[dglen@gollum.local:/Users/dglen/freesurfer/subjects/FL2/FL2surf/mri] [2006-01-20 18:12:37] 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/FL2/FL2surf/mri] [2006-01-20 18:12:37] /Applications/freesurfer/lib/mni/bin/autocrop -clobber nu.mnc /tmp/mritotal_3342/nu_crop.mnc -step 2 2 2 -extend 0,0 0,0 -25%,0 [autocrop] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FL2/FL2surf/mri] [2006-01-20 18:12:37] /Applications/freesurfer/lib/mni/bin/mincresample -clobber nu.mnc /tmp/mritotal_3342/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/FL2/FL2surf/mri] [2006-01-20 18:12:37] /Applications/freesurfer/lib/mni/bin/volume_cog /tmp/mritotal_3342/nu_crop.mnc | tail -1 Centroid of input volume: 0.836495 10.089290 -15.167766 Zero-padding data: [mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FL2/FL2surf/mri] [2006-01-20 18:12:38] /Applications/freesurfer/lib/mni/bin/autocrop -clobber /tmp/mritotal_3342/nu_crop.mnc /tmp/mritotal_3342/nu_pad.mnc -expand 22 22 22 [autocrop] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FL2/FL2surf/mri] [2006-01-20 18:12:38] /Applications/freesurfer/lib/mni/bin/mincreshape -clobber /tmp/mritotal_3342/nu_crop.mnc /tmp/mritotal_3342/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/FL2/FL2surf/mri] [2006-01-20 18:12:38] /Applications/freesurfer/lib/mni/bin/mincblur -clobber -debug /tmp/mritotal_3342/nu_pad.mnc /tmp/mritotal_3342/tmp_16 -fwhm 16 ===== Debugging information from /Applications/freesurfer/lib/mni/bin/mincblur ===== Data filename = /tmp/mritotal_3342/nu_pad.mnc Output basename = /tmp/mritotal_3342/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 254.999707 before blur min/max = 0.000000 254.999710 after blur min/max = -0.000002 125.057159 Making byte volume... [mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FL2/FL2surf/mri] [2006-01-20 18:12:41] /Applications/freesurfer/lib/mni/bin/autocrop -clobber /tmp/mritotal_3342/tmp_16_blur.mnc /tmp/mritotal_3342/nu_16_blur.mnc -expand -44 -44 -44 [autocrop] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FL2/FL2surf/mri] [2006-01-20 18:12:41] /Applications/freesurfer/lib/mni/bin/mincreshape -clobber /tmp/mritotal_3342/tmp_16_blur.mnc /tmp/mritotal_3342/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/FL2/FL2surf/mri] [2006-01-20 18:12:41] /Applications/freesurfer/lib/mni/bin/mincblur -clobber -debug /tmp/mritotal_3342/nu_pad.mnc /tmp/mritotal_3342/tmp_8 -fwhm 8 -gradient Transforming slices:......................................................................................................................................................Done ===== Debugging information from /Applications/freesurfer/lib/mni/bin/mincblur ===== Data filename = /tmp/mritotal_3342/nu_pad.mnc Output basename = /tmp/mritotal_3342/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 254.999707 before blur min/max = 0.000000 254.999710 after blur min/max = -0.000012 143.413147 Making byte volume... Making byte volume dx...dx: min = -16.332375, max = 12.793189 Making byte volume dy...dy: min = -12.451374, max = 12.265930 Making byte volume dz...dz: min = -13.170156, max = 14.327482 [mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FL2/FL2surf/mri] [2006-01-20 18:12:46] /Applications/freesurfer/lib/mni/bin/autocrop -clobber /tmp/mritotal_3342/tmp_8_blur.mnc /tmp/mritotal_3342/nu_8_blur.mnc -expand -34 -34 -34 [autocrop] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FL2/FL2surf/mri] [2006-01-20 18:12:46] /Applications/freesurfer/lib/mni/bin/mincreshape -clobber /tmp/mritotal_3342/tmp_8_blur.mnc /tmp/mritotal_3342/nu_8_blur.mnc -start 17,17,17 -count 116,116,84 Copying chunks:....................................................................................................................Done. [mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FL2/FL2surf/mri] [2006-01-20 18:12:47] /Applications/freesurfer/lib/mni/bin/autocrop -clobber /tmp/mritotal_3342/tmp_8_dxyz.mnc /tmp/mritotal_3342/nu_8_dxyz.mnc -expand -34 -34 -34 [autocrop] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FL2/FL2surf/mri] [2006-01-20 18:12:47] /Applications/freesurfer/lib/mni/bin/mincreshape -clobber /tmp/mritotal_3342/tmp_8_dxyz.mnc /tmp/mritotal_3342/nu_8_dxyz.mnc -start 17,17,17 -count 116,116,84 Copying