[dglen@gollum.local:/Users/dglen/freesurfer/subjects/EF2/EF2surf/mri] [2006-01-09 17:10:01] 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/EF2/EF2surf/mri] [2006-01-09 17:10:01] /Applications/freesurfer/lib/mni/bin/autocrop -clobber nu.mnc /tmp/mritotal_12960/nu_crop.mnc -step 2 2 2 -extend 0,0 0,0 -25%,0 [autocrop] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/EF2/EF2surf/mri] [2006-01-09 17:10:01] /Applications/freesurfer/lib/mni/bin/mincresample -clobber nu.mnc /tmp/mritotal_12960/nu_crop.mnc -start -125.2 -128 -64 -step 2 2 2 -nelements 128 128 96 Transforming slices:................................................................................................................................Done [mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/EF2/EF2surf/mri] [2006-01-09 17:10:02] /Applications/freesurfer/lib/mni/bin/volume_cog /tmp/mritotal_12960/nu_crop.mnc | tail -1 Centroid of input volume: -2.949227 7.057733 -22.334629 Zero-padding data: [mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/EF2/EF2surf/mri] [2006-01-09 17:10:03] /Applications/freesurfer/lib/mni/bin/autocrop -clobber /tmp/mritotal_12960/nu_crop.mnc /tmp/mritotal_12960/nu_pad.mnc -expand 22 22 22 [autocrop] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/EF2/EF2surf/mri] [2006-01-09 17:10:03] /Applications/freesurfer/lib/mni/bin/mincreshape -clobber /tmp/mritotal_12960/nu_crop.mnc /tmp/mritotal_12960/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/EF2/EF2surf/mri] [2006-01-09 17:10:03] /Applications/freesurfer/lib/mni/bin/mincblur -clobber -debug /tmp/mritotal_12960/nu_pad.mnc /tmp/mritotal_12960/tmp_16 -fwhm 16 ===== Debugging information from /Applications/freesurfer/lib/mni/bin/mincblur ===== Data filename = /tmp/mritotal_12960/nu_pad.mnc Output basename = /tmp/mritotal_12960/tmp_16 Input volume = 150 cols by 150 rows by 118 slices Input voxels are = 2.000 2.000 2.000 min/max value = 0.000 255.000 Apodizing data at 16.000000 Volume def min and max: = 0.000000 255.000000 before blur min/max = 0.000000 255.000000 after blur min/max = -0.000003 111.618774 Making byte volume... [mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/EF2/EF2surf/mri] [2006-01-09 17:10:07] /Applications/freesurfer/lib/mni/bin/autocrop -clobber /tmp/mritotal_12960/tmp_16_blur.mnc /tmp/mritotal_12960/nu_16_blur.mnc -expand -44 -44 -44 [autocrop] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/EF2/EF2surf/mri] [2006-01-09 17:10:07] /Applications/freesurfer/lib/mni/bin/mincreshape -clobber /tmp/mritotal_12960/tmp_16_blur.mnc /tmp/mritotal_12960/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/EF2/EF2surf/mri] [2006-01-09 17:10:07] /Applications/freesurfer/lib/mni/bin/mincblur -clobber -debug /tmp/mritotal_12960/nu_pad.mnc /tmp/mritotal_12960/tmp_8 -fwhm 8 -gradient Transforming slices:......................................................................................................................................................Done ===== Debugging information from /Applications/freesurfer/lib/mni/bin/mincblur ===== Data filename = /tmp/mritotal_12960/nu_pad.mnc Output basename = /tmp/mritotal_12960/tmp_8 Input volume = 150 cols by 150 rows by 118 slices Input voxels are = 2.000 2.000 2.000 min/max value = 0.000 255.000 Apodizing data at 8.000000 Volume def min and max: = 0.000000 255.000000 before blur min/max = 0.000000 255.000000 after blur min/max = -0.000010 154.639542 Making byte volume... Making byte volume dx...dx: min = -15.159859, max = 13.820365 Making byte volume dy...dy: min = -14.841953, max = 11.447030 Making byte volume dz...dz: min = -14.745275, max = 12.883968 [mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/EF2/EF2surf/mri] [2006-01-09 17:10:16] /Applications/freesurfer/lib/mni/bin/autocrop -clobber /tmp/mritotal_12960/tmp_8_blur.mnc /tmp/mritotal_12960/nu_8_blur.mnc -expand -34 -34 -34 [autocrop] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/EF2/EF2surf/mri] [2006-01-09 17:10:16] /Applications/freesurfer/lib/mni/bin/mincreshape -clobber /tmp/mritotal_12960/tmp_8_blur.mnc /tmp/mritotal_12960/nu_8_blur.mnc -start 17,17,17 -count 116,116,84 Copying chunks:....................................................................................................................Done. [mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/EF2/EF2surf/mri] [2006-01-09 