[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