[dglen@gollum.local:/Users/dglen/freesurfer/subjects/FL/FLsurf/mri] [2006-01-12 13:03:40] running: /Applications/freesurfer/lib/mni/bin/mritotal -verbose -debug -clobber -modeldir /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg -protocol icbm nu.mnc transforms/talairach.xfm Loading configuration file /Applications/freesurfer/lib/mni/bin/../etc/mni_autoreg/mritotal.cfg Loading protocol default (protocol file = /Applications/freesurfer/lib/mni/bin/../etc/mni_autoreg/mritotal.default.cfg) Loading protocol icbm (protocol file = /Applications/freesurfer/lib/mni/bin/../etc/mni_autoreg/mritotal.icbm.cfg) source = nu.mnc model = /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305 transform = transforms/talairach.xfm protocol = icbm: linear fit only subsample heuristically crop according to 0,0 0,0 -25%,0 blur with 16 and 8 mm FHWM kernels pad/unpad correctly (encroach on original volume) default objective function = cross-correlation Subsampling/cropping data: [mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FL/FLsurf/mri] [2006-01-12 13:03:40] /Applications/freesurfer/lib/mni/bin/autocrop -clobber nu.mnc /tmp/mritotal_19416/nu_crop.mnc -step 2 2 2 -extend 0,0 0,0 -25%,0 [autocrop] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FL/FLsurf/mri] [2006-01-12 13:03:41] /Applications/freesurfer/lib/mni/bin/mincresample -clobber nu.mnc /tmp/mritotal_19416/nu_crop.mnc -start -128.9 -128 -64 -step 2 2 2 -nelements 128 128 96 Transforming slices:................................................................................................................................Done [mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FL/FLsurf/mri] [2006-01-12 13:03:41] /Applications/freesurfer/lib/mni/bin/volume_cog /tmp/mritotal_19416/nu_crop.mnc | tail -1 Centroid of input volume: 1.479794 12.021105 -15.261126 Zero-padding data: [mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FL/FLsurf/mri] [2006-01-12 13:03:42] /Applications/freesurfer/lib/mni/bin/autocrop -clobber /tmp/mritotal_19416/nu_crop.mnc /tmp/mritotal_19416/nu_pad.mnc -expand 22 22 22 [autocrop] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FL/FLsurf/mri] [2006-01-12 13:03:42] /Applications/freesurfer/lib/mni/bin/mincreshape -clobber /tmp/mritotal_19416/nu_crop.mnc /tmp/mritotal_19416/nu_pad.mnc -start -11,-11,-11 -count 150,150,118 Copying chunks:......................................................................................................................................................Done. Intensity blurring data: [mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FL/FLsurf/mri] [2006-01-12 13:03:42] /Applications/freesurfer/lib/mni/bin/mincblur -clobber -debug /tmp/mritotal_19416/nu_pad.mnc /tmp/mritotal_19416/tmp_16 -fwhm 16 ===== Debugging information from /Applications/freesurfer/lib/mni/bin/mincblur ===== Data filename = /tmp/mritotal_19416/nu_pad.mnc Output basename = /tmp/mritotal_19416/tmp_16 Input volume = 150 cols by 150 rows by 118 slices Input voxels are = 2.000 2.000 2.000 min/max value = 0.000 248.999 Apodizing data at 16.000000 Volume def min and max: = 0.000000 248.999312 before blur min/max = 0.000000 248.999313 after blur min/max = -0.000000 133.283752 Making byte volume... [mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FL/FLsurf/mri] [2006-01-12 13:03:45] /Applications/freesurfer/lib/mni/bin/autocrop -clobber /tmp/mritotal_19416/tmp_16_blur.mnc /tmp/mritotal_19416/nu_16_blur.mnc -expand -44 -44 -44 [autocrop] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FL/FLsurf/mri] [2006-01-12 13:03:45] /Applications/freesurfer/lib/mni/bin/mincreshape -clobber /tmp/mritotal_19416/tmp_16_blur.mnc /tmp/mritotal_19416/nu_16_blur.mnc -start 22,22,22 -count 106,106,74 Copying chunks:..........................................................................................................Done. Gradient blurring data: [mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FL/FLsurf/mri] [2006-01-12 13:03:45] /Applications/freesurfer/lib/mni/bin/mincblur -clobber -debug /tmp/mritotal_19416/nu_pad.mnc /tmp/mritotal_19416/tmp_8 -fwhm 8 -gradient Transforming slices:......................................................................................................................................................Done ===== Debugging information from /Applications/freesurfer/lib/mni/bin/mincblur ===== Data filename = /tmp/mritotal_19416/nu_pad.mnc Output basename = /tmp/mritotal_19416/tmp_8 Input volume = 150 cols by 150 rows by 118 slices Input voxels are = 2.000 2.000 2.000 min/max value = 0.000 248.999 Apodizing data at 8.000000 Volume def min and max: = 0.000000 248.999312 before blur min/max = 0.000000 248.999313 after blur min/max = -0.000015 168.507477 Making byte volume... Making byte volume dx...dx: min = -17.596348, max = 15.116726 Making byte volume dy...dy: min = -14.018719, max = 12.739358 Making byte volume dz...dz: min = -14.181095, max = 15.843277 [mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FL/FLsurf/mri] [2006-01-12 13:03:52] /Applications/freesurfer/lib/mni/bin/autocrop -clobber /tmp/mritotal_19416/tmp_8_blur.mnc /tmp/mritotal_19416/nu_8_blur.mnc -expand -34 -34 -34 [autocrop] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FL/FLsurf/mri] [2006-01-12 13:03:52] /Applications/freesurfer/lib/mni/bin/mincreshape -clobber /tmp/mritotal_19416/tmp_8_blur.mnc /tmp/mritotal_19416/nu_8_blur.mnc -start 17,17,17 -count 116,116,84 Copying chunks:....................................................................................................................Done. [mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FL/FLsurf/mri] [2006-01-12 13:03:52] /Applications/freesurfer/lib/mni/bin/autocrop -clobber /tmp/mritotal_19416/tmp_8_dxyz.mnc /tmp/mritotal_19416/nu_8_dxyz.mnc -expand -34 -34 -34 [autocrop] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FL/FLsurf/mri] [2006-01-12 13:03:52] /Applications/freesurfer/lib/mni/bin/mincreshape -clobber /tmp/mritotal_19416/tmp_8_dxyz.mnc /tmp/mritotal_19416/nu_8_dxyz.mnc -start 17,17,17 -count 116,116,84 Copying chunks:....................................................................................................................Done. 16mm intensity lsq7 fit, no masks: making /tmp/mritotal_19416/nu_16.xfm [mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FL/FLsurf/mri] [2006-01-12 13:03:52] /Applications/freesurfer/lib/mni/bin/minctracc -clobber -debug /tmp/mritotal_19416/nu_16_blur.mnc /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_16_blur.mnc /tmp/mritotal_19416/nu_16.xfm -est_translations -lsq7 -xcorr -center 1.479794 12.021105 -15.261126 -step 4 4 4 -tol 0.01 -simplex 20 Source volume size: 74 by 106 by 106 Source voxel = 2.000 2.000 2.000 min/max value= -0.000 133.284 min/max voxel= 0.000 255.000 Target volume size: 58 by 110 by 86 Target voxel = 2.000 2.000 2.000 min/max value= -0.000 123.710 min/max voxel= 0.000 255.000 AFTER init_params() Transform matrix = 1.0000 0.0000 0.0000 -1.1518 0.0000 1.0000 0.0000 -29.6122 0.0000 0.0000 1.0000 24.7158 Transform center = 1.480 12.021 -15.261 Transform rotations = 0.000 0.000 0.000 Transform trans = -1.152 -29.612 24.716 Transform scale = 1.000 1.000 1.000 Transform shear = 0.000 0.000 0.000 Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -85.095 -125.510 -47.250 Lattice count = 43 55 29 ===== Debugging information from /Applications/freesurfer/lib/mni/bin/minctracc ===== Data filename = /tmp/mritotal_19416/nu_16_blur.mnc Model filename = /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_16_blur.mnc Data mask filename = Model mask filename = Input xform name = Output filename = /tmp/mritotal_19416/nu_16.xfm Step size = 4.000000 4.000000 4.000000 Sub-lattice dia = 24.000000 24.000000 24.000000 Objective function = cross correlation (threshold = 0.000000 0.000000) Transform linear = TRUE Transform inverted? = FALSE Transform type = 4 Transform matrix = 1.0000 0.0000 0.0000 0.0000 0.0000 1.0000 0.0000 0.0000 0.0000 0.0000 1.0000 0.0000 Transform center = 1.480 12.021 -15.261 Transform rotation = 0.000 0.000 0.000 Transform trans = 0.000 0.000 0.000 Transform scale = 1.000 1.000 1.000 Center of rot/scale forced: 1.479794 12.021105 -15.261126 using PAT to get initial parameters: will try to get: [trans] COG of v1 forced: 1.479794 12.021105 -15.261126 In set_up_lattice, xyzv[axes] = 2, 1, 0, -1 In set_up_lattice, xyzv[axes] = 2, 1, 0, -1 in vol to cov start = -47.25 -125.51 -85.09 count = 43 55 29 step = 4.00 4.00 4.00 direct= 1.00 0.00 0.00 direct= 0.00 1.00 0.00 direct= 0.00 0.00 1.00 In set_up_lattice, xyzv[axes] = 2, 1, 0, -1 In set_up_lattice, xyzv[axes] = 2, 1, 0, -1 COG of v2: 0.328006 -17.591131 9.454663 [trans] = -1.151788 -29.612236 24.715790 Only center & trans required, now returning from init_transformation Transform center = 1.480 12.021 -15.261 Transform rots = 0.000 0.000 0.000 Transform trans = -1.152 -29.612 24.716 Transform scale = 1.000 1.000 1.000 In set_up_lattice, xyzv[axes] = 2, 1, 0, -1 slice lim 0 36 row lim 0 52 col lim 4 49 thresh = 0.00000 0.00000 In set_up_lattice, xyzv[axes] = 2, 1, 0, -1 68585 44892 -> 0.03757206 68585 44892 -> 0.03757206 68585 40392 -> 0.08379527 68585 46139 -> 0.04656866 68585 44892 -> 0.05060920 68585 48246 -> 0.04597411 68585 44001 -> 0.04473997 68585 44077 -> 0.04533632 68585 58609 -> 0.11209173 68585 15684 -> 0.13862763 68585 54172 -> 0.06674928 68585 44742 -> 0.09625454 68585 44555 -> 0.05183155 68585 30763 -> 0.08022231 68585 50249 -> 0.04558368 68585 44633 -> 0.05877119 68585 46046 -> 0.04231211 68585 47261 -> 0.02817746 68585 47571 -> 0.04239252 68585 47861 -> 0.06162731 68585 46440 -> 0.03738227 68585 48525 -> 0.03699880 68585 40424 -> 0.04408184 68585 44517 -> 0.03264727 68585 46081 -> 0.02863226 68585 49914 -> 0.04621824 68585 43717 -> 0.03509459 68585 46184 -> 0.02114396 68585 44482 -> 0.01905007 68585 44582 -> 0.03348200 68585 45377 -> 0.02457306 68585 43757 -> 0.03175164 68585 44878 -> 0.02321010 68585 45336 -> 0.02204072 68585 44075 -> 0.03469887 68585 45364 -> 0.02343531 68585 48689 -> 0.02390069 68585 45817 -> 0.02815539 68585 42783 -> 0.01941792 68585 45888 -> 0.02330081 68585 45945 -> 0.02451286 68585 46219 -> 0.01778799 68585 41847 -> 0.02925201 68585 47299 -> 0.01808874 68585 44482 -> 0.01828753 