17:10:16] /Applications/freesurfer/lib/mni/bin/autocrop -clobber /tmp/mritotal_12960/tmp_8_dxyz.mnc /tmp/mritotal_12960/nu_8_dxyz.mnc -expand -34 -34 -34 [autocrop] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/EF2/EF2surf/mri] [2006-01-09 17:10:16] /Applications/freesurfer/lib/mni/bin/mincreshape -clobber /tmp/mritotal_12960/tmp_8_dxyz.mnc /tmp/mritotal_12960/nu_8_dxyz.mnc -start 17,17,17 -count 116,116,84 Copying chunks:....................................................................................................................Done. 16mm intensity lsq7 fit, no masks: making /tmp/mritotal_12960/nu_16.xfm [mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/EF2/EF2surf/mri] [2006-01-09 17:10:16] /Applications/freesurfer/lib/mni/bin/minctracc -clobber -debug /tmp/mritotal_12960/nu_16_blur.mnc /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_16_blur.mnc /tmp/mritotal_12960/nu_16.xfm -est_translations -lsq7 -xcorr -center -2.949227 7.057733 -22.334629 -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= -0.000 111.619 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 3.2772 0.0000 1.0000 0.0000 -24.6489 0.0000 0.0000 1.0000 31.7893 Transform center = -2.949 7.058 -22.335 Transform rotations = 0.000 0.000 0.000 Transform trans = 3.277 -24.649 31.789 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_12960/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_12960/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 = -2.949 7.058 -22.335 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: -2.949227 7.057733 -22.334629 using PAT to get initial parameters: will try to get: [trans] COG of v1 forced: -2.949227 7.057733 -22.334629 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] = 3.277233 -24.648865 31.789291 Only center & trans required, now returning from init_transformation Transform center = -2.949 7.058 -22.335 Transform rots = 0.000 0.000 0.000 Transform trans = 3.277 -24.649 31.789 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 45793 -> 0.04151581 68585 45793 -> 0.04151581 68585 40972 -> 0.08634603 68585 43386 -> 0.04092149 68585 45781 -> 0.05058362 68585 47304 -> 0.04339203 68585 45093 -> 0.04934851 68585 43750 -> 0.04650378 68585 56115 -> 0.08571665 68585 46867 -> 0.08751626 68585 45356 -> 0.05171841 68585 15284 -> 0.15493800 68585 52297 -> 0.05176543 68585 30575 -> 0.09382091 68585 50172 -> 0.03835551 68585 43849 -> 0.05812332 68585 46312 -> 0.04192089 68585 47106 -> 0.03027259 68585 47253 -> 0.05084115 68585 46896 -> 0.03866305 68585 46130 -> 0.04002752 68585 46583 -> 0.03015926 68585 45291 -> 0.04865684 68585 46531 -> 0.03034665 68585 45348 -> 0.04443854 68585 47250 -> 0.03161027 68585 51236 -> 0.03193679 68585 47196 -> 0.02626611 68585 47317 -> 0.03505893 68585 49060 -> 0.02441456 68585 49152 -> 0.03901613 68585 45985 -> 0.01461728 68585 42617 -> 0.03075902 68585 42814 -> 0.02646905 68585 45162 -> 0.01951354 68585 46287 -> 0.02879022 68585 46306 -> 0.02812318 68585 45087 -> 0.02641032 68585 45259 -> 0.02316396 68585 46916 -> 0.03085476 68585 45906 -> 0.01933705 68585 50070 -> 0.01729546 68585 47978 -> 0.03006309 68585 46175 -> 0.01778834 68585 44071 -> 0.01737974 68585 42264 -> 0.02355318 68585 44295 -> 0.01588884 68585 46516 -> 0.02544681 68585 45749 -> 0.01558068 68585 47257 -> 0.01146588 68585 48175 -> 0.01603621 68585 48153 -> 0.01886955 68585 47219 -> 0.01322332 68585 46440 -> 0.01253154 68585 47143 -> 0.02569014 68585 45791 -> 0.01158878 68585 42020 -> 0.01824897 68585 48147 -> 0.01307784 68585 48703 -> 0.01266458 68585 48572 -> 0.01514820 68585 47966 -> 0.01166287 68585 48484 -> 0.01248392 68585 47900 -> 0.00992033 68585 48338 -> 0.01206047 68585 46594 -> 0.01034935 68585 45670 -> 0.01188860 68585 47998 -> 0.01111126 68585 45701 -> 0.00952353 68585 43826 -> 0.01410863 68585 48122 -> 0.01417172 68585 46413 -> 0.00942319 68585 46092 -> 0.01078917 68585 48075 -> 0.00979175 68585 45940 -> 0.01063216 68585 45327 -> 0.01269632 68585 47377 -> 0.00906051 68585 47915 -> 0.01009716 68585 47725 -> 0.01199746 68585 46630 -> 0.00890203 68585 47597 -> 0.00905818 68585 46560 -> 0.01084407 68585 47483 -> 0.00867337 68585 46133 -> 0.00853014 68585 44978 -> 0.01116532 68585 45454 -> 0.01124604 68585 47447 -> 0.00841606 68585 48320 -> 0.01001446 68585 46369 -> 0.00838892 68585 47495 -> 0.00930935 68585 47269 -> 0.00834253 