[dglen@gollum.local:/Users/dglen/freesurfer/subjects/FK/FKsurf/mri] [2006-01-10 16:49:12] running:
  /Applications/freesurfer/lib/mni/bin/mritotal -verbose -debug -clobber -modeldir /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg -protocol icbm nu.mnc transforms/talairach.xfm

Loading configuration file /Applications/freesurfer/lib/mni/bin/../etc/mni_autoreg/mritotal.cfg
Loading protocol default (protocol file = /Applications/freesurfer/lib/mni/bin/../etc/mni_autoreg/mritotal.default.cfg)
Loading protocol icbm (protocol file = /Applications/freesurfer/lib/mni/bin/../etc/mni_autoreg/mritotal.icbm.cfg)
   source = nu.mnc
    model = /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305
transform = transforms/talairach.xfm
 protocol = icbm:
    linear fit only
    subsample heuristically
    crop according to 0,0 0,0 -25%,0
    blur with 16 and 8 mm FHWM kernels
    pad/unpad correctly (encroach on original volume)
    default objective function = cross-correlation

Subsampling/cropping data:
[mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FK/FKsurf/mri] [2006-01-10 16:49:12] /Applications/freesurfer/lib/mni/bin/autocrop -clobber nu.mnc /tmp/mritotal_16215/nu_crop.mnc -step 2 2 2 -extend 0,0 0,0 -25%,0
[autocrop] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FK/FKsurf/mri] [2006-01-10 16:49:12] /Applications/freesurfer/lib/mni/bin/mincresample -clobber nu.mnc /tmp/mritotal_16215/nu_crop.mnc -start -129.9 -128 -64 -step 2 2 2 -nelements 128 128 96
Transforming slices:................................................................................................................................Done
[mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FK/FKsurf/mri] [2006-01-10 16:49:13] /Applications/freesurfer/lib/mni/bin/volume_cog /tmp/mritotal_16215/nu_crop.mnc | tail -1
Centroid of input volume: 3.420597 3.237205 -20.482256

Zero-padding data:
[mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FK/FKsurf/mri] [2006-01-10 16:49:14] /Applications/freesurfer/lib/mni/bin/autocrop -clobber /tmp/mritotal_16215/nu_crop.mnc /tmp/mritotal_16215/nu_pad.mnc -expand 22 22 22
[autocrop] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FK/FKsurf/mri] [2006-01-10 16:49:15] /Applications/freesurfer/lib/mni/bin/mincreshape -clobber /tmp/mritotal_16215/nu_crop.mnc /tmp/mritotal_16215/nu_pad.mnc -start -11,-11,-11 -count 150,150,118
Copying chunks:......................................................................................................................................................Done.

Intensity blurring data:
[mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FK/FKsurf/mri] [2006-01-10 16:49:15] /Applications/freesurfer/lib/mni/bin/mincblur -clobber -debug /tmp/mritotal_16215/nu_pad.mnc /tmp/mritotal_16215/tmp_16 -fwhm 16
===== Debugging information from /Applications/freesurfer/lib/mni/bin/mincblur =====
Data filename     = /tmp/mritotal_16215/nu_pad.mnc
Output basename   = /tmp/mritotal_16215/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  253.999
Apodizing data at 16.000000
Volume def min and max: = 0.000000 253.998553
before blur min/max = 0.000000 253.998550
after  blur min/max = -0.000004 129.103836
Making byte volume...
[mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FK/FKsurf/mri] [2006-01-10 16:49:20] /Applications/freesurfer/lib/mni/bin/autocrop -clobber /tmp/mritotal_16215/tmp_16_blur.mnc /tmp/mritotal_16215/nu_16_blur.mnc -expand -44 -44 -44
[autocrop] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FK/FKsurf/mri] [2006-01-10 16:49:20] /Applications/freesurfer/lib/mni/bin/mincreshape -clobber /tmp/mritotal_16215/tmp_16_blur.mnc /tmp/mritotal_16215/nu_16_blur.mnc -start 22,22,22 -count 106,106,74
Copying chunks:..........................................................................................................Done.