68585 45063 -> 0.02465384 68585 46047 -> 0.01697290 68585 46291 -> 0.02223339 68585 46148 -> 0.01596514 68585 43077 -> 0.03582106 68585 46289 -> 0.01526017 68585 46082 -> 0.02603871 68585 44611 -> 0.01462362 68585 46630 -> 0.01565263 68585 45569 -> 0.02480176 68585 45725 -> 0.01428175 68585 44516 -> 0.01664884 68585 45556 -> 0.01178247 68585 45374 -> 0.01251101 68585 45501 -> 0.01245333 68585 47103 -> 0.01371667 68585 45756 -> 0.01262999 68585 44373 -> 0.01724166 68585 46336 -> 0.01273953 68585 45015 -> 0.01443169 68585 47150 -> 0.01100981 68585 47946 -> 0.01314890 68585 46649 -> 0.01550958 68585 45677 -> 0.01198321 68585 46373 -> 0.01130413 68585 44807 -> 0.01350975 68585 45422 -> 0.01147853 68585 45416 -> 0.01154193 68585 46159 -> 0.01221339 68585 46659 -> 0.01117230 68585 45978 -> 0.01306206 68585 46113 -> 0.01082404 68585 46377 -> 0.01191668 68585 46280 -> 0.01083225 68585 46836 -> 0.01048659 68585 47528 -> 0.01195985 68585 47182 -> 0.01255511 68585 45969 -> 0.01053514 68585 47615 -> 0.01093910 68585 46548 -> 0.01167253 68585 46488 -> 0.01050712 68585 46641 -> 0.01126841 68585 46627 -> 0.01049069 68585 45951 -> 0.01117902 68585 46892 -> 0.01042592 68585 45386 -> 0.01156424 68585 47009 -> 0.01039228 68585 46887 -> 0.01013876 68585 47156 -> 0.01056805 68585 47269 -> 0.01094678 68585 46401 -> 0.01032208 68585 47488 -> 0.01088815 68585 46382 -> 0.01023301 68585 46925 -> 0.01031628 68585 46916 -> 0.01013269 68585 47040 -> 0.01045500 68585 46591 -> 0.01084592 68585 46843 -> 0.01017870 68585 46651 -> 0.01017205 68585 46355 -> 0.01038831 68585 46540 -> 0.01015921 68585 47013 -> 0.01020887 68585 46546 -> 0.01034525 68585 46785 -> 0.01012990 68585 47234 -> 0.01015022 68585 46647 -> 0.01016237 68585 46764 -> 0.01011634 68585 46700 -> 0.01037520 done with simplex after 104 iterations 0 0.01014: 0.04444 -20.69719 -2.66032 -18.42463 1.85352 -3.36073 52.17292 1 0.01015:-0.10047 -21.93482 -3.77501 -18.99600 0.97165 -4.59012 52.60279 2 0.01012:-0.86968 -20.64613 -3.42079 -19.43086 2.08083 -3.64934 52.09632 3 0.01017:-0.20046 -21.27469 -3.96771 -19.54982 2.02715 -4.27924 51.98980 4 0.01016:-0.43581 -20.10667 -3.92884 -17.89363 1.30310 -4.45815 52.00851 5 0.01013:-0.67882 -21.35765 -3.38256 -16.92286 1.48596 -4.62982 52.06981 6 0.01013:-0.03458 -20.57474 -3.54537 -18.04642 0.38317 -3.32562 52.04012 7 0.01016:-0.49157 -20.70648 -2.35636 -18.01709 1.31754 -3.92761 51.73924 after parameter optimization -center 1.47979 12.02111 -15.26113 -translation -0.86968 -20.64613 -3.42079 -rotation -19.43086 2.08083 -3.64934 -scale 1.04193 1.04193 1.04193 -shear 0.00000 0.00000 0.00000 68585 46764 -> 0.01011634 Initial objective function val = 0.03757206 Final objective function value = 0.01011634 successful write 8mm intensity lsq7 fit, no masks: making /tmp/mritotal_19416/nu_8tmp1a.xfm [mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FL/FLsurf/mri] [2006-01-12 13:03:59] /Applications/freesurfer/lib/mni/bin/minctracc -clobber -debug /tmp/mritotal_19416/nu_8_blur.mnc /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_blur.mnc /tmp/mritotal_19416/nu_8tmp1a.xfm -transformation /tmp/mritotal_19416/nu_16.xfm -lsq7 -xcorr -center 1.479794 12.021105 -15.261126 -step 4 4 4 -tol 0.004 -simplex 5 Source volume size: 84 by 116 by 116 Source voxel = 2.000 2.000 2.000 min/max value= -0.000 168.507 min/max voxel= 0.000 255.000 Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 min/max value= -0.000 144.070 min/max voxel= 0.000 255.000 AFTER init_params() Transform matrix = 1.0391 0.0500 0.0577 -0.6484 -0.0663 0.9814 0.3436 -15.0800 -0.0378 -0.3464 0.9819 0.5235 Transform center = 1.480 12.021 -15.261 Transform rotations = -0.339 0.036 -0.064 Transform trans = -0.870 -20.646 -3.421 Transform scale = 1.042 1.042 1.042 Transform shear = -0.000 0.000 0.000 Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -85.095 -125.510 -57.250 Lattice count = 43 55 34 ===== Debugging information from /Applications/freesurfer/lib/mni/bin/minctracc ===== Data filename = /tmp/mritotal_19416/nu_8_blur.mnc Model filename = /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_blur.mnc Data mask filename = Model mask filename = Input xform name = /tmp/mritotal_19416/nu_16.xfm Output filename = /tmp/mritotal_19416/nu_8tmp1a.xfm Step size = 4.000000 4.000000 4.000000 Sub-lattice dia = 24.000000 24.000000 24.000000 Objective function = cross correlation (threshold = 0.000000 0.000000) Transform linear = TRUE Transform inverted? = FALSE Transform type = 4 Transform matrix = 1.0391 0.0500 0.0577 -0.6484 -0.0663 0.9814 0.3436 -15.0800 -0.0378 -0.3464 0.9819 0.5235 Transform center = 1.480 12.021 -15.261 Transform rotation = 0.000 0.000 0.000 Transform trans = 0.000 0.000 0.000 Transform scale = 1.000 1.000 1.000 Center of rot/scale forced: 1.479794 12.021105 -15.261126 using input transformation to get initial parameters: In set_up_lattice, xyzv[axes] = 2, 1, 0, -1 slice lim 0 41 row lim 0 57 col lim 8 49 thresh = 0.00000 0.00000 In set_up_lattice, xyzv[axes] = 2, 1, 0, -1 80410 57620 -> 0.02614952 80410 57620 -> 0.02614952 80410 56053 -> 0.03260488 80410 56014 -> 0.02824206 80410 58221 -> 0.03157454 80410 