[christip@varda:/home/christip/EG/EGsurf/mri] [2006-01-09 16:07:18] running: /home/christip/sw/freesurfer/lib/mni/bin/mritotal -verbose -debug -clobber -modeldir /home/christip/sw/freesurfer/lib/mni/bin/../share/mni_autoreg -protocol icbm nu.mnc transforms/talairach.xfm Loading configuration file /home/christip/sw/freesurfer/lib/mni/bin//../etc/mni_autoreg/mritotal.cfg Loading protocol default (protocol file = /home/christip/sw/freesurfer/lib/mni/bin//../etc/mni_autoreg/mritotal.default.cfg) Loading protocol icbm (protocol file = /home/christip/sw/freesurfer/lib/mni/bin//../etc/mni_autoreg/mritotal.icbm.cfg) source = nu.mnc model = /home/christip/sw/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] [christip@varda:/home/christip/EG/EGsurf/mri] [2006-01-09 16:07:18] /home/christip/sw/freesurfer/lib/mni/bin/autocrop -clobber nu.mnc /tmp/mritotal_5941/nu_crop.mnc -step 2 2 2 -extend 0,0 0,0 -25%,0 [autocrop] [christip@varda:/home/christip/EG/EGsurf/mri] [2006-01-09 16:07:18] /home/christip/sw/freesurfer/lib/mni/bin/mincresample -clobber nu.mnc /tmp/mritotal_5941/nu_crop.mnc -start -121.8 -128 -64 -step 2 2 2 -nelements 128 128 96 Transforming slices:................................................................................................................................Done [mritotal] [christip@varda:/home/christip/EG/EGsurf/mri] [2006-01-09 16:07:19] /home/christip/sw/freesurfer/lib/mni/bin/volume_cog /tmp/mritotal_5941/nu_crop.mnc | tail -1 Centroid of input volume: -8.575884 7.116868 -26.810989 Zero-padding data: [mritotal] [christip@varda:/home/christip/EG/EGsurf/mri] [2006-01-09 16:07:20] /home/christip/sw/freesurfer/lib/mni/bin/autocrop -clobber /tmp/mritotal_5941/nu_crop.mnc /tmp/mritotal_5941/nu_pad.mnc -expand 22 22 22 [autocrop] [christip@varda:/home/christip/EG/EGsurf/mri] [2006-01-09 16:07:20] /home/christip/sw/freesurfer/lib/mni/bin/mincreshape -clobber /tmp/mritotal_5941/nu_crop.mnc /tmp/mritotal_5941/nu_pad.mnc -start -11,-11,-11 -count 150,150,118 Copying chunks:......................................................................................................................................................Done. Intensity blurring data: [mritotal] [christip@varda:/home/christip/EG/EGsurf/mri] [2006-01-09 16:07:20] /home/christip/sw/freesurfer/lib/mni/bin/mincblur -clobber -debug /tmp/mritotal_5941/nu_pad.mnc /tmp/mritotal_5941/tmp_16 -fwhm 16 ===== Debugging information from /home/christip/sw/freesurfer/lib/mni/bin/mincblur ===== Data filename = /tmp/mritotal_5941/nu_pad.mnc Output basename = /tmp/mritotal_5941/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 254.999696 before blur min/max = 0.000000 254.999695 after blur min/max = -0.000005 114.182709 Making byte volume... [mritotal] [christip@varda:/home/christip/EG/EGsurf/mri] [2006-01-09 16:07:26] /home/christip/sw/freesurfer/lib/mni/bin/autocrop -clobber /tmp/mritotal_5941/tmp_16_blur.mnc /tmp/mritotal_5941/nu_16_blur.mnc -expand -44 -44 -44 [autocrop] [christip@varda:/home/christip/EG/EGsurf/mri] [2006-01-09 16:07:26] /home/christip/sw/freesurfer/lib/mni/bin/mincreshape -clobber /tmp/mritotal_5941/tmp_16_blur.mnc /tmp/mritotal_5941/nu_16_blur.mnc -start 22,22,22 -count 106,106,74 Copying chunks:..........................................................................................................Done. Gradient blurring data: [mritotal] [christip@varda:/home/christip/EG/EGsurf/mri] [2006-01-09 16:07:26] /home/christip/sw/freesurfer/lib/mni/bin/mincblur -clobber -debug /tmp/mritotal_5941/nu_pad.mnc /tmp/mritotal_5941/tmp_8 -fwhm 8 -gradient Transforming slices:......................................................................................................................................................Done ===== Debugging information from /home/christip/sw/freesurfer/lib/mni/bin/mincblur ===== Data filename = /tmp/mritotal_5941/nu_pad.mnc Output basename = /tmp/mritotal_5941/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 254.999696 before blur min/max = 0.000000 254.999695 after blur min/max = -0.000012 163.191864 Making byte volume... Making byte volume dx...dx: min = -17.271282, max = 15.649552 Making byte volume dy...dy: min = -12.861006, max = 10.949205 Making byte volume dz...dz: min = -16.431164, max = 12.921789 [mritotal] [christip@varda:/home/christip/EG/EGsurf/mri] [2006-01-09 16:07:34] /home/christip/sw/freesurfer/lib/mni/bin/autocrop -clobber /tmp/mritotal_5941/tmp_8_blur.mnc /tmp/mritotal_5941/nu_8_blur.mnc -expand -34 -34 -34 [autocrop] [christip@varda:/home/christip/EG/EGsurf/mri] [2006-01-09 16:07:34] /home/christip/sw/freesurfer/lib/mni/bin/mincreshape -clobber /tmp/mritotal_5941/tmp_8_blur.mnc /tmp/mritotal_5941/nu_8_blur.mnc -start 17,17,17 -count 116,116,84 Copying chunks:....................................................................................................................Done. [mritotal] [christip@varda:/home/christip/EG/EGsurf/mri] [2006-01-09 16:07:35] /home/christip/sw/freesurfer/lib/mni/bin/autocrop -clobber /tmp/mritotal_5941/tmp_8_dxyz.mnc /tmp/mritotal_5941/nu_8_dxyz.mnc -expand -34 -34 -34 [autocrop] [christip@varda:/home/christip/EG/EGsurf/mri] [2006-01-09 16:07:35] /home/christip/sw/freesurfer/lib/mni/bin/mincreshape -clobber /tmp/mritotal_5941/tmp_8_dxyz.mnc /tmp/mritotal_5941/nu_8_dxyz.mnc -start 17,17,17 -count 116,116,84 Copying chunks:....................................................................................................................Done. 16mm intensity lsq7 fit, no masks: making /tmp/mritotal_5941/nu_16.xfm [mritotal] [christip@varda:/home/christip/EG/EGsurf/mri] [2006-01-09 16:07:35] /home/christip/sw/freesurfer/lib/mni/bin/minctracc -clobber -debug /tmp/mritotal_5941/nu_16_blur.mnc /home/christip/sw/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_16_blur.mnc /tmp/mritotal_5941/nu_16.xfm -est_translations -lsq7 -xcorr -center -8.575884 7.116868 -26.810989 -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= -0.000 114.183 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 8.9040 0.0000 1.0000 0.0000 -24.7082 0.0000 0.0000 1.0000 36.2656 Transform center = -8.576 7.117 -26.811 Transform rotations = 0.000 0.000 0.000 Transform trans = 8.904 -24.708 36.266 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 /home/christip/sw/freesurfer/lib/mni/bin/minctracc ===== Data filename = /tmp/mritotal_5941/nu_16_blur.mnc Model filename = /home/christip/sw/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_5941/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 = -8.576 7.117 -26.811 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: -8.575884 7.116868 -26.810989 using PAT to get initial parameters: will try to get: [trans] COG of v1 forced: -8.575884 7.116868 -26.810989 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: 0.328095 -17.591330 9.454627 [trans] = 8.903978 -24.708199 36.265616 Only center & trans required, now returning from init_transformation Transform center = -8.576 7.117 -26.811 Transform rots = 0.000 0.000 0.000 Transform trans = 8.904 -24.708 36.266 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 45639 -> 0.05099371 68585 45639 -> 0.05099371 68585 40373 -> 0.09212545 68585 43211 -> 0.04510658 68585 45566 -> 0.05195214 68585 46676 -> 0.04617633 68585 44787 -> 0.05644893 68585 43518 -> 0.05604841 68585 56115 -> 0.09280854 68585 14430 -> 0.16643988 68585 52328 -> 0.05761265 68585 44554 -> 0.09566788 68585 43660 -> 0.06179931 68585 46496 -> 0.06054145 68585 46935 -> 0.04897788 68585 30041 -> 0.09382276 68585 50128 -> 0.04633863 68585 45771 -> 0.04494024 68585 43807 -> 0.05452919 68585 45490 -> 0.05096371 68585 48078 -> 0.04082805 68585 49327 -> 0.05661820 68585 46791 -> 0.05309466 68585 46690 -> 0.04429302 68585 44658 -> 0.04772466 68585 46895 -> 0.04317981 68585 44952 -> 0.05251857 68585 46195 -> 0.04305185 68585 42373 -> 0.05060041 68585 48596 -> 0.04301426 68585 45232 -> 0.03946787 68585 42998 -> 0.05557527 68585 50259 -> 0.04559639 68585 46016 -> 0.04160072 68585 46503 -> 0.03720938 68585 43978 -> 0.05293357 68585 45984 -> 0.03779707 68585 46458 -> 0.03627232 68585 45658 -> 0.04043918 68585 44745 -> 0.03800409 68585 42495 -> 0.03169404 68585 38402 -> 0.03546328 68585 45194 -> 0.03014412 68585 44420 -> 0.03263549 68585 42626 -> 0.03767049 68585 44504 -> 0.03938803 68585 44763 -> 0.03326424 68585 44800 -> 0.03185442 68585 43116 -> 0.02796910 68585 41367 -> 0.03087945 68585 47745 -> 0.04439620 68585 43621 -> 0.03127903 68585 41555 -> 0.03565627 68585 40573 -> 0.03306057 68585 44945 -> 0.03712461 68585 42548 -> 0.03027478 68585 41627 -> 0.02695396 68585 39865 -> 0.03065671 68585 45958 -> 0.03372670 68585 41988 -> 0.02877014 68585 41081 -> 0.03587342 68585 44001 -> 0.02867411 68585 43795 -> 0.02792667 68585 42813 -> 0.02715583 68585 43825 -> 0.02606727 68585 44232 -> 0.02890172 68585 40769 -> 0.02883685 68585 41949 -> 0.02664848 68585 44129 -> 0.02487068 68585 45240 -> 0.02609271 68585 41986 -> 0.02589769 68585 42444 -> 0.02664090 68585 41585 -> 0.02382517 68585 40498 -> 0.02576257 68585 42505 -> 0.02399807 68585 43284 -> 0.02816807 68585 42153 -> 0.02477449 68585 43282 -> 0.02177060 68585 43893 -> 0.02063578 68585 43267 -> 0.02336547 68585 41933 -> 0.02281153 68585 43377 -> 0.02150183 68585 41135 -> 0.02183982 68585 42966 -> 0.01804263 68585 43389 -> 0.01600789 68585 42961 -> 0.02025889 68585 44406 -> 0.01791025 68585 42154 -> 0.02076479 68585 44276 -> 0.01824954 68585 45805 -> 0.01841524 68585 44121 -> 0.01734498 68585 45658 -> 0.02119153 68585 43217 -> 0.01797150 68585 44287 -> 0.01588298 68585 44715 -> 0.01906986 68585 45627 -> 0.01442005 68585 47247 -> 0.01535486 68585 42481 -> 0.01487179 68585 43934 -> 0.01689867 68585 44948 -> 0.01532047 68585 43616 -> 0.01420915 68585 43021 -> 0.01805401 68585 44144 -> 0.01527515 68585 44318 -> 0.01422212 68585 45072 -> 0.01315054 68585 46102 -> 0.01546900 68585 44343 -> 0.01217197 68585 44480 -> 0.01365286 68585 43355 -> 0.01271856 68585 44277 -> 0.01656959 68585 44116 -> 0.01301594 68585 46204 -> 0.01535999 68585 43408 -> 0.01290833 68585 42404 -> 0.01194148 68585 40755 -> 0.01443052 68585 43324 -> 0.01387196 68585 43843 -> 0.01196130 68585 44275 -> 0.01399112 68585 43550 -> 0.01213665 68585 42116 -> 0.01341431 