68585 46617 -> 0.00811242 68585 46258 -> 0.00933885 68585 45765 -> 0.00959420 68585 47238 -> 0.00822174 68585 46856 -> 0.01063896 68585 46808 -> 0.00807074 68585 46244 -> 0.00828049 68585 47553 -> 0.00881255 68585 46498 -> 0.00806032 68585 46029 -> 0.00833776 68585 47018 -> 0.00764734 68585 47306 -> 0.00759994 68585 46040 -> 0.00766570 68585 47365 -> 0.00801105 68585 47440 -> 0.00804718 68585 46499 -> 0.00757031 68585 45927 -> 0.00816598 68585 47043 -> 0.00771851 68585 46971 -> 0.00773177 68585 47437 -> 0.00753091 68585 47923 -> 0.00824443 68585 46539 -> 0.00759847 68585 46354 -> 0.00701090 68585 45798 -> 0.00714242 68585 46498 -> 0.00729064 68585 46229 -> 0.00738973 68585 47301 -> 0.00768389 68585 46364 -> 0.00724939 68585 45746 -> 0.00726707 68585 46400 -> 0.00764389 68585 46528 -> 0.00721293 68585 46427 -> 0.00689904 68585 46458 -> 0.00718624 68585 45151 -> 0.00785203 68585 46873 -> 0.00709790 68585 46537 -> 0.00733512 68585 46462 -> 0.00707148 68585 46250 -> 0.00730032 68585 46442 -> 0.00705712 68585 47203 -> 0.00742711 68585 46104 -> 0.00702317 68585 46541 -> 0.00682913 68585 46652 -> 0.00689139 68585 46406 -> 0.00680424 68585 46355 -> 0.00688746 68585 45893 -> 0.00695510 68585 46147 -> 0.00675087 68585 45997 -> 0.00677571 68585 46093 -> 0.00670332 68585 45894 -> 0.00678011 68585 46423 -> 0.00672151 68585 46298 -> 0.00672417 68585 46742 -> 0.00671950 68585 46302 -> 0.00663121 68585 46178 -> 0.00680505 68585 46126 -> 0.00657647 68585 45932 -> 0.00673644 68585 46251 -> 0.00674459 68585 46459 -> 0.00660712 68585 46486 -> 0.00675018 68585 46311 -> 0.00656979 68585 46415 -> 0.00669704 68585 46288 -> 0.00658773 68585 45918 -> 0.00666978 68585 46411 -> 0.00651551 68585 46559 -> 0.00663362 68585 46023 -> 0.00660082 68585 46723 -> 0.00669236 68585 45997 -> 0.00656919 68585 46183 -> 0.00667369 68585 46269 -> 0.00653747 68585 45945 -> 0.00659126 68585 46349 -> 0.00672991 68585 46117 -> 0.00652050 68585 46475 -> 0.00660223 68585 46076 -> 0.00653517 68585 46010 -> 0.00666105 68585 46227 -> 0.00652255 68585 46271 -> 0.00656176 68585 46124 -> 0.00656771 done with simplex after 161 iterations 0 0.00652: 3.79832 -15.27400 5.41232 -18.80812 0.37842 -1.06792 53.77254 1 0.00657: 3.67728 -14.37224 4.73694 -18.04727 0.18875 -1.78881 53.77542 2 0.00654: 3.35301 -14.63885 5.56291 -17.82230 0.68279 -1.22416 53.67254 3 0.00657: 3.51135 -14.29987 5.33467 -18.39026 0.72972 -0.54668 53.44983 4 0.00654: 3.66813 -14.20513 5.54779 -17.72368 0.12191 -0.93216 53.46255 5 0.00656: 3.29915 -14.95315 5.61984 -18.99318 0.44673 -1.66294 53.63157 6 0.00652: 3.48135 -14.21384 5.74650 -18.39833 0.37147 -0.80641 53.62793 7 0.00652: 3.60585 -14.64230 5.70055 -18.01289 -0.24748 -0.67432 53.56624 after parameter optimization -center -2.94923 7.05773 -22.33463 -translation 3.79832 -15.27400 5.41232 -rotation -18.80812 0.37842 -1.06792 -scale 1.07545 1.07545 1.07545 -shear 0.00000 0.00000 0.00000 68585 46411 -> 0.00651551 Initial objective function val = 0.04151581 Final objective function value = 0.00651551 successful write 8mm intensity lsq7 fit, no masks: making /tmp/mritotal_12960/nu_8tmp1a.xfm [mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/EF2/EF2surf/mri] [2006-01-09 17:10:30] /Applications/freesurfer/lib/mni/bin/minctracc -clobber -debug /tmp/mritotal_12960/nu_8_blur.mnc /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_blur.mnc /tmp/mritotal_12960/nu_8tmp1a.xfm -transformation /tmp/mritotal_12960/nu_16.xfm -lsq7 -xcorr -center -2.949227 7.057733 -22.334629 -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= -0.000 154.640 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 = 1.0752 0.0167 0.0132 4.1969 -0.0200 1.0179 0.3465 -7.7196 -0.0071 -0.3467 1.0180 8.2405 Transform center = -2.949 7.058 -22.335 Transform rotations = -0.328 0.007 -0.019 Transform trans = 3.798 -15.274 5.412 Transform scale = 1.075 1.075 1.075 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_12960/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_12960/nu_16.xfm Output filename = /tmp/mritotal_12960/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 = 1.0752 0.0167 0.0132 4.1969 -0.0200 1.0179 0.3465 -7.7196 -0.0071 -0.3467 1.0180 8.2405 Transform center = -2.949 7.058 -22.335 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: -2.949227 7.057733 -22.334629 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 