57872 -> 0.02624226 80410 56897 -> 0.02851230 80410 58044 -> 0.02796547 80410 61710 -> 0.04196538 80410 49836 -> 0.04873096 80410 59795 -> 0.02949140 80410 58295 -> 0.03417355 80410 57074 -> 0.02779070 80410 57155 -> 0.02521685 80410 56540 -> 0.03098077 80410 54001 -> 0.03304859 80410 58660 -> 0.02603073 80410 58074 -> 0.02618516 80410 59716 -> 0.02718198 80410 57621 -> 0.02548125 80410 59151 -> 0.02499328 80410 59927 -> 0.02981696 80410 56235 -> 0.02729175 80410 58889 -> 0.02491445 80410 58456 -> 0.02539012 80410 58232 -> 0.02650397 80410 58238 -> 0.02457227 80410 59028 -> 0.02580733 80410 58189 -> 0.02600417 80410 58246 -> 0.02445762 80410 57504 -> 0.02549559 80410 57907 -> 0.02425228 80410 58562 -> 0.02622000 80410 57997 -> 0.02424829 80410 58043 -> 0.02620313 80410 58297 -> 0.02420254 80410 59332 -> 0.02616768 80410 57849 -> 0.02415472 80410 57196 -> 0.02622536 80410 58684 -> 0.02406620 80410 57365 -> 0.02452427 80410 57905 -> 0.02461555 80410 58107 -> 0.02404415 80410 58886 -> 0.02489897 80410 57749 -> 0.02401383 80410 57919 -> 0.02446984 80410 58160 -> 0.02401472 80410 58334 -> 0.02442758 80410 58014 -> 0.02395207 80410 58339 -> 0.02432802 80410 58086 -> 0.02395790 80410 57854 -> 0.02415320 80410 58269 -> 0.02441928 80410 57958 -> 0.02392221 80410 58356 -> 0.02418315 80410 57968 -> 0.02393705 80410 57420 -> 0.02434164 80410 58313 -> 0.02388953 80410 57972 -> 0.02403697 80410 58003 -> 0.02390831 80410 57852 -> 0.02386142 80410 57697 -> 0.02406346 80410 58290 -> 0.02414708 80410 57891 -> 0.02387930 80410 57915 -> 0.02393283 80410 57966 -> 0.02392637 80410 57994 -> 0.02384556 80410 58011 -> 0.02392753 done with simplex after 59 iterations 0 0.02393:-0.56587 -19.44756 -7.31067 -16.19764 1.49719 -3.16800 53.06545 1 0.02389:-0.53420 -20.13658 -6.59910 -16.62133 1.08950 -2.98917 53.06200 2 0.02388:-0.26170 -19.50366 -6.94521 -17.10469 1.16770 -3.38047 53.04587 3 0.02392:-0.20752 -19.80124 -6.93063 -17.07235 1.70775 -2.83009 52.97662 4 0.02385:-0.53043 -19.66368 -7.06074 -17.35910 1.67719 -3.02982 53.08693 5 0.02391:-0.27699 -19.99375 -7.14261 -16.71419 1.54215 -3.43565 53.03036 6 0.02393:-0.73926 -19.68986 -6.89516 -16.93343 1.45604 -2.78421 52.82956 7 0.02386:-0.51720 -19.66980 -6.16367 -17.16206 1.62250 -3.54829 52.87806 after parameter optimization -center 1.47979 12.02111 -15.26113 -translation -0.53043 -19.66368 -7.06074 -rotation -17.35910 1.67719 -3.02982 -scale 1.06174 1.06174 1.06174 -shear 0.00000 0.00000 0.00000 80410 57994 -> 0.02384556 Initial objective function val = 0.02614952 Final objective function value = 0.02384556 successful write 8mm gradient lsq7 fit, target masked: making /tmp/mritotal_19416/nu_8tmp1b.xfm [mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FL/FLsurf/mri] [2006-01-12 13:04:05] /Applications/freesurfer/lib/mni/bin/minctracc -clobber -debug /tmp/mritotal_19416/nu_8_dxyz.mnc /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc /tmp/mritotal_19416/nu_8tmp1b.xfm -transformation /tmp/mritotal_19416/nu_8tmp1a.xfm -lsq7 -xcorr -model_mask /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc -center 1.479794 12.021105 -15.261126 -step 4 4 4 -tol 0.004 -simplex 2 Source volume size: 84 by 116 by 116 Source voxel = 2.000 2.000 2.000 min/max value= 0.070 20.182 min/max voxel= 0.000 255.000 Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 min/max value= 0.037 11.652 min/max voxel= 0.000 255.000 AFTER init_params() Transform matrix = 1.0598 0.0443 0.0464 -0.4440 -0.0561 1.0125 0.3148 -14.9266 -0.0311 -0.3166 1.0129 -3.0108 Transform center = 1.480 12.021 -15.261 Transform rotations = -0.303 0.029 -0.053 Transform trans = -0.530 -19.664 -7.061 Transform scale = 1.062 1.062 1.062 Transform shear = -0.000 0.000 0.000 Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -65.095 -105.510 -57.250 Lattice count = 35 46 34 ===== Debugging information from /Applications/freesurfer/lib/mni/bin/minctracc ===== Data filename = /tmp/mritotal_19416/nu_8_dxyz.mnc Model filename = /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc Data mask filename = Model mask filename = /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc Input xform name = /tmp/mritotal_19416/nu_8tmp1a.xfm Output filename = /tmp/mritotal_19416/nu_8tmp1b.xfm Step size = 4.000000 4.000000 4.000000 Sub-lattice dia = 24.000000 24.000000 24.000000 Objective function = cross correlation (threshold = 0.000000 0.000000) Transform linear = TRUE Transform inverted? = FALSE Transform type = 4 Transform matrix = 1.0598 0.0443 0.0464 -0.4440 -0.0561 1.0125 0.3148 -14.9266 -0.0311 -0.3166 1.0129 -3.0108 Transform center = 1.480 12.021 -15.261 Transform rotation = 0.000 0.000 0.000 Transform trans = 0.000 0.000 0.000 Transform scale = 1.000 1.000 1.000 Center of rot/scale forced: 1.479794 12.021105 -15.261126 using input transformation to get initial parameters: In set_up_lattice, xyzv[axes] = 2, 1, 0, -1 slice lim 0 41 row lim 0 57 col lim 0 57 thresh = 0.00000 0.00000 In set_up_lattice, xyzv[axes] = 2, 1, 0, -1 29440 25832 -> 0.13408650 29440 25832 -> 0.13408650 29440 25814 -> 0.14936821 29440 25446 -> 0.12951148 29440 25951 -> 0.14478505 29440 25965 -> 0.13080958 