68585 44311 -> 0.01195414 68585 43046 -> 0.01152910 68585 42459 -> 0.01330908 68585 43753 -> 0.01034498 68585 44014 -> 0.01031210 68585 44035 -> 0.01201480 68585 42818 -> 0.01197795 68585 43380 -> 0.01015762 68585 43286 -> 0.01067276 68585 42661 -> 0.01310867 68585 43686 -> 0.01083198 68585 44202 -> 0.01099314 68585 43205 -> 0.01186015 68585 42405 -> 0.00999029 68585 41354 -> 0.01103735 68585 44565 -> 0.00991821 68585 45904 -> 0.01119742 68585 44032 -> 0.01085718 68585 44716 -> 0.01142536 68585 44200 -> 0.01019900 68585 43397 -> 0.01069035 68585 43253 -> 0.01170025 68585 43844 -> 0.00995106 68585 43607 -> 0.00969486 68585 43351 -> 0.01082307 68585 44137 -> 0.01011745 68585 43432 -> 0.00915468 68585 43146 -> 0.00937610 68585 43103 -> 0.00941910 68585 43795 -> 0.00988205 68585 42958 -> 0.00981946 68585 44833 -> 0.01005937 68585 42989 -> 0.00940613 68585 43091 -> 0.00957712 68585 42005 -> 0.00952174 68585 42317 -> 0.01016430 68585 43403 -> 0.00930655 68585 43318 -> 0.00948015 68585 42562 -> 0.01005154 68585 43325 -> 0.00918970 68585 43036 -> 0.00963477 68585 43090 -> 0.00921331 68585 44432 -> 0.00981489 68585 42625 -> 0.00915486 68585 43040 -> 0.00967182 68585 43225 -> 0.00916708 68585 43246 -> 0.00934726 68585 43380 -> 0.00895124 68585 43557 -> 0.00911508 68585 43211 -> 0.00922545 68585 42983 -> 0.00904346 68585 43119 -> 0.00917837 68585 43199 -> 0.00912518 68585 42952 -> 0.00909386 68585 43146 -> 0.00922101 68585 43109 -> 0.00899332 68585 42981 -> 0.00898205 68585 43644 -> 0.00928872 68585 42888 -> 0.00895793 68585 42681 -> 0.00918392 68585 43249 -> 0.00896906 68585 42944 -> 0.00886520 68585 42809 -> 0.00903243 68585 43211 -> 0.00902942 68585 43263 -> 0.00910600 68585 43046 -> 0.00890681 68585 42967 -> 0.00908822 68585 43149 -> 0.00890878 68585 43076 -> 0.00881524 68585 43051 -> 0.00885707 68585 43228 -> 0.00909793 68585 43042 -> 0.00886725 68585 42877 -> 0.00899139 68585 43166 -> 0.00887894 68585 43336 -> 0.00876771 68585 43563 -> 0.00873794 68585 42897 -> 0.00892145 68585 43018 -> 0.00884329 68585 43096 -> 0.00879933 68585 43214 -> 0.00874944 68585 43104 -> 0.00871160 68585 43073 -> 0.00872181 68585 43248 -> 0.00870171 68585 43362 -> 0.00873541 68585 43425 -> 0.00880693 68585 43469 -> 0.00871301 68585 43537 -> 0.00868054 68585 43766 -> 0.00874276 68585 43203 -> 0.00874971 68585 43576 -> 0.00871361 68585 43566 -> 0.00877371 68585 43296 -> 0.00869945 68585 43583 -> 0.00869581 done with simplex after 204 iterations 0 0.00871: 9.10500 -9.67871 5.03474 -32.10827 -2.05249 2.36214 54.10399 1 0.00871: 8.64994 -8.39735 5.06524 -30.89435 -1.76262 1.91853 53.76764 2 0.00870: 8.49897 -8.69944 4.70589 -30.55206 -1.65089 2.09383 54.05931 3 0.00874: 8.59949 -9.49377 5.62983 -31.41583 -1.45867 2.53662 53.84953 4 0.00871: 9.04562 -9.05275 5.40274 -30.66164 -1.88623 2.45805 54.02457 5 0.00870: 9.07829 -9.65465 4.93236 -30.96259 -2.41019 2.37097 54.09815 6 0.00868: 8.98684 -9.14928 5.69477 -30.63751 -1.52997 1.73670 53.97486 7 0.00870: 8.67632 -8.95404 4.78497 -31.19007 -1.24711 2.04771 53.99167 after parameter optimization -center -8.57588 7.11687 -26.81099 -translation 8.98684 -9.14928 5.69477 -rotation -30.63751 -1.52997 1.73670 -scale 1.07950 1.07950 1.07950 -shear 0.00000 0.00000 0.00000 68585 43537 -> 0.00868054 Initial objective function val = 0.05099371 Final objective function value = 0.00868054 successful write 8mm intensity lsq7 fit, no masks: making /tmp/mritotal_5941/nu_8tmp1a.xfm [mritotal] [christip@varda:/home/christip/EG/EGsurf/mri] [2006-01-09 16:07:54] /home/christip/sw/freesurfer/lib/mni/bin/minctracc -clobber -debug /tmp/mritotal_5941/nu_8_blur.mnc /home/christip/sw/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_blur.mnc /tmp/mritotal_5941/nu_8tmp1a.xfm -transformation /tmp/mritotal_5941/nu_16.xfm -lsq7 -xcorr -center -8.575884 7.116868 -26.810989 -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= -0.000 163.192 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 = 1.0786 -0.0135 -0.0415 8.6453 0.0327 0.9288 0.5491 6.3600 0.0288 -0.5499 0.9285 7.9381 Transform center = -8.576 7.117 -26.811 Transform rotations = -0.535 -0.027 0.030 Transform trans = 8.987 -9.149 5.695 Transform scale = 1.079 1.079 1.079 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 /home/christip/sw/freesurfer/lib/mni/bin/minctracc ===== Data filename = /tmp/mritotal_5941/nu_8_blur.mnc Model filename = /home/christip/sw/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_blur.mnc Data mask filename = Model mask filename = Input xform name = /tmp/mritotal_5941/nu_16.xfm Output filename = /tmp/mritotal_5941/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 = 1.0786 -0.0135 -0.0415 8.6453 0.0327 0.9288 0.5491 6.3600 0.0288 -0.5499 0.9285 7.9381 Transform center = -8.576 7.117 -26.811 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: -8.575884 7.116868 -26.810989 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 54852 -> 0.02678547 80410 54852 -> 0.02678547 80410 53386 -> 0.03429403 80410 53100 -> 0.03064284 80410 55862 -> 0.03306828 80410 54869 -> 0.02760373 80410 54331 -> 0.02940238 80410 54220 -> 0.02881335 80410 57965 -> 