 run 2 t= 4.1 run 3 t= 8.3 run 4 t=12.4 Found 13887 zero-valued voxels Computing contrasts Starting contrasts distractor.avg-v-base J=1 ------------- /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/workmem.sm05.lh/distractor.avg-v-base exists, deleting Saving efficiency 33.4862 Testing Motion Correction Parameters -5.39 0.39 -0.26 -0.32 -1.44 -1.97 0.62 0.41 2.09 3.04 2.40 -0.44 -0.49 -0.46 0.64 0.43 -0.59 -0.38 emot.dist-v-base J=1 ------------- /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/workmem.sm05.lh/emot.dist-v-base exists, deleting Saving efficiency 33.4862 Testing Motion Correction Parameters -5.39 0.39 -0.26 -0.32 -1.44 -1.97 0.62 0.41 2.09 3.04 2.40 -0.44 -0.49 -0.46 0.64 0.43 -0.59 -0.38 emot.dist-v-neut.dist J=1 ------------- /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/workmem.sm05.lh/emot.dist-v-neut.dist exists, deleting Saving efficiency 21.8536 Testing Motion Correction Parameters -3.11 2.42 -2.33 0.05 -1.30 -1.27 -0.79 -0.75 0.39 4.67 0.12 -0.79 0.31 -0.67 -0.78 -0.72 0.82 0.77 encode-v-base J=1 ------------- /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/workmem.sm05.lh/encode-v-base exists, deleting Saving efficiency 55.0851 Testing Motion Correction Parameters -0.72 -1.01 2.05 0.10 -0.96 -3.23 1.99 1.42 2.97 -0.26 2.40 0.52 -2.47 -1.60 2.01 1.48 -1.94 -1.37 probe.avg-v-base J=1 ------------- /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/workmem.sm05.lh/probe.avg-v-base exists, deleting Saving efficiency 55.1902 Testing Motion Correction Parameters 0.33 -0.32 0.02 -0.96 1.67 -0.89 1.93 1.86 0.61 -0.49 -0.20 -0.33 0.89 0.15 1.90 1.89 -1.93 -1.86 Saving h.dat to /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01/bold/workmem.sm05.lh/h.dat cputime-min 1.963000 fast_selxavg3 done for /autofs/cluster/pubftp/data/tutorial_data/fsfast-functional/sess01 ans = 0 >> >> >> >> >> ------------------------------------------ Started at Sun Mar 27 21:37:16 EDT 2016 Ended at Sun Mar 27 22:03:32 EDT 2016 selxavg3-sess completed