29440 25836 -> 0.14361411 29440 25832 -> 0.13664575 29440 26342 -> 0.16399169 29440 25245 -> 0.13073826 29440 25639 -> 0.12637332 29440 25538 -> 0.13183075 29440 25411 -> 0.12311057 29440 25143 -> 0.13248952 29440 25410 -> 0.11984246 29440 25197 -> 0.12368599 29440 25304 -> 0.11595447 29440 25037 -> 0.11594618 29440 25056 -> 0.11214072 29440 24638 -> 0.11699695 29440 24652 -> 0.11364093 29440 25236 -> 0.11669910 29440 24976 -> 0.12634249 29440 24572 -> 0.11963730 29440 25133 -> 0.11780505 29440 24607 -> 0.11355720 29440 24383 -> 0.11413245 29440 25177 -> 0.12220902 29440 24718 -> 0.10978885 29440 24489 -> 0.12937614 29440 24973 -> 0.10895188 29440 24293 -> 0.13059527 29440 25009 -> 0.10844965 29440 24500 -> 0.10547966 29440 24220 -> 0.11012907 29440 25192 -> 0.11981345 29440 24581 -> 0.10839717 29440 24914 -> 0.10620242 29440 25038 -> 0.11117592 29440 24586 -> 0.10549077 29440 24475 -> 0.11486926 29440 24897 -> 0.10635591 29440 24842 -> 0.10899612 29440 24812 -> 0.10585623 29440 24534 -> 0.10656762 29440 24364 -> 0.10265308 29440 24028 -> 0.10460050 29440 24734 -> 0.10580579 29440 24842 -> 0.10626130 29440 24457 -> 0.10707036 29440 24786 -> 0.10406344 29440 24503 -> 0.10704143 29440 24754 -> 0.10394052 29440 24379 -> 0.10389197 29440 24354 -> 0.10188577 29440 24126 -> 0.10371872 29440 24327 -> 0.10617702 29440 24635 -> 0.10321477 29440 24498 -> 0.10457891 29440 24581 -> 0.10326307 29440 24607 -> 0.10682295 29440 24528 -> 0.10261799 29440 24232 -> 0.10133534 29440 23955 -> 0.10240610 29440 24117 -> 0.10203794 29440 24431 -> 0.10243344 29440 24174 -> 0.10390504 29440 24478 -> 0.10183887 29440 24078 -> 0.10325423 29440 24493 -> 0.10184311 29440 24391 -> 0.10293103 29440 24372 -> 0.10171875 29440 24186 -> 0.10317292 29440 24439 -> 0.10162678 29440 24292 -> 0.10341850 29440 24391 -> 0.10143015 29440 24669 -> 0.10241419 29440 24253 -> 0.10151463 29440 24406 -> 0.10139854 29440 24239 -> 0.10134390 29440 24186 -> 0.10162615 29440 24246 -> 0.10124411 29440 24187 -> 0.10202694 29440 24118 -> 0.10150065 done with simplex after 75 iterations 0 0.10150:-1.08622 -13.53271 -9.40249 -15.90683 1.32475 -2.98381 51.66500 1 0.10140:-1.18855 -14.33192 -8.92156 -15.59253 1.51664 -3.21662 51.85033 2 0.10151:-1.29796 -14.23718 -9.22871 -16.16763 1.52694 -2.63501 51.63509 3 0.10134:-1.10127 -14.06595 -9.12450 -16.45066 1.26362 -2.60167 51.73621 4 0.10143:-1.10948 -14.41881 -9.05880 -15.33807 1.21108 -3.17929 51.70916 5 0.10134:-1.02352 -14.09846 -9.17515 -15.88477 1.52556 -2.98159 51.60022 6 0.10163:-1.24571 -13.99249 -8.91193 -15.93510 1.35482 -2.64640 51.45551 7 0.10124:-1.08952 -14.05005 -9.24191 -16.16003 1.33646 -2.38232 51.75355 after parameter optimization -center 1.47979 12.02111 -15.26113 -translation -1.08952 -14.05005 -9.24191 -rotation -16.16003 1.33646 -2.38232 -scale 1.03507 1.03507 1.03507 -shear 0.00000 0.00000 0.00000 29440 24246 -> 0.10124411 Initial objective function val = 0.13408650 Final objective function value = 0.10124411 successful write 8mm gradient lsq9 fit, target masked: making /tmp/mritotal_19416/nu_8tmp2a.xfm [mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FL/FLsurf/mri] [2006-01-12 13:04:10] /Applications/freesurfer/lib/mni/bin/minctracc -clobber -debug /tmp/mritotal_19416/nu_8_dxyz.mnc /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc /tmp/mritotal_19416/nu_8tmp2a.xfm -transformation /tmp/mritotal_19416/nu_8tmp1b.xfm -lsq9 -xcorr -model_mask /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc -center 1.479794 12.021105 -15.261126 -step 4 4 4 -tol 0.004 -simplex 2 Source volume size: 84 by 116 by 116 Source voxel = 2.000 2.000 2.000 min/max value= 0.070 20.182 min/max voxel= 0.000 255.000 Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 min/max value= 0.037 11.652 min/max voxel= 0.000 255.000 AFTER init_params() Transform matrix = 1.0339 0.0346 0.0351 -1.0194 -0.0430 0.9936 0.2869 -9.5314 -0.0241 -0.2880 0.9939 -5.8371 Transform center = 1.480 12.021 -15.261 Transform rotations = -0.282 0.023 -0.042 Transform trans = -1.090 -14.050 -9.242 Transform scale = 1.035 1.035 1.035 Transform shear = 0.000 0.000 0.000 Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -65.095 -105.510 -57.250 Lattice count = 35 46 34 ===== Debugging information from /Applications/freesurfer/lib/mni/bin/minctracc ===== Data filename = /tmp/mritotal_19416/nu_8_dxyz.mnc Model filename = /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc Data mask filename = Model mask filename = /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc Input xform name = /tmp/mritotal_19416/nu_8tmp1b.xfm Output filename = /tmp/mritotal_19416/nu_8tmp2a.xfm Step size = 4.000000 4.000000 4.000000 Sub-lattice dia = 24.000000 24.000000 24.000000 Objective function = cross correlation (threshold = 0.000000 0.000000) Transform linear = TRUE Transform inverted? = FALSE Transform type = 5 Transform matrix = 1.0339 0.0346 0.0351 -1.0194 -0.0430 0.9936 0.2869 -9.5314 -0.0241 -0.2880 0.9939 -5.8371 Transform center = 1.480 12.021 -15.261 Transform rotation = 0.000 0.000 0.000 Transform trans = 0.000 0.000 0.000 Transform scale = 1.000 1.000 1.000 Center of rot/scale forced: 1.479794 