Gradient blurring data:
[mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FK/FKsurf/mri] [2006-01-10 16:49:21] /Applications/freesurfer/lib/mni/bin/mincblur -clobber -debug /tmp/mritotal_16215/nu_pad.mnc /tmp/mritotal_16215/tmp_8 -fwhm 8 -gradient
Transforming slices:......................................................................................................................................................Done
===== Debugging information from /Applications/freesurfer/lib/mni/bin/mincblur =====
Data filename     = /tmp/mritotal_16215/nu_pad.mnc
Output basename   = /tmp/mritotal_16215/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  253.999
Apodizing data at 8.000000
Volume def min and max: = 0.000000 253.998553
before blur min/max = 0.000000 253.998550
after  blur min/max = -0.000014 159.178040
Making byte volume...
Making byte volume dx...dx: min = -16.101101, max = 16.658909
Making byte volume dy...dy: min = -15.791716, max = 10.807730
Making byte volume dz...dz: min = -17.701569, max = 15.462411
[mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FK/FKsurf/mri] [2006-01-10 16:49:32] /Applications/freesurfer/lib/mni/bin/autocrop -clobber /tmp/mritotal_16215/tmp_8_blur.mnc /tmp/mritotal_16215/nu_8_blur.mnc -expand -34 -34 -34
[autocrop] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FK/FKsurf/mri] [2006-01-10 16:49:32] /Applications/freesurfer/lib/mni/bin/mincreshape -clobber /tmp/mritotal_16215/tmp_8_blur.mnc /tmp/mritotal_16215/nu_8_blur.mnc -start 17,17,17 -count 116,116,84
Copying chunks:....................................................................................................................Done.
[mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FK/FKsurf/mri] [2006-01-10 16:49:32] /Applications/freesurfer/lib/mni/bin/autocrop -clobber /tmp/mritotal_16215/tmp_8_dxyz.mnc /tmp/mritotal_16215/nu_8_dxyz.mnc -expand -34 -34 -34
[autocrop] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FK/FKsurf/mri] [2006-01-10 16:49:33] /Applications/freesurfer/lib/mni/bin/mincreshape -clobber /tmp/mritotal_16215/tmp_8_dxyz.mnc /tmp/mritotal_16215/nu_8_dxyz.mnc -start 17,17,17 -count 116,116,84
Copying chunks:....................................................................................................................Done.

16mm intensity lsq7 fit, no masks: making /tmp/mritotal_16215/nu_16.xfm
[mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FK/FKsurf/mri] [2006-01-10 16:49:33] /Applications/freesurfer/lib/mni/bin/minctracc -clobber -debug /tmp/mritotal_16215/nu_16_blur.mnc /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_16_blur.mnc /tmp/mritotal_16215/nu_16.xfm -est_translations -lsq7 -xcorr -center 3.420597 3.237205 -20.482256 -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  129.104
min/max voxel=    0.000  255.000

Target volume size:  58  by 110  by 86 
Target voxel =    2.000    2.000    2.000
min/max value=   -0.000  123.710
min/max voxel=    0.000  255.000


AFTER init_params()
Transform matrix    =    1.0000    0.0000    0.0000   -3.0926 
                         0.0000    1.0000    0.0000  -20.8283 
                         0.0000    0.0000    1.0000   29.9369 

Transform center   =    3.421    3.237  -20.482
Transform rotations  =    0.000    0.000    0.000
Transform trans    =   -3.093  -20.828   29.937
Transform scale    =    1.000    1.000    1.000
Transform shear    =    0.000    0.000    0.000

Target volume is smallest
Lattice step size  =    4.000    4.000    4.000
Lattice start      =  -85.095 -125.510  -47.250
Lattice count      =       43       55       29