0.04088827 80410 48037 -> 0.04803212 80410 56630 -> 0.03178756 80410 54832 -> 0.03396273 80410 55173 -> 0.02948960 80410 54031 -> 0.02638991 80410 53083 -> 0.03107994 80410 51396 -> 0.03170991 80410 53111 -> 0.02795624 80410 55866 -> 0.02976871 80410 55260 -> 0.02740674 80410 53384 -> 0.02966014 80410 54910 -> 0.02746663 80410 53766 -> 0.02766514 80410 54248 -> 0.02618758 80410 53688 -> 0.02954732 80410 55945 -> 0.02585343 80410 56908 -> 0.02758463 80410 54758 -> 0.02794969 80410 54422 -> 0.02624427 80410 54747 -> 0.02613384 80410 54915 -> 0.02496733 80410 54875 -> 0.02621336 80410 54208 -> 0.02594749 80410 54516 -> 0.02692205 80410 54913 -> 0.02558802 80410 55433 -> 0.02694638 80410 54470 -> 0.02539569 80410 54530 -> 0.02534155 80410 55161 -> 0.02680950 80410 54773 -> 0.02524478 80410 54779 -> 0.02575738 80410 55595 -> 0.02619696 80410 54594 -> 0.02515185 80410 53315 -> 0.02570094 80410 54166 -> 0.02619378 80410 54741 -> 0.02511585 80410 55890 -> 0.02575067 80410 54039 -> 0.02511541 80410 54452 -> 0.02580705 80410 54824 -> 0.02508200 80410 54659 -> 0.02512589 80410 54122 -> 0.02569234 80410 54766 -> 0.02501085 80410 54644 -> 0.02496362 80410 54581 -> 0.02542068 80410 54474 -> 0.02510470 80410 54489 -> 0.02527050 80410 54682 -> 0.02489974 80410 54688 -> 0.02498737 80410 55378 -> 0.02486670 80410 55973 -> 0.02506623 80410 54909 -> 0.02499387 80410 54943 -> 0.02506552 80410 54938 -> 0.02484423 80410 54957 -> 0.02483022 80410 54940 -> 0.02529243 80410 54663 -> 0.02528468 80410 54929 -> 0.02479425 80410 55165 -> 0.02507675 80410 54843 -> 0.02482088 80410 54828 -> 0.02501713 80410 54951 -> 0.02483919 80410 55292 -> 0.02490266 80410 55143 -> 0.02477769 80410 55178 -> 0.02503483 80410 54890 -> 0.02479139 80410 54491 -> 0.02489495 80410 55174 -> 0.02475450 80410 54985 -> 0.02481922 done with simplex after 69 iterations 0 0.02482: 8.74233 -9.47836 2.26067 -28.60569 -1.84169 1.71895 54.63404 1 0.02484: 8.75852 -9.28099 1.51356 -28.20055 -1.64225 1.47019 54.79215 2 0.02479: 8.61338 -8.88917 1.72143 -28.71727 -1.78363 1.31057 54.93586 3 0.02479: 8.70857 -9.02969 1.78363 -28.26288 -1.59502 0.58784 54.79219 4 0.02482: 8.68122 -9.07314 1.46938 -29.04083 -1.24332 1.12150 54.75415 5 0.02483: 9.08839 -9.65108 1.38742 -28.63002 -2.36793 1.71296 54.78183 6 0.02478: 8.58565 -9.61129 1.78826 -28.44678 -1.50670 1.19171 54.79149 7 0.02475: 8.79874 -9.58476 1.78578 -28.48967 -1.63823 1.07703 54.90938 after parameter optimization -center -8.57588 7.11687 -26.81099 -translation 8.79874 -9.58476 1.78578 -rotation -28.48967 -1.63823 1.07703 -scale 1.09819 1.09819 1.09819 -shear 0.00000 0.00000 0.00000 80410 55174 -> 0.02475450 Initial objective function val = 0.02678547 Final objective function value = 0.02475450 successful write 8mm gradient lsq7 fit, target masked: making /tmp/mritotal_5941/nu_8tmp1b.xfm [mritotal] [christip@varda:/home/christip/EG/EGsurf/mri] [2006-01-09 16:08:05] /home/christip/sw/freesurfer/lib/mni/bin/minctracc -clobber -debug /tmp/mritotal_5941/nu_8_dxyz.mnc /home/christip/sw/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc /tmp/mritotal_5941/nu_8tmp1b.xfm -transformation /tmp/mritotal_5941/nu_8tmp1a.xfm -lsq7 -xcorr -model_mask /home/christip/sw/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc -center -8.575884 7.116868 -26.810989 -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= 0.048 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 = 1.0975 -0.0032 -0.0374 8.6542 0.0206 0.9653 0.5232 4.8672 0.0314 -0.5236 0.9648 4.8380 Transform center = -8.576 7.117 -26.811 Transform rotations = -0.497 -0.029 0.019 Transform trans = 8.799 -9.585 1.786 Transform scale = 1.098 1.098 1.098 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 /home/christip/sw/freesurfer/lib/mni/bin/minctracc ===== Data filename = /tmp/mritotal_5941/nu_8_dxyz.mnc Model filename = /home/christip/sw/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc Data mask filename = Model mask filename = /home/christip/sw/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc Input xform name = /tmp/mritotal_5941/nu_8tmp1a.xfm Output filename = /tmp/mritotal_5941/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 = 1.0975 -0.0032 -0.0374 8.6542 0.0206 0.9653 0.5232 4.8672 0.0314 -0.5236 0.9648 4.8380 Transform center = -8.576 7.117 -26.811 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: -8.575884 7.116868 -26.810989 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 23247 -> 0.11921287 29440 23247 -> 0.11921287 29440 23248 -> 0.12528235 29440 22831 -> 0.12405353 29440 23478 -> 0.13530323 29440 23272 -> 0.11095246 29440 23251 -> 0.12583525 29440 23247 -> 0.12037960 29440 23811 -> 0.14179139 29440 22647 -> 0.11569243 29440 22765 -> 0.10819674 29440 22403 -> 0.11151736 29440 22858 -> 0.10780641 29440 22678 -> 0.10737358 29440 22659 -> 0.10944690 29440 23060 -> 0.10984283 29440 22543 -> 0.10256267 29440 22230 -> 0.11118826 29440 22376 -> 0.10586482 29440 22949 -> 0.10319889 29440 22075 -> 0.11111049 29440 23019 -> 0.10444253 29440 22400 -> 0.10097115 29440 22006 -> 0.10672184 29440 22663 -> 0.10012987 29440 22668 -> 0.11238398 29440 22553 -> 