12.021105 -15.261126 using input transformation to get initial parameters: In set_up_lattice, xyzv[axes] = 2, 1, 0, -1 slice lim 0 41 row lim 0 57 col lim 0 57 thresh = 0.00000 0.00000 In set_up_lattice, xyzv[axes] = 2, 1, 0, -1 29440 24246 -> 0.10124412 29440 24246 -> 0.10124412 29440 24233 -> 0.11229771 29440 23810 -> 0.10450254 29440 24372 -> 0.10767739 29440 24397 -> 0.10258489 29440 24249 -> 0.10677955 29440 24235 -> 0.10596451 29440 24246 -> 0.10528158 29440 24744 -> 0.10743678 29440 24336 -> 0.10976212 29440 24351 -> 0.11330431 29440 24262 -> 0.10462289 29440 24231 -> 0.10806009 29440 24261 -> 0.10221629 29440 24173 -> 0.11227744 29440 24320 -> 0.10304677 29440 23683 -> 0.09761832 29440 23116 -> 0.10063918 29440 24082 -> 0.10395803 29440 24056 -> 0.10109901 29440 24002 -> 0.10777859 29440 24185 -> 0.10051960 29440 23972 -> 0.10215674 29440 24462 -> 0.09901930 29440 24275 -> 0.10270416 29440 24027 -> 0.10117500 29440 24018 -> 0.10337403 29440 24209 -> 0.09956159 29440 23853 -> 0.09900168 29440 23887 -> 0.09739716 29440 23690 -> 0.10144833 29440 24159 -> 0.10281194 29440 24022 -> 0.09893154 29440 23826 -> 0.09752937 29440 24025 -> 0.10076274 29440 23984 -> 0.09806313 29440 24006 -> 0.10113437 29440 24021 -> 0.09776702 29440 23798 -> 0.09520762 29440 23588 -> 0.09832821 29440 23687 -> 0.09684531 29440 23251 -> 0.10033312 29440 24166 -> 0.09647001 29440 23934 -> 0.09639476 29440 23752 -> 0.09700418 29440 23742 -> 0.09625182 29440 23635 -> 0.09688545 29440 23971 -> 0.09857021 29440 23754 -> 0.09548800 29440 23800 -> 0.09742331 29440 23809 -> 0.09558477 29440 23726 -> 0.09675728 29440 23860 -> 0.09722646 29440 23776 -> 0.09540098 29440 24006 -> 0.09657706 29440 24034 -> 0.09808587 29440 23772 -> 0.09507342 29440 23992 -> 0.09819486 29440 23794 -> 0.09504820 29440 23669 -> 0.09686687 29440 23923 -> 0.09520130 29440 23447 -> 0.09519112 29440 23587 -> 0.09570482 29440 23742 -> 0.09824868 29440 23741 -> 0.09472957 29440 23937 -> 0.09656812 29440 23670 -> 0.09483548 29440 23670 -> 0.09505911 29440 23709 -> 0.09450927 29440 23692 -> 0.09559274 29440 23672 -> 0.09450728 29440 23621 -> 0.09551132 29440 23629 -> 0.09505243 29440 23434 -> 0.09497503 29440 23903 -> 0.09540333 29440 23561 -> 0.09464803 29440 23539 -> 0.09492461 29440 23604 -> 0.09472941 29440 23646 -> 0.09554342 29440 23633 -> 0.09456004 29440 23445 -> 0.09569781 29440 23707 -> 0.09445442 29440 23864 -> 0.09488399 29440 23837 -> 0.09532273 29440 23611 -> 0.09445637 29440 23448 -> 0.09487712 29440 23555 -> 0.09434994 29440 23616 -> 0.09454138 29440 23522 -> 0.09474815 29440 23684 -> 0.09445108 29440 23674 -> 0.09455587 29440 23741 -> 0.09417874 29440 23824 -> 0.09456933 29440 23695 -> 0.09449907 29440 23657 -> 0.09462100 29440 23671 -> 0.09433571 29440 23727 -> 0.09482396 29440 23643 -> 0.09426600 done with simplex after 88 iterations 0 0.09434:-0.91937 -13.78678 -8.19757 -14.82075 1.57822 -2.67887 53.09937 49.26117 51.14585 1 0.09451:-1.00268 -13.61276 -8.20912 -15.06792 1.47082 -2.74616 52.82770 49.48238 51.11086 2 0.09418:-0.84076 -13.89224 -8.08448 -14.78944 1.35489 -2.83372 53.11662 49.40971 51.05672 3 0.09435:-0.83567 -13.74562 -8.27218 -14.81773 1.42587 -2.69701 53.17402 48.86399 51.25059 4 0.09427:-0.89721 -13.83397 -8.15960 -14.53155 1.36616 -2.73798 53.06792 49.02636 51.28405 5 0.09446:-0.79025 -13.76539 -8.19483 -14.78601 1.56796 -2.79319 52.98253 49.03716 51.24642 6 0.09445:-0.84670 -13.81537 -8.33935 -14.79770 1.38105 -2.82865 53.01169 49.28038 51.38084 7 0.09450:-1.03896 -13.91668 -8.12926 -14.66825 1.65717 -2.88182 52.98812 49.19812 51.04409 8 0.09451:-0.98105 -14.21837 -8.02665 -14.84281 1.44209 -2.71145 53.26231 49.01215 51.16028 9 0.09445:-0.87513 -14.02217 -8.28700 -14.81861 1.48187 -2.40193 53.00309 49.20866 51.25412 after parameter optimization -center 1.47979 12.02111 -15.26113 -translation -0.84076 -13.89224 -8.08448 -rotation -14.78944 1.35489 -2.83372 -scale 1.06233 0.98819 1.02113 -shear 0.00000 0.00000 0.00000 29440 23741 -> 0.09417874 Initial objective function val = 0.10124412 Final objective function value = 0.09417874 successful write checking z-scale: making /tmp/mritotal_19416/nu_8tmp2b.xfm [mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FL/FLsurf/mri] [2006-01-12 13:04:15] /Applications/freesurfer/lib/mni/bin/check_scale /tmp/mritotal_19416/nu_8tmp2a.xfm /tmp/mritotal_19416/nu_8tmp2b.xfm 8mm gradient lsq9 fit, target masked: making /tmp/mritotal_19416/nu_8tmp2c.xfm [mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FL/FLsurf/mri] [2006-01-12 13:04:15] /Applications/freesurfer/lib/mni/bin/minctracc -clobber -debug /tmp/mritotal_19416/nu_8_dxyz.mnc /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc /tmp/mritotal_19416/nu_8tmp2c.xfm -transformation /tmp/mritotal_19416/nu_8tmp2b.xfm -lsq9 -xcorr -model_mask /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc -center 1.479794 12.021105 -15.261126 -step 4 4 4 -tol 0.004 -simplex 2 Source volume size: 84 by 116 by 116 Source voxel = 2.000 2.000 2.000 min/max value= 0.070 20.182 min/max voxel= 0.000 255.000 Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 min/max value= 0.037 11.652 min/max voxel= 