57724 -> 0.02173338 80410 57724 -> 0.02173338 80410 56161 -> 0.03087613 80410 56011 -> 0.02391154 80410 58339 -> 0.02842896 80410 57973 -> 0.02256186 80410 56977 -> 0.02458551 80410 57590 -> 0.02359989 80410 60582 -> 0.03889754 80410 50813 -> 0.04522604 80410 59395 -> 0.02757980 80410 57891 -> 0.02922712 80410 58231 -> 0.02409855 80410 57356 -> 0.02067546 80410 56846 -> 0.02580926 80410 54690 -> 0.02589571 80410 56279 -> 0.02199169 80410 56808 -> 0.02275872 80410 56209 -> 0.02157553 80410 58428 -> 0.02471381 80410 56623 -> 0.02130051 80410 56139 -> 0.02034176 80410 55066 -> 0.02423834 80410 55886 -> 0.02422244 80410 57229 -> 0.02060292 80410 55648 -> 0.02072151 80410 56992 -> 0.02126945 80410 55813 -> 0.02197750 80410 57169 -> 0.02028647 80410 57094 -> 0.02217964 80410 56551 -> 0.02011018 80410 56861 -> 0.01970485 80410 57033 -> 0.02179971 80410 56410 -> 0.02075088 80410 56591 -> 0.01971822 80410 57979 -> 0.02105545 80410 56230 -> 0.01971913 80410 55786 -> 0.02141913 80410 57013 -> 0.01965784 80410 55929 -> 0.02049832 80410 56395 -> 0.01969804 80410 57053 -> 0.02156130 80410 56460 -> 0.01952407 80410 56102 -> 0.02031965 80410 56868 -> 0.01959328 80410 56675 -> 0.01952630 80410 57124 -> 0.01967534 80410 56949 -> 0.01997880 80410 56707 -> 0.01942730 80410 56608 -> 0.02011906 80410 56779 -> 0.01940603 80410 57136 -> 0.01946001 80410 56485 -> 0.01965795 80410 56627 -> 0.01941850 80410 56599 -> 0.01940041 80410 56193 -> 0.01996716 80410 56631 -> 0.01960490 80410 56810 -> 0.01936965 80410 56754 -> 0.01980556 80410 56709 -> 0.01932415 80410 57078 -> 0.01932056 80410 57522 -> 0.02001761 80410 56376 -> 0.01949719 80410 56939 -> 0.01933020 80410 56916 -> 0.01928647 80410 57021 -> 0.01955263 80410 57023 -> 0.01932279 80410 56936 -> 0.01948109 80410 56818 -> 0.01929144 80410 57302 -> 0.01954687 80410 56775 -> 0.01927353 80410 56968 -> 0.01942150 80410 56838 -> 0.01927776 80410 56780 -> 0.01928018 80410 57046 -> 0.01924260 80410 57230 -> 0.01937416 80410 56678 -> 0.01934229 80410 56956 -> 0.01924986 80410 56647 -> 0.01945699 80410 56882 -> 0.01923929 80410 56954 -> 0.01927288 80410 56878 -> 0.01928620 80410 56882 -> 0.01923831 done with simplex after 74 iterations 0 0.01928: 3.39326 -13.23863 1.93475 -17.00605 0.29995 -0.97388 53.93348 1 0.01924: 3.45565 -13.64177 1.56537 -17.16166 -0.32729 -0.93035 54.01563 2 0.01927: 3.13967 -13.45578 1.83180 -17.37943 0.01198 -1.26083 53.96971 3 0.01927: 3.28544 -13.12559 1.86426 -16.82456 0.08968 -1.50014 53.82895 4 0.01925: 3.26930 -13.47983 1.44132 -16.82498 0.16156 -1.30945 54.01060 5 0.01928: 3.33573 -13.25834 1.17221 -17.40426 0.23567 -1.37181 53.99072 6 0.01924: 3.18112 -13.46528 1.52890 -17.29871 0.33109 -0.62509 54.02615 7 0.01924: 3.33019 -13.51210 1.66425 -17.12112 0.20455 -1.08760 53.89111 after parameter optimization -center -2.94923 7.05773 -22.33463 -translation 3.33019 -13.51210 1.66425 -rotation -17.12112 0.20455 -1.08760 -scale 1.07782 1.07782 1.07782 -shear 0.00000 0.00000 0.00000 80410 56882 -> 0.01923831 Initial objective function val = 0.02173338 Final objective function value = 0.01923831 successful write 8mm gradient lsq7 fit, target masked: making /tmp/mritotal_12960/nu_8tmp1b.xfm [mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/EF2/EF2surf/mri] [2006-01-09 17:10:40] /Applications/freesurfer/lib/mni/bin/minctracc -clobber -debug /tmp/mritotal_12960/nu_8_dxyz.mnc /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc /tmp/mritotal_12960/nu_8tmp1b.xfm -transformation /tmp/mritotal_12960/nu_8tmp1a.xfm -lsq7 -xcorr -model_mask /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc -center -2.949227 7.057733 -22.334629 -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= 0.046 18.160 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 = 1.0776 0.0184 0.0097 3.6457 -0.0205 1.0299 0.3172 -6.6994 -0.0038 -0.3173 1.0301 4.5635 Transform center = -2.949 7.058 -22.335 Transform rotations = -0.299 0.004 -0.019 Transform trans = 3.330 -13.512 1.664 Transform scale = 1.078 1.078 1.078 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_12960/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_12960/nu_8tmp1a.xfm Output filename = /tmp/mritotal_12960/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 = 1.0776 0.0184 0.0097 3.6457 -0.0205 1.0299 0.3172 -6.6994 -0.0038 -0.3173 1.0301 4.5635 Transform center = -2.949 7.058 -22.335 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: -2.949227 7.057733 -22.334629 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 24804 -> 0.12029067 29440 24804 -> 0.12029067 29440 24796 -> 0.13334647 29440 24374 -> 0.12055791 29440 24931 -> 0.13189422 29440 24921 -> 0.11399738 29440 24795 -> 0.12918408 29440 24795 -> 0.12262522 29440 25317 -> 0.15566404 29440 24205 -> 0.12203062 29440 24595 -> 0.11327502 29440 24464 -> 0.11899173 29440 24353 -> 0.11033130 29440 24068 -> 0.11853747 29440 24337 -> 0.10330542 29440 24118 -> 0.10502210 29440 24233 -> 0.10047285 29440 23957 -> 0.09817658 29440 24755 -> 0.11909904 29440 24694 -> 0.10555542 29440 24236 -> 0.09663823 29440 23952 -> 0.10353882 29440 24132 -> 0.12134616 29440 24595 -> 0.10665796 29440 23852 -> 0.09905943 29440 24009 -> 0.09802711 29440 24141 -> 0.10282581 29440 23744 -> 0.10911883 29440 24388 -> 0.09833996 29440 23552 -> 0.09178370 29440 22950 -> 0.09861843 29440 23712 -> 0.10768217 29440 24186 -> 0.09619249 29440 23915 -> 0.10257652 29440 23970 -> 0.09616570 29440 24232 -> 0.09339156 29440 23640 -> 0.09603184 29440 24008 -> 0.09448462 29440 23947 -> 0.09513124 29440 23624 -> 0.09157054 29440 23305 -> 0.09653210 29440 23513 -> 0.09125618 29440 23174 -> 0.09677322 29440 23592 -> 0.08761647 29440 23402 -> 0.08999721 29440 23922 -> 0.09245609 29440 23610 -> 0.09052705 29440 23443 -> 0.09224134 29440 22968 -> 0.09404371 29440 23920 -> 0.08942343 29440 23291 -> 0.10058628 29440 23758 -> 0.08839913 29440 23863 -> 0.09383436 29440 23549 -> 0.08961035 29440 23756 -> 0.09217682 29440 23600 -> 0.08919526 29440 23685 -> 0.08841679 29440 23835 -> 0.08794742 29440 23798 -> 0.09306706 29440 23656 -> 0.08801365 29440 23900 -> 0.08841840 29440 23514 -> 0.08920083 29440 23616 -> 0.08778051 29440 23843 -> 0.08703836 29440 23964 -> 0.08869397 29440 23525 -> 0.08778816 29440 23704 -> 0.08858690 29440 23686 -> 0.08736306 29440 23601 -> 0.08928119 29440 23711 -> 0.08731189 29440 23712 -> 0.08856648 29440 23671 -> 0.08718205 29440 23498 -> 0.08779103 29440 23578 -> 0.08708245 29440 23824 -> 0.08818352 29440 23598 -> 0.08712248 29440 23726 -> 0.08698725 29440 23781 -> 0.08785553 29440 23786 -> 0.08711766 29440 23722 -> 0.08673081 29440 23738 -> 0.08717453 29440 23688 -> 0.08719361 29440 23697 -> 0.08670487 29440 23740 -> 0.08653983 29440 23777 -> 0.08690413 29440 23858 -> 0.08706047 29440 23691 -> 0.08658231 29440 23929 -> 0.08730662 29440 23667 -> 0.08662479 29440 23596 -> 0.08698864 29440 23536 -> 0.08764493 29440 23766 -> 0.08659784 29440 23837 -> 0.08697101 29440 23738 -> 0.08674032 29440 23599 -> 0.08680780 29440 23659 -> 0.08655418 29440 23674 -> 0.08701701 29440 23722 -> 0.08643751 29440 23693 -> 0.08697172 29440 23716 -> 0.08649874 done with simplex after 91 iterations 0 0.08650: 3.50565 -9.37729 0.48616 -13.39058 -2.00610 -2.42481 52.59777 1 0.08654: 3.49743 -9.23437 0.50278 -12.99879 -1.96731 -2.63654 52.70519 2 0.08660: 3.39905 -9.44735 0.51017 -13.08349 -2.08767 -2.44640 52.64287 3 0.08658: 3.51711 -9.28421 0.69490 -12.99987 -2.13384 -2.25661 52.46003 4 0.08644: 3.44954 -9.28532 0.39856 -13.07233 -2.14889 -2.35375 52.63886 5 0.08662: 3.29597 -9.25684 0.45749 -13.27354 -1.76791 -2.45652 52.50131 6 0.08655: 3.41334 -9.19541 0.60677 -13.26107 -2.07831 -2.49485 52.48995 7 0.08670: 3.46879 -9.30864 0.35289 -13.15301 -1.91334 -2.73672 52.54787 after parameter optimization -center -2.94923 7.05773 -22.33463 -translation 3.44954 -9.28532 0.39856 -rotation -13.07233 -2.14889 -2.35375 -scale 1.05278 1.05278 1.05278 -shear 0.00000 0.00000 0.00000 29440 23722 -> 0.08643751 Initial objective function val = 0.12029067 Final objective function value = 0.08643751 successful write 8mm gradient lsq9 fit, target masked: making /tmp/mritotal_12960/nu_8tmp2a.xfm [mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/EF2/EF2surf/mri] [2006-01-09 17:10:48] /Applications/freesurfer/lib/mni/bin/minctracc -clobber -debug /tmp/mritotal_12960/nu_8_dxyz.mnc /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc /tmp/mritotal_12960/nu_8tmp2a.xfm -transformation /tmp/mritotal_12960/nu_8tmp1b.xfm -lsq9 -xcorr -model_mask /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc -center -2.949227 7.057733 -22.334629 -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= 0.046 18.160 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 = 1.0511 