chunks:....................................................................................................................Done. 16mm intensity lsq7 fit, no masks: making /tmp/mritotal_3342/nu_16.xfm [mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FL2/FL2surf/mri] [2006-01-20 18:12:47] /Applications/freesurfer/lib/mni/bin/minctracc -clobber -debug /tmp/mritotal_3342/nu_16_blur.mnc /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_16_blur.mnc /tmp/mritotal_3342/nu_16.xfm -est_translations -lsq7 -xcorr -center 0.836495 10.089290 -15.167766 -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= -0.000 125.057 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 -0.5085 0.0000 1.0000 0.0000 -27.6804 0.0000 0.0000 1.0000 24.6224 Transform center = 0.836 10.089 -15.168 Transform rotations = 0.000 0.000 0.000 Transform trans = -0.508 -27.680 24.622 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_3342/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_3342/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 = 0.836 10.089 -15.168 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: 0.836495 10.089290 -15.167766 using PAT to get initial parameters: will try to get: [trans] COG of v1 forced: 0.836495 10.089290 -15.167766 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] = -0.508489 -27.680420 24.622429 Only center & trans required, now returning from init_transformation Transform center = 0.836 10.089 -15.168 Transform rots = 0.000 0.000 0.000 Transform trans = -0.508 -27.680 24.622 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 45772 -> 0.03757607 68585 45772 -> 0.03757607 68585 40731 -> 0.07888532 68585 44556 -> 0.04156344 68585 45708 -> 0.04799088 68585 47848 -> 0.04389396 68585 45011 -> 0.04148751 68585 43772 -> 0.04529915 68585 57362 -> 0.09315009 68585 15494 -> 0.14628050 68585 53443 -> 0.05569467 68585 44541 -> 0.09276663 68585 44154 -> 0.04924679 68585 30385 -> 0.08275072 68585 50244 -> 0.03958551 68585 44583 -> 0.05589889 68585 45626 -> 0.04001577 68585 47090 -> 0.02812400 68585 47266 -> 0.04560101 68585 45750 -> 0.03559577 68585 47332 -> 0.03330667 68585 48137 -> 0.04844349 68585 46341 -> 0.03409278 68585 48104 -> 0.03564108 68585 47806 -> 0.02736836 68585 46995 -> 0.03260422 68585 42988 -> 0.02388356 68585 37976 -> 0.03413337 68585 44413 -> 0.03288447 68585 44342 -> 0.02872361 68585 44069 -> 0.02644937 68585 44448 -> 0.02278115 68585 42017 -> 0.04037824 68585 45563 -> 0.03031492 68585 43880 -> 0.03007261 68585 47143 -> 0.02897136 68585 45237 -> 0.03777233 68585 45588 -> 0.02179171 68585 45537 -> 0.02829558 68585 46552 -> 0.02035682 68585 45975 -> 0.03322510 68585 47672 -> 0.02423692 68585 43403 -> 0.02331070 68585 41718 -> 0.02632344 68585 44834 -> 0.01613149 68585 43622 -> 0.02281694 68585 47489 -> 0.02720449 68585 44060 -> 0.01878849 68585 42410 -> 0.03016243 68585 46639 -> 0.01864749 68585 46288 -> 0.01681496 68585 46732 -> 0.02993211 68585 44720 -> 0.01660917 68585 45227 -> 0.02135405 68585 45087 -> 0.01698581 68585 43999 -> 0.02197587 68585 46041 -> 0.01621536 68585 44745 -> 0.01847267 68585 47356 -> 0.01448362 68585 48658 -> 0.01992334 68585 44906 -> 0.01205952 68585 43577 -> 0.01552798 68585 46834 -> 0.02119046 68585 45320 -> 0.01408809 68585 45918 -> 0.01573242 68585 43511 -> 0.02064578 68585 46270 -> 0.01339630 68585 47232 -> 0.01116841 68585 48109 -> 0.01389464 68585 45477 -> 0.01298721 68585 46671 -> 0.01644735 68585 45692 -> 0.01265280 68585 45907 -> 0.01324150 68585 44327 -> 0.01352920 68585 46504 -> 0.01080661 68585 47406 -> 0.01479589 68585 47591 -> 0.01328292 68585 45936 -> 0.01122717 68585 44120 -> 0.01227451 68585 45087 -> 0.01491437 68585 45927 -> 0.01067872 68585 46194 -> 0.01392331 68585 45605 -> 0.01073239 68585 45737 -> 0.01056339 68585 45361 -> 0.01387435 68585 47489 -> 0.01253411 68585 45114 -> 0.01032339 68585 46836 -> 0.01078896 68585 46358 -> 0.01153092 68585 46059 -> 0.00993599 68585 44480 -> 0.01371647 68585 46721 -> 0.00964531 68585 45707 -> 0.01000206 68585 44553 -> 0.01219189 68585 46388 -> 0.00968746 68585 46391 -> 0.00993418 68585 46042 -> 0.00978424 68585 45837 -> 0.01240654 68585 45967 -> 0.00949216 68585 47227 -> 0.00961080 68585 47272 -> 0.01069142 68585 46035 -> 0.00937435 68585 46790 -> 0.00903421 68585 47134 -> 0.00946948 68585 46496 -> 0.01003545 68585 46416 -> 0.00930743 68585 46903 -> 0.00979034 68585 46264 -> 0.00927683 68585 46656 -> 0.00892193 68585 46709 -> 0.00923554 68585 46272 -> 0.00965841 68585 46619 -> 0.00916194 68585 45483 -> 0.00971690 68585 46806 -> 0.00915107 68585 46918 -> 0.00974419 68585 46252 -> 0.00911446 68585 47046 -> 0.00930910 68585 46821 -> 0.00907049 68585 46758 -> 0.00881276 68585 46876 -> 0.00884028 68585 46985 -> 0.00896003 68585 46859 -> 0.00893983 68585 46570 -> 0.00892694 68585 47260 -> 0.00896312 68585 46914 -> 0.00869497 68585 46982 -> 0.00875059 68585 46909 -> 0.00886016 68585 46308 -> 0.00896018 68585 46583 -> 0.00881073 68585 46484 -> 0.00870917 68585 46505 -> 0.00870176 68585 46765 -> 0.00873663 68585 46816 -> 0.00854620 68585 46930 -> 0.00859939 68585 46394 -> 0.00889602 68585 46812 -> 0.00867181 68585 46632 -> 0.00880603 68585 46851 -> 0.00856101 68585 46831 -> 0.00877323 68585 46800 -> 0.00862718 68585 46664 -> 0.00881846 68585 46754 -> 0.00861523 68585 47040 -> 0.00873358 68585 46640 -> 0.00861495 68585 47065 -> 0.00867072 68585 46743 -> 0.00850887 68585 46629 -> 0.00851103 68585 46790 -> 0.00862058 68585 46505 -> 0.00861563 68585 46673 -> 0.00848305 68585 46610 -> 0.00847423 68585 46566 -> 0.00865225 68585 46781 -> 0.00854380 68585 47020 -> 0.00862327 68585 46623 -> 0.00854028 68585 46683 -> 0.00851463 68585 46825 -> 0.00846730 68585 46900 -> 0.00853276 68585 46551 -> 0.00849982 68585 46549 -> 0.00844949 68585 46389 -> 0.00846946 68585 46555 -> 0.00842973 68585 46428 -> 0.00844165 68585 46683 -> 0.00842485 68585 46706 -> 0.00846440 68585 46623 -> 0.00846942 68585 46510 -> 0.00846552 68585 46672 -> 0.00849581 68585 46656 -> 0.00844157 done with simplex after 160 iterations 0 0.00847: 0.45940 -19.77040 -1.91186 -20.09601 2.77538 -4.11417 52.93394 1 0.00847: 0.35890 -19.08304 -2.02624 -19.91765 2.25132 -5.25706 53.01627 2 0.00847: 0.71038 -19.18774 -2.51919 -20.85297 1.71580 -4.16686 52.94124 3 0.00842: 0.33508 -19.67633 -2.72334 -21.05848 2.66787 -4.94760 53.03938 4 0.00845: 0.46113 -19.37156 -2.37466 -20.14466 2.41061 -4.92867 52.84251 5 0.00847: 0.14492 -19.16994 -2.38284 -21.47427 3.31128 -4.46004 52.87284 6 0.00844: 0.33360 -19.39833 -2.13456 -21.23515 2.26978 -4.35641 52.87684 7 0.00843: 0.34721 -18.95551 -2.71212 -20.01040 2.59141 -4.39330 52.93047 after parameter optimization -center 0.83649 10.08929 -15.16777 -translation 0.33508 -19.67633 -2.72334 -rotation -21.05848 2.66787 -4.94760 -scale 1.06079 1.06079 1.06079 -shear 0.00000 0.00000 0.00000 68585 46683 -> 0.00842485 Initial objective function val = 0.03757607 Final objective function value = 0.00842485 successful write 8mm intensity lsq7 fit, no masks: making /tmp/mritotal_3342/nu_8tmp1a.xfm [mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FL2/FL2surf/mri] [2006-01-20 18:12:55] /Applications/freesurfer/lib/mni/bin/minctracc -clobber -debug /tmp/mritotal_3342/nu_8_blur.mnc /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_blur.mnc /tmp/mritotal_3342/nu_8tmp1a.xfm -transformation /tmp/mritotal_3342/nu_16.xfm -lsq7 -xcorr -center 0.836495 10.089290 -15.167766 -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= -0.000 143.413 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 = 1.0557 0.0677 0.0788 0.8003 -0.0914 0.9878 0.3758 -13.7771 -0.0494 -0.3807 0.9889 0.9906 Transform center = 0.836 10.089 -15.168 Transform rotations = -0.368 0.047 -0.086 Transform trans = 0.335 -19.676 -2.723 Transform scale = 1.061 1.061 1.061 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_3342/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_3342/nu_16.xfm Output filename = /tmp/mritotal_3342/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 = 1.0557 0.0677 0.0788 0.8003 -0.0914 0.9878 0.3758 -13.7771 -0.0494 -0.3807 0.9889 0.9906 Transform center = 0.836 10.089 -15.168 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: 0.836495 10.089290 -15.167766 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 57438 -> 0.02396842 80410 57438 -> 0.02396842 80410 55954 -> 0.03342842 80410 55836 -> 0.02627104 80410 58141 -> 0.02884546 80410 57627 -> 0.02375344 80410 56826 -> 0.02691068 80410 58298 -> 0.02483972 80410 61512 -> 0.03869300 80410 50825 -> 0.04350122 80410 59543 -> 0.02873720 80410 58654 -> 0.02935378 80410 58345 -> 0.02501262 80410 57300 -> 0.02300865 80410 56853 -> 0.02676614 80410 54776 -> 0.02760657 80410 56212 -> 0.02411060 80410 57765 -> 0.02420130 80410 59447 -> 0.02439953 80410 57002 -> 0.02498672 80410 57447 -> 0.02311157 80410 57002 -> 0.02304959 80410 55197 -> 0.02461191 80410 58381 -> 0.02268177 80410 56794 -> 0.02720700 80410 57601 -> 0.02241199 80410 58773 -> 0.02263539 80410 58145 -> 0.02320679 80410 57938 -> 0.02260499 80410 57540 -> 0.02299127 80410 58052 -> 0.02250264 80410 58925 -> 0.02339271 80410 57463 -> 0.02204202 80410 58446 -> 0.02372567 80410 57699 -> 0.02202493 80410 58578 -> 0.02319016 80410 57774 -> 0.02207552 80410 57401 -> 0.02292475 80410 58125 -> 0.02194721 80410 56781 -> 0.02248907 80410 57365 -> 0.02330907 80410 57731 -> 0.02186367 80410 57045 -> 0.02307984 80410 57823 -> 0.02189591 80410 58660 -> 0.02262908 80410 57268 -> 0.02192908 80410 57749 -> 0.02259064 80410 57633 -> 0.02189465 80410 57613 -> 0.02199163 80410 57948 -> 0.02210389 80410 57595 -> 0.02181580 80410 57675 -> 0.02222885 80410 57695 -> 0.02178865 80410 57813 -> 0.02206088 80410 57652 -> 0.02180124 80410 57129 -> 0.02202558 80410 57881 -> 0.02178623 80410 58177 -> 0.02188527 80410 57684 -> 0.02191781 80410 57787 -> 0.02175963 80410 57944 -> 0.02207499 80410 57712 -> 0.02175161 80410 57277 -> 0.02193258 80410 57947 -> 0.02176494 80410 57739 -> 0.02197305 80410 57736 -> 0.02175433 80410 57936 -> 0.02176700 80410 57980 -> 0.02179915 80410 57887 -> 0.02174001 done with simplex after 60 iterations 0 0.02174:-0.54422 -18.88681 -5.95658 -18.58196 2.24059 -3.50441 53.60794 1 0.02176:-0.82449 -18.64152 -6.09793 -18.35029 2.37010 -3.95521 53.62912 2 0.02179:-0.66254 -19.10578 -5.68029 -18.31361 2.40513 -3.46059 53.42867 3 0.02179:-0.58615 -18.55190 -6.26052 -18.57323 2.82257 -3.52091 53.58635 4 0.02175:-0.71170 -18.64204 -6.58412 -18.39767 2.27831 -3.36914 53.55312 5 0.02175:-0.61037 -18.58381 -5.67620 -18.32496 2.07240 -3.55151 53.42511 6 0.02177:-0.73365 -18.66076 -6.27137 -18.50911 2.30411 -2.94747 53.66347 7 0.02176:-0.56192 -18.91510 -6.14604 -17.79537 2.13352 -3.77469 53.66471 after parameter optimization -center 0.83649 10.08929 -15.16777 -translation -0.54422 -18.88681 -5.95658 -rotation -18.58196 2.24059 -3.50441 -scale 1.07216 1.07216 1.07216 -shear 0.00000 0.00000 0.00000 80410 57887 -> 0.02174001 Initial objective function val = 0.02396842 Final objective function value = 0.02174001 successful write 8mm gradient lsq7 fit, target masked: making /tmp/mritotal_3342/nu_8tmp1b.xfm [mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FL2/FL2surf/mri] [2006-01-20 18:13:00] /Applications/freesurfer/lib/mni/bin/minctracc -clobber -debug /tmp/mritotal_3342/nu_8_dxyz.mnc /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc /tmp/mritotal_3342/nu_8tmp1b.xfm -transformation /tmp/mritotal_3342/nu_8tmp1a.xfm -lsq7 -xcorr -model_mask /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc -center 0.836495 10.089290 -15.167766 -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= 0.047 18.715 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 = 1.0693 0.0488 0.0605 -0.1762 -0.0655 1.0152 0.3386 -13.8496 -0.0419 -0.3414 1.0155 -2.2422 Transform center = 0.836 10.089 -15.168 Transform rotations = -0.324 0.039 -0.061 Transform trans = -0.544 -18.887 -5.957 Transform scale = 1.072 1.072 1.072 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_3342/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_3342/nu_8tmp1a.xfm Output filename = /tmp/mritotal_3342/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 = 1.0693 0.0488 0.0605 -0.1762 -0.0655 1.0152 0.3386 -13.8496 -0.0419 -0.3414 1.0155 -2.2422 Transform center = 0.836 10.089 -15.168 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: 0.836495 10.089290 -15.167766 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 25782 -> 0.16528980 29440 25782 -> 0.16528980 29440 25762 -> 0.18205656 29440 25395 -> 0.16504754 29440 25908 -> 0.17663038 29440 25902 -> 0.15982662 29440 25777 -> 0.17530014 29440 25767 -> 0.16503549 29440 26276 -> 0.19739328 29440 25212 -> 0.15259771 29440 24634 -> 0.16481131 29440 25587 -> 0.15195091 29440 25493 -> 0.15342785 29440 25355 -> 0.14756435 29440 25072 -> 0.14487579 29440 25282 -> 0.13733479 29440 25023 -> 0.13453962 29440 25052 -> 0.13209161 29440 24670 -> 0.12782703 29440 25276 -> 0.14460360 29440 24717 -> 0.13456279 29440 24202 -> 0.14862412 29440 24672 -> 0.14516801 29440 24027 -> 0.18984444 29440 25196 -> 0.13405679 29440 25665 -> 