0.000 255.000 AFTER init_params() Transform matrix = 1.0607 0.0444 0.0377 -0.8893 -0.0488 0.9546 0.2508 -9.4461 -0.0241 -0.2606 0.9870 -5.1141 Transform center = 1.480 12.021 -15.261 Transform rotations = -0.258 0.024 -0.049 Transform trans = -0.841 -13.892 -8.084 Transform scale = 1.062 0.988 1.021 Transform shear = 0.000 -0.000 -0.000 Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -65.095 -105.510 -57.250 Lattice count = 35 46 34 ===== Debugging information from /Applications/freesurfer/lib/mni/bin/minctracc ===== Data filename = /tmp/mritotal_19416/nu_8_dxyz.mnc Model filename = /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc Data mask filename = Model mask filename = /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc Input xform name = /tmp/mritotal_19416/nu_8tmp2b.xfm Output filename = /tmp/mritotal_19416/nu_8tmp2c.xfm Step size = 4.000000 4.000000 4.000000 Sub-lattice dia = 24.000000 24.000000 24.000000 Objective function = cross correlation (threshold = 0.000000 0.000000) Transform linear = TRUE Transform inverted? = FALSE Transform type = 5 Transform matrix = 1.0607 0.0444 0.0377 -0.8893 -0.0488 0.9546 0.2508 -9.4461 -0.0241 -0.2606 0.9870 -5.1141 Transform center = 1.480 12.021 -15.261 Transform rotation = 0.000 0.000 0.000 Transform trans = 0.000 0.000 0.000 Transform scale = 1.000 1.000 1.000 Center of rot/scale forced: 1.479794 12.021105 -15.261126 using input transformation to get initial parameters: In set_up_lattice, xyzv[axes] = 2, 1, 0, -1 slice lim 0 41 row lim 0 57 col lim 0 57 thresh = 0.00000 0.00000 In set_up_lattice, xyzv[axes] = 2, 1, 0, -1 29440 23741 -> 0.09417874 29440 23741 -> 0.09417874 29440 23720 -> 0.10836613 29440 23286 -> 0.09949479 29440 23854 -> 0.10157076 29440 23878 -> 0.09669920 29440 23738 -> 0.10212105 29440 23728 -> 0.09761219 29440 23739 -> 0.10450301 29440 24268 -> 0.09824083 29440 23814 -> 0.10286666 29440 23837 -> 0.10660478 29440 23810 -> 0.09825663 29440 23840 -> 0.10177168 29440 23774 -> 0.10253347 29440 23781 -> 0.09585212 29440 23862 -> 0.10364709 29440 23766 -> 0.09642171 29440 23738 -> 0.10330461 29440 23814 -> 0.09662461 29440 23725 -> 0.10428227 29440 23820 -> 0.09634227 29440 24402 -> 0.09873101 29440 24132 -> 0.09521580 29440 23954 -> 0.09988230 29440 23848 -> 0.09521548 29440 23386 -> 0.09698173 29440 23872 -> 0.09799222 29440 23763 -> 0.09509951 29440 24275 -> 0.09822843 29440 23613 -> 0.09460781 29440 23756 -> 0.09875606 29440 23846 -> 0.09466644 29440 23804 -> 0.09592528 29440 23867 -> 0.09550405 29440 23824 -> 0.09821030 29440 23824 -> 0.09463008 29440 23835 -> 0.09623349 29440 23812 -> 0.09472196 29440 23868 -> 0.09603209 29440 23805 -> 0.09464049 29440 23773 -> 0.09618008 29440 23840 -> 0.09442766 29440 23446 -> 0.09443195 29440 23637 -> 0.09524398 29440 23795 -> 0.09438621 29440 23736 -> 0.09485700 29440 23739 -> 0.09420004 29440 23660 -> 0.09451646 29440 23596 -> 0.09460898 29440 23584 -> 0.09455956 29440 23519 -> 0.09433219 29440 23729 -> 0.09466515 29440 23629 -> 0.09402674 29440 23709 -> 0.09573340 29440 23635 -> 0.09405391 29440 23751 -> 0.09469582 29440 23625 -> 0.09409945 29440 23666 -> 0.09455745 29440 23660 -> 0.09410927 29440 23928 -> 0.09456334 29440 23567 -> 0.09408724 29440 23468 -> 0.09453624 29440 23749 -> 0.09415358 29440 23506 -> 0.09415375 29440 23777 -> 0.09427311 29440 23716 -> 0.09401026 done with simplex after 56 iterations 0 0.09418:-0.84076 -13.89224 -8.08448 -14.78943 1.35489 -2.83372 53.11662 49.40972 51.05671 1 0.09415:-0.87283 -13.51352 -7.80540 -14.44422 1.24299 -2.70400 53.00354 48.74831 50.89265 2 0.09409:-1.01057 -13.37056 -7.78603 -14.37266 1.38742 -2.49066 53.16275 49.06451 50.91426 3 0.09401:-0.95919 -13.72205 -7.61433 -14.42132 1.42442 -2.59932 53.08022 49.29926 50.93985 4 0.09403:-1.08026 -13.56420 -7.63358 -14.66217 1.43566 -2.43448 53.07665 49.16714 50.89553 5 0.09415:-1.06382 -13.80181 -7.70249 -14.27465 1.33216 -2.38656 53.10655 49.33531 50.91251 6 0.09420:-1.05797 -13.71535 -7.64272 -14.13568 1.51158 -2.81528 53.16459 49.32479 50.83546 7 0.09411:-1.02770 -13.51745 -7.73392 -14.28852 1.40725 -2.55778 52.91665 49.24900 51.00444 8 0.09405:-1.05503 -13.68403 -7.68201 -14.22562 1.60355 -2.35732 52.97672 48.99857 50.97168 9 0.09410:-1.03520 -13.61446 -7.72731 -14.42271 1.34269 -2.56946 53.11135 49.04644 51.11646 after parameter optimization -center 1.47979 12.02111 -15.26113 -translation -0.95919 -13.72205 -7.61433 -rotation -14.42132 1.42442 -2.59932 -scale 1.06160 0.98599 1.01880 -shear 0.00000 0.00000 0.00000 29440 23716 -> 0.09401026 Initial objective function val = 0.09417874 Final objective function value = 0.09401026 successful write final linear fit: 8mm gradient lsq9 fit, target masked: making transforms/talairach.xfm [mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FL/FLsurf/mri] [2006-01-12 13:04:19] /Applications/freesurfer/lib/mni/bin/minctracc -clobber -debug /tmp/mritotal_19416/nu_8_dxyz.mnc /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc transforms/talairach.xfm -transformation /tmp/mritotal_19416/nu_8tmp2c.xfm -lsq9 -xcorr -model_mask /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc -center 1.479794 