0.0510 -0.0286 2.6005 -0.0432 1.0243 0.2395 -4.2349 0.0395 -0.2380 1.0248 2.7477 Transform center = -2.949 7.058 -22.335 Transform rotations = -0.228 -0.038 -0.041 Transform trans = 3.450 -9.285 0.399 Transform scale = 1.053 1.053 1.053 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_12960/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_12960/nu_8tmp1b.xfm Output filename = /tmp/mritotal_12960/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 = 1.0511 0.0510 -0.0286 2.6005 -0.0432 1.0243 0.2395 -4.2349 0.0395 -0.2380 1.0248 2.7477 Transform center = -2.949 7.058 -22.335 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: -2.949227 7.057733 -22.334629 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 23722 -> 0.08643750 29440 23722 -> 0.08643750 29440 23699 -> 0.09686114 29440 23262 -> 0.09032836 29440 23830 -> 0.09267534 29440 23867 -> 0.09004117 29440 23721 -> 0.09183197 29440 23719 -> 0.09014750 29440 23724 -> 0.09752660 29440 24216 -> 0.08930866 29440 23782 -> 0.08850694 29440 23796 -> 0.09085234 29440 23833 -> 0.09364221 29440 23803 -> 0.08768486 29440 23712 -> 0.09173673 29440 23800 -> 0.09127022 29440 23849 -> 0.09348366 29440 23742 -> 0.08684705 29440 23731 -> 0.09129449 29440 23791 -> 0.08723225 29440 23742 -> 0.09847823 29440 23782 -> 0.08593479 29440 24373 -> 0.08896828 29440 24096 -> 0.08727824 29440 23984 -> 0.08799729 29440 23561 -> 0.08649427 29440 23228 -> 0.09018096 29440 24091 -> 0.08580973 29440 23895 -> 0.09060177 29440 23811 -> 0.08577992 29440 23673 -> 0.08999965 29440 23900 -> 0.08570003 29440 23857 -> 0.08472355 29440 23892 -> 0.08770124 29440 23532 -> 0.08862783 29440 23948 -> 0.08516629 29440 23863 -> 0.08568351 29440 23938 -> 0.08673835 29440 23890 -> 0.08521531 29440 24178 -> 0.08761349 29440 23723 -> 0.08494022 29440 24021 -> 0.08661720 29440 23797 -> 0.08500852 29440 23976 -> 0.08666906 29440 23828 -> 0.08491067 29440 23602 -> 0.08508424 29440 23835 -> 0.08518644 29440 23729 -> 0.08607923 29440 23861 -> 0.08469836 29440 23767 -> 0.08567959 29440 23792 -> 0.08485412 29440 23722 -> 0.08503640 29440 23750 -> 0.08557075 29440 23813 -> 0.08455102 29440 23609 -> 0.08499990 29440 23953 -> 0.08599283 29440 23688 -> 0.08443413 29440 23827 -> 0.08524195 29440 23747 -> 0.08449125 29440 23738 -> 0.08479176 29440 23959 -> 0.08501140 29440 23695 -> 0.08456925 29440 23841 -> 0.08525792 29440 23753 -> 0.08444540 29440 23716 -> 0.08429731 29440 23658 -> 0.08466803 29440 23734 -> 0.08474177 29440 23788 -> 0.08472239 29440 23804 -> 0.08493248 29440 23751 -> 0.08445832 29440 23651 -> 0.08499563 29440 23811 -> 0.08433028 29440 23732 -> 0.08475114 29440 23773 -> 0.08442825 29440 23641 -> 0.08481549 29440 23804 -> 0.08446738 29440 23827 -> 0.08435055 29440 23714 -> 0.08442896 done with simplex after 67 iterations 0 0.08443: 3.59548 -9.25252 0.05379 -12.97472 -2.16375 -2.46454 52.06358 52.80731 53.54103 1 0.08433: 3.84608 -9.28382 -0.11268 -12.81683 -2.38321 -2.44458 51.88747 52.89617 53.76945 2 0.08443: 3.62118 -8.94849 0.17233 -13.01515 -2.12652 -2.61082 51.90905 52.71192 53.71423 3 0.08449: 3.60750 -8.97865 -0.00155 -12.79865 -2.20090 -2.39473 51.90678 52.92656 53.47173 4 0.08447: 3.50695 -9.18981 0.14139 -13.00894 -2.15335 -2.37587 51.91641 52.96144 53.67098 5 0.08446: 3.70490 -9.21084 -0.09942 -12.97979 -2.10732 -2.41681 51.81735 52.76828 53.81007 6 0.08435: 3.54955 -9.20899 -0.04856 -12.75511 -2.19898 -2.76860 51.95284 52.98824 53.75938 7 0.08430: 3.76559 -9.09721 -0.22321 -12.99673 -2.51232 -2.63835 51.83784 52.73063 53.98929 8 0.08445: 3.45317 -9.19631 0.19356 -12.75697 -2.16675 -2.26356 51.85062 52.64911 53.76870 9 0.08443: 3.67083 -9.05475 -0.13134 -12.98774 -2.34454 -2.41942 52.04227 52.74236 53.97028 after parameter optimization -center -2.94923 7.05773 -22.33463 -translation 3.76559 -9.09721 -0.22321 -rotation -12.99673 -2.51232 -2.63835 -scale 1.03676 1.05461 1.07979 -shear 0.00000 0.00000 0.00000 29440 23716 -> 0.08429731 Initial objective function val = 0.08643750 Final objective function value = 0.08429731 successful write checking z-scale: making /tmp/mritotal_12960/nu_8tmp2b.xfm [mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/EF2/EF2surf/mri] [2006-01-09 17:10:54] /Applications/freesurfer/lib/mni/bin/check_scale /tmp/mritotal_12960/nu_8tmp2a.xfm /tmp/mritotal_12960/nu_8tmp2b.xfm 8mm gradient lsq9 fit, target masked: making /tmp/mritotal_12960/nu_8tmp2c.xfm [mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/EF2/EF2surf/mri] [2006-01-09 17:10:54] /Applications/freesurfer/lib/mni/bin/minctracc -clobber -debug /tmp/mritotal_12960/nu_8_dxyz.mnc /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc /tmp/mritotal_12960/nu_8tmp2c.xfm -transformation /tmp/mritotal_12960/nu_8tmp2b.xfm -lsq9 -xcorr -model_mask /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc -center -2.949227 7.057733 -22.334629 -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= 0.046 18.160 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 = 1.0347 0.0567 -0.0335 2.7193 -0.0485 1.0260 0.2390 -4.0860 0.0473 -0.2426 1.0511 2.7702 Transform center = -2.949 7.058 -22.335 Transform rotations = -0.227 -0.044 -0.046 Transform trans = 3.766 -9.097 -0.223 Transform scale = 1.037 1.055 1.080 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_12960/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_12960/nu_8tmp2b.xfm Output filename = /tmp/mritotal_12960/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 = 1.0347 0.0567 -0.0335 2.7193 -0.0485 1.0260 0.2390 -4.0860 0.0473 -0.2426 1.0511 2.7702 Transform center = -2.949 7.058 -22.335 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: -2.949227 7.057733 -22.334629 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 -> 0.08429731 29440 23716 -> 0.08429731 29440 23689 -> 0.09634950 29440 23253 -> 0.08956338 29440 23821 -> 0.09146230 29440 23857 -> 0.08692119 29440 23711 -> 0.08983494 29440 23711 -> 0.08756673 29440 23715 -> 0.09264322 29440 24220 -> 0.08754497 29440 23775 -> 0.09098528 29440 23812 -> 0.09432051 29440 23784 -> 0.08752508 29440 23804 -> 0.09404612 29440 23739 -> 0.08722605 29440 23690 -> 0.09040067 29440 23708 -> 0.09215334 29440 23759 -> 0.08675133 29440 23816 -> 0.09059416 29440 23719 -> 0.08645291 29440 23790 -> 0.09321497 29440 23733 -> 0.08606563 29440 24342 -> 0.08811878 29440 24070 -> 0.08560303 29440 23993 -> 0.08870040 29440 23763 -> 0.08534049 29440 23366 -> 0.08748675 29440 23716 -> 0.08853535 29440 23767 -> 0.08547120 29440 24210 -> 0.08741491 29440 24006 -> 0.08555432 29440 23905 -> 0.08648719 29440 23790 -> 0.08784158 29440 23842 -> 0.08523737 29440 23915 -> 0.08674724 29440 23875 -> 0.08521412 29440 23762 -> 0.08679125 29440 23867 -> 0.08514435 29440 23980 -> 0.08521184 29440 24020 -> 0.08630461 29440 23802 -> 0.08490212 29440 23623 -> 0.08516956 29440 23607 -> 0.08524265 29440 23812 -> 0.08600154 29440 23776 -> 0.08475544 29440 23801 -> 0.08525272 29440 23796 -> 0.08468778 29440 24013 -> 0.08538045 29440 23704 -> 0.08470684 29440 23748 -> 0.08467274 29440 23697 -> 0.08526618 29440 23831 -> 0.08451945 29440 23544 -> 0.08586042 29440 23871 -> 0.08452363 29440 23958 -> 0.08507334 29440 23734 -> 0.08452850 29440 23596 -> 0.08501182 29440 23682 -> 0.08457749 29440 23718 -> 0.08461849 29440 23735 -> 0.08462018 29440 23810 -> 0.08453159 29440 23726 -> 0.08459529 29440 23771 -> 0.08444504 29440 23788 -> 0.08472623 29440 23749 -> 0.08437958 29440 23811 -> 0.08470777 29440 23745 -> 0.08442485 done with simplex after 56 iterations 0 0.08430: 3.76559 -9.09721 -0.22321 -12.99673 -2.51232 -2.63835 51.83784 52.73063 53.98928 1 0.08438: 3.69153 -9.15703 0.08750 -12.88103 -2.29208 -2.54199 51.72993 52.74406 53.72544 2 0.08458: 3.62648 -8.77281 0.00105 -12.73808 -2.23155 -2.45375 51.77656 52.79694 53.84864 3 0.08452: 3.60512 -9.32779 0.18092 -12.59781 -2.21104 -2.33309 51.75172 52.95892 53.95780 4 0.08445: 3.76160 -9.18205 0.09701 -12.51243 -2.58706 -2.68134 51.94816 52.69188 53.75407 5 0.08442: 3.57955 -9.11103 0.09509 -12.80172 -2.41560 -2.47954 51.78050 52.72547 53.79481 6 0.08460: 3.66976 -9.14997 0.18893 -13.41703 -2.40592 -2.25631 51.87400 52.79769 53.68047 7 0.08453: 3.55442 -9.22470 0.24391 -12.94230 -2.14017 -2.54605 52.08883 52.59531 53.76184 8 0.08453: 3.67366 -9.15207 0.13602 -13.16489 -2.32413 -2.73347 51.80309 53.05686 53.70959 9 0.08452: 3.57574 -9.13235 -0.26680 -12.53594 -2.12960 -2.26215 51.80348 53.03878 53.89685 after parameter optimization -center -2.94923 7.05773 -22.33463 -translation 3.76559 -9.09721 -0.22321 -rotation -12.99673 -2.51232 -2.63835 -scale 1.03676 1.05461 1.07979 -shear 0.00000 0.00000 0.00000 29440 23716 -> 0.08429731 Initial objective function val = 0.08429731 Final objective function value = 0.08429731 successful write