0.10976260 29440 22740 -> 0.10133911 29440 22687 -> 0.10239810 29440 23046 -> 0.10533047 29440 22841 -> 0.10052022 29440 22320 -> 0.09908311 29440 21973 -> 0.10617078 29440 22287 -> 0.10817505 29440 22763 -> 0.09883582 29440 22687 -> 0.10059466 29440 22556 -> 0.10518233 29440 22658 -> 0.09863855 29440 22542 -> 0.09845378 29440 22469 -> 0.10295830 29440 22941 -> 0.10546679 29440 22476 -> 0.09784078 29440 22557 -> 0.10008756 29440 22285 -> 0.10053889 29440 22737 -> 0.09803078 29440 22514 -> 0.09982455 29440 22601 -> 0.10083219 29440 22577 -> 0.09782460 29440 22668 -> 0.09973583 29440 22630 -> 0.09757267 29440 22934 -> 0.09906051 29440 22754 -> 0.09764846 29440 22493 -> 0.09767432 29440 22535 -> 0.09810603 29440 22797 -> 0.10052040 29440 22568 -> 0.09722170 29440 22673 -> 0.09895864 29440 22579 -> 0.09738940 29440 22450 -> 0.09665985 29440 22309 -> 0.09685788 29440 22661 -> 0.09844574 29440 22551 -> 0.09720708 29440 22590 -> 0.09770662 29440 22586 -> 0.09707022 29440 22675 -> 0.09830126 29440 22547 -> 0.09711378 29440 22337 -> 0.09786091 29440 22655 -> 0.09704259 29440 22490 -> 0.09731994 29440 22528 -> 0.09669689 29440 22618 -> 0.09752084 29440 22530 -> 0.09697344 29440 22532 -> 0.09684391 29440 22538 -> 0.09660812 29440 22544 -> 0.09688886 29440 22556 -> 0.09663979 29440 22500 -> 0.09645692 29440 22451 -> 0.09669720 29440 22361 -> 0.09630091 29440 22204 -> 0.09684729 29440 22460 -> 0.09616127 29440 22425 -> 0.09626150 29440 22439 -> 0.09677717 29440 22460 -> 0.09651374 29440 22423 -> 0.09624171 29440 22489 -> 0.09605876 29440 22503 -> 0.09593312 29440 22382 -> 0.09626149 29440 22341 -> 0.09605081 29440 22386 -> 0.09593849 29440 22327 -> 0.09586574 29440 22242 -> 0.09630655 29440 22446 -> 0.09567815 29440 22486 -> 0.09574083 29440 22446 -> 0.09578986 29440 22405 -> 0.09577626 29440 22366 -> 0.09563056 29440 22318 -> 0.09594303 29440 22480 -> 0.09572870 29440 22458 -> 0.09541501 29440 22501 -> 0.09564021 29440 22334 -> 0.09536677 29440 22237 -> 0.09573325 29440 22514 -> 0.09573638 29440 22415 -> 0.09588522 29440 22435 -> 0.09553609 29440 22452 -> 0.09524101 29440 22476 -> 0.09528835 29440 22339 -> 0.09576870 29440 22466 -> 0.09541028 29440 22368 -> 0.09547745 29440 22378 -> 0.09544334 29440 22465 -> 0.09509975 29440 22514 -> 0.09538223 29440 22402 -> 0.09495699 29440 22388 -> 0.09482406 29440 22467 -> 0.09549441 29440 22394 -> 0.09525762 29440 22467 -> 0.09539301 29440 22383 -> 0.09540257 29440 22362 -> 0.09527257 29440 22428 -> 0.09524783 29440 22344 -> 0.09511566 29440 22473 -> 0.09514727 29440 22477 -> 0.09556071 29440 22390 -> 0.09505553 29440 22443 -> 0.09492192 29440 22412 -> 0.09497524 29440 22390 -> 0.09473904 29440 22324 -> 0.09457769 29440 22325 -> 0.09503302 29440 22446 -> 0.09486092 29440 22299 -> 0.09462696 29440 22364 -> 0.09452284 29440 22348 -> 0.09454178 29440 22468 -> 0.09475160 29440 22367 -> 0.09495688 29440 22392 -> 0.09486289 29440 22301 -> 0.09451353 29440 22238 -> 0.09494922 29440 22390 -> 0.09466732 29440 22231 -> 0.09453711 done with simplex after 133 iterations 0 0.09475: 9.81680 -6.91728 0.24111 -24.28456 -3.15158 1.31903 53.96875 1 0.09463: 9.89274 -6.55332 0.28251 -24.27390 -3.12462 1.20197 53.71409 2 0.09451: 9.76775 -6.61678 0.34092 -24.15692 -2.87097 1.50524 53.64809 3 0.09467: 9.77197 -6.79546 0.35966 -24.45825 -3.08246 1.36118 53.72938 4 0.09454: 9.58702 -6.24556 0.28883 -24.07420 -2.96071 1.32278 53.78420 5 0.09458: 9.87924 -6.63813 0.12125 -24.35659 -3.06910 1.53737 53.78710 6 0.09452: 9.82556 -6.68315 0.30383 -24.37015 -2.93176 1.40366 53.82065 7 0.09482: 9.67743 -6.83639 0.18123 -24.54327 -2.91177 1.04546 53.83962 after parameter optimization -center -8.57588 7.11687 -26.81099 -translation 9.76775 -6.61678 0.34092 -rotation -24.15692 -2.87097 1.50524 -scale 1.07296 1.07296 1.07296 -shear 0.00000 0.00000 0.00000 29440 22301 -> 0.09451353 Initial objective function val = 0.11921287 Final objective function value = 0.09451353 successful write 8mm gradient lsq9 fit, target masked: making /tmp/mritotal_5941/nu_8tmp2a.xfm [mritotal] [christip@varda:/home/christip/EG/EGsurf/mri] [2006-01-09 16:08:14] /home/christip/sw/freesurfer/lib/mni/bin/minctracc -clobber -debug /tmp/mritotal_5941/nu_8_dxyz.mnc /home/christip/sw/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc /tmp/mritotal_5941/nu_8tmp2a.xfm -transformation /tmp/mritotal_5941/nu_8tmp1b.xfm -lsq9 -xcorr -model_mask /home/christip/sw/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc -center -8.575884 7.116868 -26.810989 -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= 0.048 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 = 1.0712 -0.0037 -0.0606 8.7818 0.0281 0.9792 0.4377 5.5064 0.0537 -0.4385 0.9778 3.3269 Transform center = -8.576 7.117 -26.811 Transform rotations = -0.422 -0.050 0.026 Transform trans = 9.768 -6.617 0.341 Transform scale = 1.073 1.073 1.073 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 /home/christip/sw/freesurfer/lib/mni/bin/minctracc ===== Data filename = /tmp/mritotal_5941/nu_8_dxyz.mnc Model filename = /home/christip/sw/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc Data mask filename = Model mask filename = /home/christip/sw/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc Input xform name = /tmp/mritotal_5941/nu_8tmp1b.xfm Output filename = /tmp/mritotal_5941/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 = 1.0712 -0.0037 -0.0606 8.7818 0.0281 0.9792 0.4377 5.5064 0.0537 -0.4385 0.9778 3.3269 Transform center = -8.576 7.117 -26.811 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: -8.575884 7.116868 -26.810989 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 22301 -> 0.09451354 29440 22301 -> 0.09451354 29440 22302 -> 0.10305750 29440 21840 -> 0.09755524 29440 22524 -> 0.10093124 29440 22431 -> 0.09758864 29440 22306 -> 0.10079658 29440 22318 -> 0.09649816 29440 22301 -> 0.10742749 29440 22765 -> 0.09423068 29440 22455 -> 0.08883291 29440 22418 -> 0.08680514 29440 22471 -> 0.09387540 29440 22431 -> 0.09364091 29440 22222 -> 0.09223259 29440 22410 -> 0.09136713 29440 22272 -> 0.09001883 29440 22937 -> 0.08523165 29440 23459 -> 0.09113371 29440 22633 -> 0.08246532 29440 22796 -> 0.08511262 29440 22695 -> 0.08028866 29440 22882 -> 0.07991703 29440 22253 -> 0.07938274 29440 21983 -> 0.08430178 29440 22573 -> 0.07728986 29440 22631 -> 0.08419942 29440 22861 -> 0.08903049 29440 22775 -> 0.08103546 29440 22995 -> 0.07726265 29440 23358 -> 0.08650516 29440 22472 -> 0.08563715 29440 22866 -> 0.07883226 29440 23001 -> 0.07722848 29440 23285 -> 0.08902018 29440 23070 -> 0.08714256 29440 22620 -> 0.07750093 29440 22530 -> 0.07529408 29440 22310 -> 0.08522455 29440 22821 -> 0.07765687 29440 22703 -> 0.07964397 29440 22523 -> 0.07621071 29440 22694 -> 0.08070253 29440 22694 -> 0.07457648 29440 23207 -> 0.07769444 29440 22686 -> 0.07506026 29440 22211 -> 0.08016553 29440 22969 -> 0.07345139 29440 22647 -> 0.07880491 29440 22776 -> 0.07354821 29440 22883 -> 0.07405815 29440 22992 -> 0.07823131 29440 22677 -> 0.07328822 29440 22489 -> 0.07312611 29440 22220 -> 0.07904103 29440 22369 -> 0.07928137 29440 22849 -> 0.07287056 29440 22919 -> 0.07757743 29440 22625 -> 0.07246982 29440 22955 -> 0.07797990 29440 22631 -> 0.07233211 29440 22777 -> 0.07706897 29440 22705 -> 0.07233862 29440 22781 -> 0.07344197 29440 22564 -> 0.07543063 29440 22799 -> 0.07224021 29440 22676 -> 0.07160432 29440 22618 -> 0.07362308 29440 22418 -> 0.07305958 29440 22531 -> 0.07430212 29440 22715 -> 0.07182273 29440 22637 -> 0.07256210 29440 22836 -> 0.07415016 29440 22582 -> 0.07177030 29440 22967 -> 0.07265214 29440 22558 -> 0.07307865 29440 22775 -> 0.07165167 29440 22400 -> 0.07296327 29440 22822 -> 0.07167675 29440 22773 -> 0.07376581 29440 22669 -> 0.07146312 29440 22791 -> 0.07374506 29440 22666 -> 0.07142197 29440 22701 -> 0.07194290 29440 22791 -> 0.07129185 29440 22879 -> 0.07269804 29440 22622 -> 0.07146843 29440 22700 -> 0.07254990 29440 22700 -> 0.07119649 29440 22687 -> 0.07166280 29440 22845 -> 0.07126772 29440 22606 -> 0.07124856 29440 22726 -> 0.07153758 29440 22617 -> 0.07115171 29440 22545 -> 0.07232373 29440 22714 -> 0.07132057 29440 22663 -> 0.07145970 29440 22780 -> 0.07163560 29440 22660 -> 0.07095891 29440 22726 -> 0.07127730 29440 22744 -> 0.07146397 29440 22684 -> 0.07104210 29440 22741 -> 0.07111505 29440 22703 -> 0.07164638 29440 22712 -> 0.07095832 29440 22607 -> 0.07106548 29440 22650 -> 0.07151700 29440 22707 -> 0.07087991 29440 22498 -> 0.07154100 29440 22756 -> 0.07088120 29440 22766 -> 0.07132298 29440 22649 -> 0.07083148 29440 22669 -> 0.07123195 29440 22694 -> 0.07092600 29440 22756 -> 0.07145610 29440 22657 -> 0.07082655 29440 22616 -> 0.07122098 29440 22713 -> 0.07087887 29440 22775 -> 0.07127701 29440 22653 -> 0.07081512 29440 22700 -> 0.07090444 done with simplex after 110 iterations 0 0.07088: 9.55357 -6.32861 -2.40981 -23.84275 -2.87668 1.55295 50.90815 55.42720 58.07460 1 0.07088: 9.66868 -6.43092 -2.16725 -23.73452 -2.89415 1.61575 50.94270 55.27322 57.71227 2 0.07082: 9.48154 -6.13763 -2.11303 -23.71571 -2.74674 1.46166 50.87020 55.28910 57.74326 3 0.07096: 9.51284 -6.19414 -2.17491 -23.77442 -2.75129 1.69789 50.99971 55.29685 57.80654 4 0.07088: 9.56240 -6.43934 -1.94134 -23.55597 -2.85203 1.49035 50.94654 55.33133 57.78061 5 0.07090: 9.66428 -6.30964 -2.11055 -23.91685 -2.80565 1.44021 50.97006 55.30827 57.89616 6 0.07096: 9.49043 -6.41688 -2.11193 -23.70296 -2.75360 1.87295 50.81037 55.21399 57.96866 7 0.07083: 9.73889 -6.23357 -2.26359 -23.79017 -2.90425 1.48498 50.89124 55.23189 57.97941 8 0.07083: 9.53517 -6.19860 -2.21648 -23.80806 -2.94899 1.60664 51.00556 55.23189 57.91307 9 0.07093: 9.53026 -6.16686 -2.05919 -23.73721 -2.83873 1.68706 50.77982 55.39322 57.84869 after parameter optimization -center -8.57588 7.11687 -26.81099 -translation 9.48154 -6.13763 -2.11303 -rotation -23.71571 -2.74674 1.46166 -scale 1.01740 1.10578 1.15487 -shear 0.00000 0.00000 0.00000 29440 22653 -> 0.07081512 Initial objective function val = 0.09451354 Final objective function value = 0.07081512 successful write checking z-scale: making /tmp/mritotal_5941/nu_8tmp2b.xfm [mritotal] [christip@varda:/home/christip/EG/EGsurf/mri] [2006-01-09 16:08:21] /home/christip/sw/freesurfer/lib/mni/bin/check_scale /tmp/mritotal_5941/nu_8tmp2a.xfm /tmp/mritotal_5941/nu_8tmp2b.xfm 8mm gradient lsq9 fit, target masked: making /tmp/mritotal_5941/nu_8tmp2c.xfm [mritotal] [christip@varda:/home/christip/EG/EGsurf/mri] [2006-01-09 16:08:21] /home/christip/sw/freesurfer/lib/mni/bin/minctracc -clobber -debug /tmp/mritotal_5941/nu_8_dxyz.mnc /home/christip/sw/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc /tmp/mritotal_5941/nu_8tmp2c.xfm -transformation /tmp/mritotal_5941/nu_8tmp2b.xfm -lsq9 -xcorr -model_mask /home/christip/sw/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc -center -8.575884 7.116868 -26.810989 -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= 0.048 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 = 1.0159 -0.0042 -0.0551 8.1713 0.0282 1.0126 0.4434 5.9012 0.0553 -0.4640 1.0561 3.1682 Transform center = -8.576 7.117 -26.811 Transform rotations = -0.414 -0.048 0.026 Transform trans = 9.482 -6.138 -2.113 Transform scale = 1.017 1.106 1.155 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 /home/christip/sw/freesurfer/lib/mni/bin/minctracc ===== Data filename = /tmp/mritotal_5941/nu_8_dxyz.mnc Model filename = /home/christip/sw/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc Data mask filename = Model mask filename = /home/christip/sw/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc Input xform name = /tmp/mritotal_5941/nu_8tmp2b.xfm Output filename = /tmp/mritotal_5941/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 = 1.0159 -0.0042 -0.0551 8.1713 0.0282 1.0126 0.4434 5.9012 0.0553 -0.4640 1.0561 3.1682 Transform center = -8.576 7.117 -26.811 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: -8.575884 7.116868 -26.810989 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 22653 -> 0.07081512 29440 22653 -> 0.07081512 29440 22654 -> 0.08385934 29440 22188 -> 0.07601732 29440 22845 -> 0.07721985 29440 22773 -> 0.07475330 29440 22652 -> 0.07900372 29440 22648 -> 0.07463765 29440 22651 -> 0.08091171 29440 23107 -> 0.07441152 29440 22785 -> 0.07509258 29440 22741 -> 0.08150800 29440 22721 -> 0.07460747 29440 22765 -> 0.07930288 29440 22735 -> 0.07412567 29440 22789 -> 0.07943875 29440 22682 -> 0.07335873 29440 22561 -> 0.07691395 29440 22626 -> 0.07306339 29440 23296 -> 0.07595745 29440 23026 -> 0.07286093 29440 22765 -> 0.07849550 29440 22785 -> 0.07253976 29440 22782 -> 0.07541499 29440 22772 -> 0.07249577 29440 22938 -> 0.07511714 29440 22726 -> 0.07247642 29440 22864 -> 0.07599746 29440 22753 -> 0.07244287 29440 22387 -> 0.07375899 29440 22688 -> 0.07384179 29440 22702 -> 0.07242233 29440 23099 -> 0.07481275 29440 22564 -> 0.07222604 29440 22794 -> 0.07360845 29440 22709 -> 0.07200661 29440 22854 -> 0.07245136 29440 22422 -> 0.07226923 29440 22585 -> 0.07248730 29440 22555 -> 0.07201976 29440 22731 -> 0.07279419 29440 22621 -> 0.07170806 29440 22573 -> 0.07197761 29440 22375 -> 0.07312541 29440 22735 -> 0.07168272 29440 22472 -> 0.07208306 29440 22485 -> 0.07198700 29440 22769 -> 0.07157782 29440 22677 -> 0.07179632 29440 22806 -> 0.07205147 29440 22724 -> 0.07142875 29440 22771 -> 0.07160935 29440 22630 -> 0.07132710 29440 22889 -> 0.07200243 29440 22583 -> 0.07133952 29440 22792 -> 0.07152847 29440 22726 -> 0.07204560 29440 22684 -> 0.07122932 29440 22791 -> 0.07136666 29440 22666 -> 0.07113225 29440 22632 -> 0.07131558 29440 22630 -> 0.07166421 29440 22727 -> 0.07107507 29440 22567 -> 0.07165643 29440 22737 -> 0.07112858 29440 22631 -> 0.07094179 29440 22542 -> 0.07127887 29440 22734 -> 0.07088856 29440 22713 -> 0.07156450 29440 22650 -> 0.07096888 29440 22707 -> 0.07133757 29440 22653 -> 0.07101706 29440 22825 -> 0.07124452 29440 22756 -> 0.07098807 29440 22697 -> 0.07089788 29440 22701 -> 0.07088180 29440 22643 -> 0.07068706 29440 22597 -> 0.07078019 29440 22647 -> 0.07074048 29440 22706 -> 0.07073404 29440 22581 -> 0.07075249 29440 22653 -> 0.07070883 29440 22706 -> 0.07084212 done with simplex after 72 iterations 0 0.07082: 9.48154 -6.13763 -2.11303 -23.71571 -2.74674 1.46166 50.87020 55.28910 57.74326 1 0.07084: 9.44506 -6.48626 -2.18804 -23.98603 -3.01228 1.62789 50.93531 55.29571 57.67033 2 0.07074: 9.59482 -6.43042 -1.86357 -24.20546 -3.03428 1.36635 50.90239 55.01635 57.40664 3 0.07088: 9.43916 -6.58775 -1.81689 -23.94463 -2.74274 1.86709 50.95552 54.98421 57.78583 4 0.07073: 9.60680 -6.58822 -1.92598 -23.79016 -2.91215 1.20951 50.84475 55.05068 57.55809 5 0.07071: 9.69639 -6.60309 -2.14480 -24.14357 -3.02201 1.50095 50.80592 55.11571 57.57362 6 0.07069: 9.46711 -6.56453 -1.93390 -24.06516 -2.72233 1.33876 50.91918 54.86168 57.67099 7 0.07089: 9.46728 -6.65784 -1.89726 -24.09967 -2.73625 1.55080 50.92878 55.23886 57.36717 8 0.07090: 9.49240 -6.59158 -1.89833 -23.98887 -2.75897 1.48078 50.67876 55.08050 57.52047 9 0.07075: 9.53665 -6.42659 -2.02213 -24.00652 -2.95884 1.58970 50.92393 54.82711 57.48153 after parameter optimization -center -8.57588 7.11687 -26.81099 -translation 9.46711 -6.56453 -1.93390 -rotation -24.06516 -2.72233 1.33876 -scale 1.01838 1.09723 1.15342 -shear 0.00000 0.00000 0.00000 29440 22643 -> 0.07068706 Initial objective function val = 0.07081512 Final