0.14099053 29440 25496 -> 0.15667032 29440 24888 -> 0.13258958 29440 25039 -> 0.14224961 29440 24800 -> 0.12945244 29440 24942 -> 0.13627979 29440 24077 -> 0.13326520 29440 24576 -> 0.14543018 29440 24863 -> 0.12639832 29440 24869 -> 0.13898663 29440 24758 -> 0.12729488 29440 24481 -> 0.12923995 29440 24090 -> 0.13537614 29440 24930 -> 0.12722571 29440 25429 -> 0.13477057 29440 24428 -> 0.12683229 29440 24533 -> 0.12382022 29440 24340 -> 0.13102455 29440 24540 -> 0.14606199 29440 24734 -> 0.12352698 29440 24920 -> 0.13019066 29440 24594 -> 0.12526387 29440 24713 -> 0.12312628 29440 24733 -> 0.12687950 29440 24602 -> 0.12352699 29440 24328 -> 0.12002384 29440 24034 -> 0.12047370 29440 24818 -> 0.12697881 29440 24524 -> 0.12307484 29440 24284 -> 0.12331414 29440 24476 -> 0.12342455 29440 24533 -> 0.12414996 29440 24527 -> 0.12201121 29440 24417 -> 0.12319693 29440 24202 -> 0.12296623 29440 24385 -> 0.12703751 29440 24453 -> 0.12159323 29440 24621 -> 0.12214344 29440 24547 -> 0.12341803 29440 24450 -> 0.12169223 29440 24177 -> 0.12132005 29440 24260 -> 0.12123533 29440 24608 -> 0.12069695 29440 24180 -> 0.12194408 29440 24178 -> 0.11989687 29440 24013 -> 0.12095892 29440 24523 -> 0.12138648 29440 24274 -> 0.11935887 29440 24183 -> 0.12051434 29440 24222 -> 0.12024163 29440 24067 -> 0.12058305 29440 24381 -> 0.11911659 29440 24482 -> 0.12103727 29440 24331 -> 0.11950293 29440 23909 -> 0.12098549 29440 24425 -> 0.11925943 29440 24552 -> 0.12129367 29440 24187 -> 0.11913572 29440 24382 -> 0.12007423 29440 24341 -> 0.11924222 29440 24268 -> 0.11865946 29440 24236 -> 0.11960794 29440 24454 -> 0.12076303 29440 24247 -> 0.11906767 29440 24276 -> 0.12132794 29440 24316 -> 0.11879934 29440 24352 -> 0.11875530 29440 24169 -> 0.11865764 29440 24034 -> 0.11938114 29440 24202 -> 0.11825655 29440 24135 -> 0.11818557 29440 24350 -> 0.11849334 29440 24148 -> 0.11881466 29440 24247 -> 0.11805758 29440 24251 -> 0.11874266 29440 24381 -> 0.11891728 29440 24203 -> 0.11820307 29440 24169 -> 0.11882755 29440 24280 -> 0.11830480 29440 24125 -> 0.11819658 29440 24159 -> 0.11818279 29440 24264 -> 0.11824114 29440 24059 -> 0.11876906 29440 24275 -> 0.11809102 29440 24118 -> 0.11814350 done with simplex after 101 iterations 0 0.11820:-1.49096 -13.72953 -7.76172 -15.66653 1.32268 -2.30559 51.47177 1 0.11818:-1.49664 -13.50243 -8.23001 -15.48762 1.45436 -2.64494 51.54060 2 0.11824:-1.01540 -13.80179 -8.25953 -15.47583 0.90489 -2.44163 51.68366 3 0.11809:-1.42395 -13.85665 -8.07129 -15.70891 1.23634 -2.73224 51.68467 4 0.11814:-1.03395 -13.22970 -8.19344 -15.42724 0.91091 -2.76762 51.58740 5 0.11819:-1.21829 -13.51335 -8.00142 -15.66806 1.41790 -2.83171 51.44408 6 0.11820:-1.10017 -13.37822 -8.12313 -15.96628 1.21096 -2.74232 51.60680 7 0.11806:-1.34503 -13.61766 -7.94106 -15.46475 1.19235 -2.39080 51.69770 after parameter optimization -center 0.83649 10.08929 -15.16777 -translation -1.34503 -13.61766 -7.94106 -rotation -15.46475 1.19235 -2.39080 -scale 1.03395 1.03395 1.03395 -shear 0.00000 0.00000 0.00000 29440 24247 -> 0.11805758 Initial objective function val = 0.16528980 Final objective function value = 0.11805758 successful write 8mm gradient lsq9 fit, target masked: making /tmp/mritotal_3342/nu_8tmp2a.xfm [mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FL2/FL2surf/mri] [2006-01-20 18:13:05] /Applications/freesurfer/lib/mni/bin/minctracc -clobber -debug /tmp/mritotal_3342/nu_8_dxyz.mnc /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc /tmp/mritotal_3342/nu_8tmp2a.xfm -transformation /tmp/mritotal_3342/nu_8tmp1b.xfm -lsq9 -xcorr -model_mask /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc -center 0.836495 10.089290 -15.167766 -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= 0.047 18.715 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 = 1.0328 0.0358 0.0322 -1.2454 -0.0431 0.9959 0.2746 -9.3751 -0.0215 -0.2756 0.9963 -5.1981 Transform center = 0.836 10.089 -15.168 Transform rotations = -0.270 0.021 -0.042 Transform trans = -1.345 -13.618 -7.941 Transform scale = 1.034 1.034 1.034 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_3342/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_3342/nu_8tmp1b.xfm Output filename = /tmp/mritotal_3342/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 = 1.0328 0.0358 0.0322 -1.2454 -0.0431 0.9959 0.2746 -9.3752 -0.0215 -0.2756 0.9963 -5.1981 Transform center = 0.836 10.089 -15.168 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: 0.836495 10.089290 -15.167766 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 24247 -> 0.11805750 29440 24247 -> 0.11805750 29440 24232 -> 0.12915100 29440 23807 -> 0.12208112 29440 24372 -> 0.12647115 29440 24392 -> 0.11968728 29440 24239 -> 0.12354690 29440 24233 -> 0.12330275 29440 24248 -> 0.12250728 29440 24742 -> 0.12465195 29440 24328 -> 0.12725346 29440 24345 -> 0.13123697 29440 24261 -> 0.12206899 29440 24233 -> 0.12393786 29440 24171 -> 0.12957914 29440 24318 -> 0.12062144 29440 23676 -> 0.11490349 29440 23127 -> 0.11809015 29440 24084 -> 0.12397990 29440 24198 -> 0.11905240 29440 24069 -> 0.12190311 29440 24043 -> 0.11894146 29440 23977 -> 0.12421833 29440 24183 -> 0.11794929 29440 24502 -> 0.11746682 29440 24108 -> 0.11752614 29440 24309 -> 0.12041754 29440 24055 -> 0.11764885 29440 24006 -> 0.12074322 29440 24239 -> 0.11706497 29440 23896 -> 0.11603113 29440 24008 -> 0.11405715 29440 23910 -> 0.11678635 29440 24163 -> 0.11763463 29440 23927 -> 0.11438455 29440 23942 -> 0.11590867 29440 24053 -> 0.11538589 29440 23918 -> 0.11566087 29440 23935 -> 0.12145997 29440 24066 -> 0.11422620 29440 23425 -> 0.11497410 29440 23513 -> 0.11315499 29440 23149 -> 0.11860447 29440 23778 -> 0.11309300 29440 23706 -> 0.11758294 29440 23695 -> 0.11877542 29440 23880 -> 0.11299068 29440 23722 -> 0.11440476 29440 23503 -> 0.11538176 29440 23637 -> 0.11307713 29440 24177 -> 0.11606158 29440 23609 -> 0.11273696 29440 23907 -> 0.11529721 29440 23736 -> 0.11307011 29440 23881 -> 0.11561589 29440 23751 -> 0.11259209 29440 23624 -> 0.11394146 29440 23389 -> 0.11310729 29440 23305 -> 0.11419561 29440 23832 -> 0.11255679 29440 23738 -> 0.11487732 29440 23650 -> 0.11254681 29440 23881 -> 0.11529935 29440 23604 -> 0.11205500 29440 24053 -> 0.11408449 29440 23556 -> 0.11223779 29440 23619 -> 0.11396452 29440 23735 -> 0.11220025 29440 23775 -> 0.11270349 29440 23684 -> 0.11244416 29440 23499 -> 0.11301724 29440 23783 -> 0.11224098 29440 23812 -> 0.11284003 29440 23659 -> 0.11209229 29440 23615 -> 0.11297249 29440 23734 -> 0.11208061 29440 23633 -> 0.11266626 29440 23727 -> 0.11215077 29440 23533 -> 0.11224490 29440 23684 -> 0.11244019 29440 23650 -> 0.11266872 29440 23675 -> 0.11200264 29440 23650 -> 0.11254057 29440 23674 -> 0.11200068 done with simplex after 73 iterations 0 0.11200:-1.39917 -13.60389 -7.18706 -14.25250 1.63983 -2.37311 53.16843 49.08311 51.02684 1 0.11224:-1.32291 -13.35285 -7.39736 -14.27012 1.64455 -2.46937 53.01588 48.85447 51.26147 2 0.11209:-1.45938 -13.27468 -7.31764 -14.50800 1.66770 -2.54363 52.98519 49.37750 51.12036 3 0.11208:-1.39264 -13.60747 -7.18064 -14.54698 1.53536 -2.35452 52.85958 49.35279 51.23673 4 0.11220:-1.42798 -13.51753 -7.24076 -13.80517 1.54392 -2.47068 52.87251 49.24876 51.23769 5 0.11206:-1.29943 -13.35489 -7.16443 -14.51368 1.32915 -2.43101 53.25333 49.09368 50.98747 6 0.11215:-1.47189 -13.59696 -7.38204 -14.40840 1.56108 -2.19704 52.97871 49.33356 51.18884 7 0.11224:-1.36954 -13.66832 -7.29178 -14.32702 1.61096 -2.48874 52.89114 49.47462 51.04944 8 0.11200:-1.48350 -13.58831 -7.19699 -14.27235 1.52230 -2.57017 53.09187 49.07928 51.14292 9 0.11224:-1.51184 -13.35441 -7.06714 -14.26174 1.68810 -2.11632 52.97515 48.74439 50.90574 after parameter optimization -center 0.83649 10.08929 -15.16777 -translation -1.39917 -13.60389 -7.18706 -rotation -14.25250 1.63983 -2.37311 -scale 1.06337 0.98166 1.02054 -shear 0.00000 0.00000 0.00000 29440 23674 -> 0.11200068 Initial objective function val = 0.11805750 Final objective function value = 0.11200068 successful write checking z-scale: making /tmp/mritotal_3342/nu_8tmp2b.xfm [mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FL2/FL2surf/mri] [2006-01-20 18:13:09] /Applications/freesurfer/lib/mni/bin/check_scale /tmp/mritotal_3342/nu_8tmp2a.xfm /tmp/mritotal_3342/nu_8tmp2b.xfm 8mm gradient lsq9 fit, target masked: making /tmp/mritotal_3342/nu_8tmp2c.xfm [mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FL2/FL2surf/mri] [2006-01-20 18:13:09] /Applications/freesurfer/lib/mni/bin/minctracc -clobber -debug /tmp/mritotal_3342/nu_8_dxyz.mnc /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc /tmp/mritotal_3342/nu_8tmp2c.xfm -transformation /tmp/mritotal_3342/nu_8tmp2b.xfm -lsq9 -xcorr -model_mask /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc -center 0.836495 10.089290 -15.167766 -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= 0.047 18.715 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 = 1.0620 0.0352 0.0403 -1.1947 -0.0406 0.9509 0.2403 -9.4292 -0.0292 -0.2511 0.9887 -4.7998 Transform center = 0.836 10.089 -15.168 Transform rotations = -0.249 0.029 -0.041 Transform trans = -1.399 -13.604 -7.187 Transform scale = 1.063 0.982 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_3342/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_3342/nu_8tmp2b.xfm Output filename = /tmp/mritotal_3342/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 = 1.0620 0.0352 0.0403 -1.1947 -0.0406 0.9509 0.2403 -9.4292 -0.0292 -0.2511 0.9887 -4.7998 Transform center = 0.836 10.089 -15.168 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: 0.836495 10.089290 -15.167766 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 23674 -> 0.11200069 29440 23674 -> 0.11200069 29440 23660 -> 0.12741846 29440 23218 -> 0.11681964 29440 23789 -> 0.11907886 29440 23812 -> 0.11516941 29440 23673 -> 0.12100655 29440 23644 -> 0.11717422 29440 23674 -> 0.12250303 29440 24197 -> 0.11545502 29440 23745 -> 0.11982776 29440 23767 -> 0.12486833 29440 23744 -> 0.11611256 29440 23773 -> 0.11868803 29440 23795 -> 0.12268786 29440 23705 -> 0.11487310 29440 23708 -> 0.11978833 29440 23720 -> 0.11389899 29440 23664 -> 0.12225269 29440 23756 -> 0.11402693 29440 23669 -> 0.12170318 29440 23747 -> 0.11437144 29440 23807 -> 0.11686277 29440 23768 -> 0.11372808 29440 24355 -> 0.11672383 29440 24072 -> 0.11347268 29440 23913 -> 0.11702879 29440 23786 -> 0.11326136 29440 23350 -> 0.11537487 29440 23574 -> 0.11299258 29440 23704 -> 0.11632574 29440 23787 -> 0.11290199 29440 23827 -> 0.11437570 29440 23799 -> 0.11289445 29440 23798 -> 0.11385571 29440 23798 -> 0.11540128 29440 23766 -> 0.11257713 29440 23838 -> 0.11421553 29440 23751 -> 0.11261144 29440 23756 -> 0.11422141 29440 23785 -> 0.11268904 29440 23790 -> 0.11396772 29440 23775 -> 0.11259302 29440 23407 -> 0.11271569 29440 23619 -> 0.11290555 29440 23842 -> 0.11286844 29440 23847 -> 0.11370470 29440 23669 -> 0.11219783 29440 23653 -> 0.11279061 29440 23609 -> 0.11290006 29440 23749 -> 0.11232061 29440 23548 -> 0.11261358 29440 23712 -> 0.11305713 29440 23664 -> 0.11222199 29440 24013 -> 0.11302089 29440 23560 -> 0.11220895 29440 23582 -> 0.11252829 29440 23835 -> 0.11257762 29440 23643 -> 0.11231343 29440 23593 -> 0.11189201 29440 23504 -> 0.11245210 29440 23482 -> 0.11257226 29440 23485 -> 0.11213099 29440 23769 -> 0.11253101 29440 23689 -> 0.11207413 29440 23693 -> 0.11254157 29440 23611 -> 0.11205592 29440 23496 -> 0.11196076 29440 23569 -> 0.11247292 29440 23625 -> 0.11199345 done with simplex after 59 iterations 0 0.11200:-1.39917 -13.60389 -7.18706 -14.25250 1.63983 -2.37311 53.16844 49.08311 51.02683 1 0.11220:-1.40141 -13.33078 -6.73033 -13.56069 1.68802 -2.47570 53.02040 49.07414 50.72762 2 0.11221:-1.58134 -12.99784 -6.76855 -13.76647 1.71028 -2.41463 53.14788 48.97194 50.83342 3 0.11213:-1.41484 -13.07659 -7.09771 -14.07445 1.47991 -2.50548 52.99912 48.77365 50.83197 4 0.11222:-1.59396 -13.22215 -6.64746 -14.09866 1.68576 -2.45574 53.14111 49.25832 50.74245 5 0.11196:-1.26987 -13.13328 -7.04058 -14.30200 1.52602 -2.50473 53.12494 48.80574 50.90670 6 0.11189:-1.33451 -13.29532 -6.77289 -14.17201 1.36462 -2.15833 53.07568 48.96888 50.79764 7 0.11206:-1.47450 -13.14398 -6.79785 -13.99756 1.66830 -2.34786 52.89024 49.10563 50.88974 8 0.11207:-1.40684 -13.23118 -6.94556 -13.95286 1.46743 -2.48196 53.06543 49.38374 50.80695 9 0.11199:-1.41945 -13.24136 -6.84902 -14.02877 1.53311 -2.56015 53.07919 49.07267 50.99602 after parameter optimization -center 0.83649 10.08929 -15.16777 -translation -1.33451 -13.29532 -6.77289 -rotation -14.17201 1.36462 -2.15833 -scale 1.06151 0.97938 1.01595 -shear 0.00000 0.00000 0.00000 29440 23593 -> 0.11189201 Initial objective function val = 0.11200069 Final objective function value = 0.11189201 successful write final linear fit: 8mm gradient lsq9 fit, target masked: making transforms/talairach.xfm [mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FL2/FL2surf/mri] [2006-01-20 18:13:12] /Applications/freesurfer/lib/mni/bin/minctracc -clobber -debug /tmp/mritotal_3342/nu_8_dxyz.mnc /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc transforms/talairach.xfm -transformation /tmp/mritotal_3342/nu_8tmp2c.xfm -lsq9 -xcorr -model_mask /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc -center 0.836495 10.089290 -15.167766 -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= 0.047 18.715 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 = 1.0605 0.0326 0.0343 -1.1938 -0.0369 0.9491 0.2388 -9.1295 -0.0242 -0.2487 0.9848 -4.4750 Transform center = 0.836 10.089 -15.168 Transform rotations = -0.247 0.024 -0.038 Transform trans = -1.335 -13.295 -6.773 Transform scale = 1.062 0.979 1.016 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_3342/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_3342/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 = 1.0605 0.0326 0.0343 -1.1938 -0.0369 0.9491 0.2388 -9.1295 -0.0242 -0.2487 0.9848 -4.4750 Transform center = 0.836 10.089 -15.168 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: 0.836495 10.089290 -15.167766 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 23593 -> 0.11189201 29440 23593 -> 0.11189201 29440 23577 -> 0.12585923 29440 23132 -> 0.11812092 29440 23706 -> 0.12098996 29440 23729 -> 0.11426073 29440 23593 -> 0.11931435 29440 23590 -> 0.11816883 29440 23592 -> 0.12199042 29440 24121 -> 0.11556342 29440 23661 -> 0.12019048 29440 23685 -> 0.12647267 29440 23605 -> 0.11641002 29440 23679 -> 0.12039451 29440 23565 -> 0.11963245 29440 23559 -> 0.12225154 29440 23646 -> 0.11527473 29440 23580 -> 0.12824191 29440 23639 -> 0.11473873 29440 23696 -> 0.11938398 29440 23660 -> 0.11464982 29440 23681 -> 0.11883436 29440 23657 -> 0.11456586 29440 23716 -> 0.11681215 29440 24271 -> 0.11624634 29440 23823 -> 0.11882578 29440 23746 -> 0.11367563 29440 23963 -> 0.11628138 29440 23876 -> 0.11387490 29440 23199 -> 0.11802142 29440 24005 -> 0.11354556 29440 23322 -> 0.11560454 29440 23925 -> 0.11359721 29440 23867 -> 0.11495933 29440 23821 -> 0.11328933 29440 23918 -> 0.11405967 29440 23951 -> 0.11485318 29440 23731 -> 0.11308223 29440 23974 -> 0.11354110 29440 23958 -> 0.11576071 29440 23788 -> 0.11263392 29440 23738 -> 0.11435975 29440 23874 -> 0.11285532 29440 23783 -> 0.11308838 29440 23926 -> 0.11348709 29440 23740 -> 0.11347254 29440 23594 -> 0.11314977 29440 23546 -> 0.11349121 29440 23653 -> 0.11251029 29440 23537 -> 0.11280484 29440 23671 -> 0.11406072 29440 23725 -> 0.11238921 29440 23578 -> 0.11287007 29440 23800 -> 0.11303098 29440 23615 -> 0.11332887 29440 23739 -> 0.11234832 29440 23664 -> 0.11281689 29440 23570 -> 0.11350340 29440 23736 -> 0.11219985 29440 23824 -> 0.11291251 29440 23641 -> 0.11229702 29440 23477 -> 0.11224511 29440 23646 -> 0.11284009 29440 23661 -> 0.11225854 29440 23799 -> 0.11340087 29440 23602 -> 0.11220112 29440 23510 -> 0.11232844 29440 23610 -> 0.11265133 29440 23642 -> 0.11211715 29440 23521 -> 0.11207645 29440 23455 -> 0.11193271 29440 23680 -> 0.11247447 29440 23551 -> 0.11210098 29440 23527 -> 0.11194173 done with simplex after 63 iterations 0 0.11189:-1.33451 -13.29532 -6.77289 -14.17201 1.36462 -2.15833 53.07568 48.96887 50.79763 1 0.11193:-1.17235 -13.01522 -6.73445 -13.90289 1.16174 -2.26310 53.03234 48.61510 50.79856 2 0.11220:-1.05773 -13.35956 -6.51110 -13.52338 1.21352 -2.30819 52.93372 49.23645 50.86769 3 0.11226:-1.13278 -13.30820 -6.67548 -13.37447 1.24430 -2.46730 53.12185 48.98586 50.66785 4 0.11210:-1.06451 -13.19497 -6.56333 -13.97587 1.23652 -2.38594 53.17017 48.80910 50.68670 5 0.11212:-1.17054 -13.27061 -6.51779 -13.61904 1.15264 -2.18903 53.21588 48.99232 50.68918 6 0.11220:-1.12622 -13.03650 -6.51009 -13.48427 1.23547 -2.59694 53.14079 48.98292 50.78486 7 0.11194:-1.07090 -13.12246 -6.81217 -14.02415 1.09693 -2.30445 53.16366 48.79691 51.02825 8 0.11208:-0.99482 -12.92666 -6.75617 -14.04435 1.21317 -2.33652 53.02552 48.98085 50.78150 9 0.11225:-1.05601 -13.14498 -6.75089 -13.61384 1.37271 -2.37585 53.23757 48.49429 50.90083 after parameter optimization -center 0.83649 10.08929 -15.16777 -translation -1.33451 -13.29532 -6.77289 -rotation -14.17201 1.36462 -2.15833 -scale 1.06151 0.97938 1.01595 -shear 0.00000 0.00000 0.00000 29440 23593 -> 0.11189201 Initial objective function val = 0.11189201 Final objective function value = 0.11189201 successful write