final linear fit: 8mm gradient lsq9 fit, target masked: making transforms/talairach.xfm [mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/EF2/EF2surf/mri] [2006-01-09 17:10:59] /Applications/freesurfer/lib/mni/bin/minctracc -clobber -debug /tmp/mritotal_12960/nu_8_dxyz.mnc /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc transforms/talairach.xfm -transformation /tmp/mritotal_12960/nu_8tmp2c.xfm -lsq9 -xcorr -model_mask /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc -center -2.949227 7.057733 -22.334629 -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= 0.046 18.160 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 = 1.0347 0.0567 -0.0335 2.7193 -0.0485 1.0260 0.2390 -4.0860 0.0473 -0.2426 1.0511 2.7702 Transform center = -2.949 7.058 -22.335 Transform rotations = -0.227 -0.044 -0.046 Transform trans = 3.766 -9.097 -0.223 Transform scale = 1.037 1.055 1.080 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_12960/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_12960/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 = 1.0347 0.0567 -0.0335 2.7193 -0.0485 1.0260 0.2390 -4.0860 0.0473 -0.2426 1.0511 2.7702 Transform center = -2.949 7.058 -22.335 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: -2.949227 7.057733 -22.334629 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 -> 0.08429731 29440 23716 -> 0.08429731 29440 23689 -> 0.09634949 29440 23253 -> 0.08956338 29440 23821 -> 0.09146228 29440 23857 -> 0.08692119 29440 23711 -> 0.08983494 29440 23711 -> 0.08756673 29440 23715 -> 0.09264325 29440 24220 -> 0.08754498 29440 23775 -> 0.09098526 29440 23812 -> 0.09432051 29440 23784 -> 0.08752507 29440 23804 -> 0.09404606 29440 23739 -> 0.08722606 29440 23690 -> 0.09040070 29440 23708 -> 0.09215338 29440 23759 -> 0.08675133 29440 23816 -> 0.09059414 29440 23719 -> 0.08645292 29440 23790 -> 0.09321499 29440 23733 -> 0.08606563 29440 24342 -> 0.08811878 29440 24070 -> 0.08560304 29440 23993 -> 0.08870042 29440 23763 -> 0.08534049 29440 23366 -> 0.08748676 29440 23716 -> 0.08853537 29440 23767 -> 0.08547121 29440 24210 -> 0.08741491 29440 24006 -> 0.08555432 29440 23905 -> 0.08648717 29440 23789 -> 0.08784244 29440 23842 -> 0.08523737 29440 23915 -> 0.08674726 29440 23875 -> 0.08521412 29440 23762 -> 0.08679128 29440 23867 -> 0.08514434 29440 23980 -> 0.08521184 29440 24020 -> 0.08630461 29440 23802 -> 0.08490212 29440 23623 -> 0.08516955 29440 23607 -> 0.08524264 29440 23812 -> 0.08600154 29440 23776 -> 0.08475544 29440 23801 -> 0.08525271 29440 23796 -> 0.08468778 29440 24013 -> 0.08538044 29440 23704 -> 0.08470684 29440 23748 -> 0.08467273 29440 23697 -> 0.08526617 29440 23831 -> 0.08451945 29440 23544 -> 0.08586044 29440 23871 -> 0.08452362 29440 23958 -> 0.08507334 29440 23734 -> 0.08452850 29440 23596 -> 0.08501182 29440 23682 -> 0.08457749 29440 23718 -> 0.08461848 29440 23735 -> 0.08462017 29440 23810 -> 0.08453159 29440 23726 -> 0.08459529 29440 23771 -> 0.08444504 29440 23788 -> 0.08472623 29440 23749 -> 0.08437958 29440 23811 -> 0.08470777 29440 23745 -> 0.08442485 done with simplex after 56 iterations 0 0.08430: 3.76559 -9.09721 -0.22321 -12.99673 -2.51232 -2.63835 51.83784 52.73063 53.98927 1 0.08438: 3.69153 -9.15703 0.08750 -12.88103 -2.29208 -2.54199 51.72994 52.74406 53.72543 2 0.08458: 3.62648 -8.77281 0.00105 -12.73808 -2.23155 -2.45375 51.77657 52.79694 53.84864 3 0.08452: 3.60512 -9.32779 0.18092 -12.59781 -2.21104 -2.33309 51.75173 52.95892 53.95779 4 0.08445: 3.76160 -9.18205 0.09701 -12.51244 -2.58706 -2.68134 51.94817 52.69188 53.75406 5 0.08442: 3.57955 -9.11103 0.09509 -12.80172 -2.41560 -2.47954 51.78051 52.72547 53.79480 6 0.08460: 3.66976 -9.14997 0.18893 -13.41703 -2.40592 -2.25631 51.87400 52.79769 53.68046 7 0.08453: 3.55442 -9.22470 0.24391 -12.94230 -2.14017 -2.54605 52.08883 52.59531 53.76184 8 0.08453: 3.67366 -9.15207 0.13602 -13.16489 -2.32413 -2.73347 51.80310 53.05686 53.70958 9 0.08452: 3.57574 -9.13235 -0.26680 -12.53594 -2.12960 -2.26215 51.80349 53.03878 53.89684 after parameter optimization -center -2.94923 7.05773 -22.33463 -translation 3.76559 -9.09721 -0.22321 -rotation -12.99673 -2.51232 -2.63835 -scale 1.03676 1.05461 1.07979 -shear 0.00000 0.00000 0.00000 29440 23716 -> 0.08429731 Initial objective function val = 0.08429731 Final objective function value = 0.08429731 successful write