objective function value = 0.07068706 successful write final linear fit: 8mm gradient lsq9 fit, target masked: making transforms/talairach.xfm [mritotal] [christip@varda:/home/christip/EG/EGsurf/mri] [2006-01-09 16:08:28] /home/christip/sw/freesurfer/lib/mni/bin/minctracc -clobber -debug /tmp/mritotal_5941/nu_8_dxyz.mnc /home/christip/sw/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc transforms/talairach.xfm -transformation /tmp/mritotal_5941/nu_8tmp2c.xfm -lsq9 -xcorr -model_mask /home/christip/sw/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc -center -8.575884 7.116868 -26.810989 -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= 0.048 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 = 1.0170 -0.0020 -0.0539 8.1829 0.0256 1.0021 0.4462 5.6030 0.0548 -0.4698 1.0520 3.2730 Transform center = -8.576 7.117 -26.811 Transform rotations = -0.420 -0.048 0.023 Transform trans = 9.467 -6.565 -1.934 Transform scale = 1.018 1.097 1.153 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 /home/christip/sw/freesurfer/lib/mni/bin/minctracc ===== Data filename = /tmp/mritotal_5941/nu_8_dxyz.mnc Model filename = /home/christip/sw/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc Data mask filename = Model mask filename = /home/christip/sw/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc Input xform name = /tmp/mritotal_5941/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 = 1.0170 -0.0020 -0.0539 8.1829 0.0256 1.0021 0.4462 5.6030 0.0548 -0.4698 1.0520 3.2730 Transform center = -8.576 7.117 -26.811 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: -8.575884 7.116868 -26.810989 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 22643 -> 0.07068706 29440 22643 -> 0.07068706 29440 22645 -> 0.08319058 29440 22179 -> 0.07470877 29440 22839 -> 0.07804277 29440 22760 -> 0.07413088 29440 22640 -> 0.07861485 29440 22640 -> 0.07390738 29440 22644 -> 0.08004779 29440 23088 -> 0.07322678 29440 22768 -> 0.07473474 29440 22732 -> 0.08105042 29440 22712 -> 0.07414857 29440 22753 -> 0.07896790 29440 22725 -> 0.07359178 29440 22766 -> 0.07908473 29440 22675 -> 0.07299144 29440 22552 -> 0.07487713 29440 22621 -> 0.07176324 29440 22568 -> 0.07656351 29440 22721 -> 0.07201656 29440 23275 -> 0.07621292 29440 22458 -> 0.07198892 29440 22698 -> 0.07496981 29440 22708 -> 0.07182283 29440 22651 -> 0.07543754 29440 22736 -> 0.07167690 29440 22784 -> 0.07465246 29440 22677 -> 0.07164085 29440 22681 -> 0.07369083 29440 22714 -> 0.07169010 29440 22212 -> 0.07359996 29440 22871 -> 0.07165202 29440 22692 -> 0.07241254 29440 22689 -> 0.07122283 29440 22633 -> 0.07218859 29440 22703 -> 0.07122018 29440 22958 -> 0.07195551 29440 22832 -> 0.07133659 29440 22729 -> 0.07156548 29440 22850 -> 0.07177401 29440 22677 -> 0.07109160 29440 22737 -> 0.07149526 29440 22731 -> 0.07138259 29440 22549 -> 0.07129982 29440 22722 -> 0.07094293 29440 22664 -> 0.07178968 29440 22715 -> 0.07093440 29440 22650 -> 0.07131485 29440 22651 -> 0.07170220 29440 22712 -> 0.07094315 29440 22517 -> 0.07088068 29440 22668 -> 0.07129864 29440 22790 -> 0.07169431 29440 22611 -> 0.07082798 29440 22663 -> 0.07134722 29440 22669 -> 0.07080680 29440 22635 -> 0.07081658 29440 22601 -> 0.07090302 29440 22623 -> 0.07051374 29440 22580 -> 0.07079320 29440 22569 -> 0.07093970 29440 22513 -> 0.07104588 29440 22679 -> 0.07064429 29440 22698 -> 0.07096220 29440 22617 -> 0.07068848 29440 22525 -> 0.07086948 29440 22617 -> 0.07097537 29440 22601 -> 0.07065295 29440 22721 -> 0.07100476 29440 22571 -> 0.07064562 29440 22724 -> 0.07091463 29440 22568 -> 0.07062354 29440 22625 -> 0.07083523 29440 22616 -> 0.07062867 29440 22597 -> 0.07101870 29440 22622 -> 0.07059927 29440 22555 -> 0.07069864 29440 22592 -> 0.07058269 29440 22633 -> 0.07050194 29440 22644 -> 0.07057977 29440 22577 -> 0.07074887 29440 22619 -> 0.07053021 done with simplex after 72 iterations 0 0.07053: 9.51648 -6.51039 -2.12564 -24.06061 -2.80328 1.36853 50.89612 54.87224 57.83610 1 0.07062: 9.54343 -6.43460 -2.33005 -24.08134 -2.89652 1.32500 50.95010 54.76068 57.96863 2 0.07065: 9.54648 -6.24506 -2.31560 -24.03246 -2.88739 1.45452 50.83459 54.88070 58.06449 3 0.07051: 9.69961 -6.59262 -2.23732 -24.24491 -3.09233 1.30496 50.90025 54.79478 57.98697 4 0.07050: 9.50534 -6.48694 -2.21971 -24.22989 -2.85069 1.44129 50.87838 54.93119 57.98238 5 0.07060: 9.58714 -6.50442 -2.33924 -24.03515 -2.72632 1.41179 50.88352 54.90391 58.02835 6 0.07064: 9.51933 -6.45701 -2.38567 -23.84672 -2.89083 1.28621 50.85345 55.09721 58.10393 7 0.07058: 9.59890 -6.49497 -2.28026 -24.12795 -2.86485 1.27245 50.82356 54.75935 57.94922 8 0.07063: 9.50822 -6.43391 -2.29904 -23.90340 -2.84827 1.61845 50.87017 54.86995 58.03926 9 0.07065: 9.58432 -6.45667 -2.44947 -24.00277 -2.90080 1.47004 50.86354 54.94745 57.88758 after parameter optimization -center -8.57588 7.11687 -26.81099 -translation 9.50534 -6.48694 -2.21971 -rotation -24.22989 -2.85069 1.44129 -scale 1.01757 1.09862 1.15965 -shear 0.00000 0.00000 0.00000 29440 22633 -> 0.07050194 Initial objective function val = 0.07068706 Final objective function value = 0.07050194 successful write