12.021105 -15.261126 -step 4 4 4 -tol 0.004 -simplex 2 Source volume size: 84 by 116 by 116 Source voxel = 2.000 2.000 2.000 min/max value= 0.070 20.182 min/max voxel= 0.000 255.000 Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 min/max value= 0.037 11.652 min/max voxel= 0.000 255.000 AFTER init_params() Transform matrix = 1.0602 0.0401 0.0375 -0.9572 -0.0447 0.9542 0.2442 -9.3782 -0.0253 -0.2537 0.9864 -4.7354 Transform center = 1.480 12.021 -15.261 Transform rotations = -0.252 0.025 -0.045 Transform trans = -0.959 -13.722 -7.614 Transform scale = 1.062 0.986 1.019 Transform shear = 0.000 0.000 -0.000 Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -65.095 -105.510 -57.250 Lattice count = 35 46 34 ===== Debugging information from /Applications/freesurfer/lib/mni/bin/minctracc ===== Data filename = /tmp/mritotal_19416/nu_8_dxyz.mnc Model filename = /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc Data mask filename = Model mask filename = /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc Input xform name = /tmp/mritotal_19416/nu_8tmp2c.xfm Output filename = transforms/talairach.xfm Step size = 4.000000 4.000000 4.000000 Sub-lattice dia = 24.000000 24.000000 24.000000 Objective function = cross correlation (threshold = 0.000000 0.000000) Transform linear = TRUE Transform inverted? = FALSE Transform type = 5 Transform matrix = 1.0602 0.0401 0.0375 -0.9572 -0.0447 0.9542 0.2442 -9.3782 -0.0253 -0.2537 0.9864 -4.7354 Transform center = 1.480 12.021 -15.261 Transform rotation = 0.000 0.000 0.000 Transform trans = 0.000 0.000 0.000 Transform scale = 1.000 1.000 1.000 Center of rot/scale forced: 1.479794 12.021105 -15.261126 using input transformation to get initial parameters: In set_up_lattice, xyzv[axes] = 2, 1, 0, -1 slice lim 0 41 row lim 0 57 col lim 0 57 thresh = 0.00000 0.00000 In set_up_lattice, xyzv[axes] = 2, 1, 0, -1 29440 23716 -> 0.09401026 29440 23716 -> 0.09401026 29440 23701 -> 0.10732047 29440 23261 -> 0.09979578 29440 23832 -> 0.10355741 29440 23854 -> 0.09627553 29440 23719 -> 0.10134520 29440 23651 -> 0.09796411 29440 23717 -> 0.10387810 29440 24249 -> 0.09805255 29440 23790 -> 0.10362256 29440 23816 -> 0.10784873 29440 23731 -> 0.09853698 29440 23807 -> 0.10308307 29440 23735 -> 0.10400650 29440 23778 -> 0.09821505 29440 23691 -> 0.10210986 29440 23683 -> 0.10353243 29440 23777 -> 0.09737955 29440 23822 -> 0.10322644 29440 23723 -> 0.09656148 29440 23799 -> 0.09965665 29440 24366 -> 0.09947136 29440 23963 -> 0.10260960 29440 23841 -> 0.09576461 29440 23265 -> 0.09936503 29440 23549 -> 0.09590300 29440 23868 -> 0.09824392 29440 23835 -> 0.09578439 29440 23834 -> 0.09890167 29440 23795 -> 0.09572173 29440 23235 -> 0.09731290 29440 23702 -> 0.09821133 29440 23700 -> 0.09558424 29440 23617 -> 0.09656809 29440 24219 -> 0.09820445 29440 23490 -> 0.09493863 29440 23828 -> 0.09726338 29440 23673 -> 0.09483277 29440 23710 -> 0.09686048 29440 23718 -> 0.09501037 29440 23552 -> 0.09864116 29440 23780 -> 0.09455296 29440 23908 -> 0.09572464 29440 23637 -> 0.09492321 29440 23588 -> 0.09554216 29440 23444 -> 0.09560269 29440 23486 -> 0.09614614 29440 23712 -> 0.09466854 29440 23891 -> 0.09585796 29440 23557 -> 0.09460223 29440 23604 -> 0.09494366 29440 23720 -> 0.09510617 29440 23684 -> 0.09442661 29440 23583 -> 0.09437389 29440 23692 -> 0.09526400 29440 23626 -> 0.09434990 29440 23835 -> 0.09487440 29440 23733 -> 0.09509084 29440 23660 -> 0.09432207 29440 23503 -> 0.09482832 29440 23624 -> 0.09458342 29440 23825 -> 0.09481737 29440 23741 -> 0.09424511 29440 23611 -> 0.09421492 29440 23784 -> 0.09449106 29440 23751 -> 0.09493682 29440 23656 -> 0.09425866 29440 23569 -> 0.09428551 29440 23520 -> 0.09457947 29440 23717 -> 0.09416321 29440 23616 -> 0.09457483 29440 23666 -> 0.09416229 29440 23744 -> 0.09437484 29440 23622 -> 0.09411845 29440 23697 -> 0.09401716 done with simplex after 65 iterations 0 0.09401:-0.95919 -13.72205 -7.61433 -14.42132 1.42442 -2.59932 53.08021 49.29925 50.93985 1 0.09432:-0.68246 -13.59698 -7.74285 -13.82824 1.26603 -2.26767 53.17531 49.06054 51.12945 2 0.09416:-0.77511 -13.71316 -7.59277 -13.74643 1.13915 -2.67691 53.11892 49.11179 51.06972 3 0.09412:-0.80505 -13.56850 -7.54601 -13.82120 1.22539 -2.55147 53.20449 48.89690 51.08051 4 0.09429:-0.63402 -13.60700 -7.58218 -14.45485 1.14476 -2.79312 53.24055 48.83816 51.07369 5 0.09416:-0.76013 -13.44475 -7.70029 -13.86766 1.18974 -2.49712 53.08620 49.22009 51.10826 6 0.09402:-0.69080 -13.72708 -7.40572 -14.22176 1.08273 -2.56186 53.14221 49.15190 50.93178 7 0.09426:-0.76368 -13.53832 -7.56535 -13.82594 1.40495 -2.57257 52.97683 49.05167 51.09982 8 0.09425:-0.77208 -13.60617 -7.59540 -13.94142 1.36463 -2.67320 53.19963 49.35082 51.05728 9 0.09421:-0.73783 -13.50881 -7.61453 -13.67647 1.23507 -2.73817 53.19209 48.91360 50.86933 after parameter optimization -center 1.47979 12.02111 -15.26113 -translation -0.95919 -13.72205 -7.61433 -rotation -14.42132 1.42442 -2.59932 -scale 1.06160 0.98599 1.01880 -shear 0.00000 0.00000 0.00000 29440 23716 -> 0.09401026 Initial objective function val = 0.09401026 Final objective function value = 0.09401026 successful write