===== Debugging information from /Applications/freesurfer/lib/mni/bin/minctracc =====
Data filename       = /tmp/mritotal_16215/nu_16_blur.mnc
Model filename      = /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_16_blur.mnc
Data mask filename  = 
Model mask filename = 
Input xform name    = 
Output filename     = /tmp/mritotal_16215/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   =    3.421    3.237  -20.482
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: 3.420597 3.237205 -20.482256
  using PAT to get initial parameters:
  will try to get: [trans]
COG of v1 forced: 3.420597 3.237205 -20.482256
In set_up_lattice, xyzv[axes] = 2, 1, 0, -1
In set_up_lattice, xyzv[axes] = 2, 1, 0, -1
in vol to cov
start =   -47.25  -125.51   -85.09 
count =       43       55       29 
step  =     4.00     4.00     4.00 
direct=     1.00     0.00     0.00 
direct=     0.00     1.00     0.00 
direct=     0.00     0.00     1.00 
In set_up_lattice, xyzv[axes] = 2, 1, 0, -1
In set_up_lattice, xyzv[axes] = 2, 1, 0, -1
COG of v2: 0.328006 -17.591131 9.454663
   [trans] = -3.092591 -20.828337 29.936920
Only center & trans required, now returning from init_transformation
Transform center   =    3.421    3.237  -20.482
Transform rots    =    0.000    0.000    0.000
Transform trans    =   -3.093  -20.828   29.937
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   46006 -> 0.05257604
  68585   46006 -> 0.05257604
  68585   41255 -> 0.09704002
  68585   42345 -> 0.04094364
  68585   46016 -> 0.05752872
  68585   47210 -> 0.05085681
  68585   45028 -> 0.05648582
  68585   43365 -> 0.05513421
  68585   53621 -> 0.08539180
  68585   45425 -> 0.09189089
  68585   47441 -> 0.05800883
  68585   16082 -> 0.16789368
  68585   50850 -> 0.05400874
  68585   42456 -> 0.06692665
  68585   47488 -> 0.04623422
  68585   47901 -> 0.03644054
  68585   48886 -> 0.05256664
  68585   47170 -> 0.04553588
  68585   47687 -> 0.05297660
  68585   38443 -> 0.07000673
  68585   49101 -> 0.04220989
  68585   41981 -> 0.05946403
  68585   47679 -> 0.04259360
  68585   47037 -> 0.05226578
  68585   47244 -> 0.04343842
  68585   45176 -> 0.04307374
  68585   45480 -> 0.03860059
  68585   45024 -> 0.03400181
  68585   43164 -> 0.04252447
  68585   45191 -> 0.02651577
  68585   43924 -> 0.02170646
  68585   45059 -> 0.04281159
  68585   46366 -> 0.03466039
  68585   43986 -> 0.02603398
  68585   39453 -> 0.02720909
  68585   46547 -> 0.02972945
  68585   43439 -> 0.03924789
  68585   45234 -> 0.02910991
  68585   40309 -> 0.03422982
  68585   40003 -> 0.03425441
  68585   41773 -> 0.02607354
  68585   46962 -> 0.02884949
  68585   42820 -> 0.01864864
  68585   40915 -> 0.02597883
  68585   40811 -> 0.02930581
  68585   42200 -> 0.02349859
  68585   40501 -> 0.02370745
  68585   37294 -> 0.03718873
  68585   44657 -> 0.02222965
  68585   45791 -> 0.01864890
  68585   44690 -> 0.02028616
  68585   43018 -> 0.01198455
  68585   42236 -> 0.00912941
  68585   46431 -> 0.02072871
  68585   46360 -> 0.01249283
  68585   44847 -> 0.01141067
  68585   45067 -> 0.01406248
  68585   42423 -> 0.01758862
  68585   42918 -> 0.01498500
  68585   41266 -> 0.02038047
  68585   44889 -> 0.01265218
  68585   46145 -> 0.00960030
  68585   46826 -> 0.01464544
  68585   46703 -> 0.01695771
  68585   44128 -> 0.01055244
  68585   42739 -> 0.01654536
  68585   45814 -> 0.01039731
  68585   44984 -> 0.01695629
  68585   45024 -> 0.00970259
  68585   44840 -> 0.00928668
  68585   43011 -> 0.01042719
  68585   43852 -> 0.01114403
  68585   44188 -> 0.00892296
  68585   44714 -> 0.00821271
  68585   44876 -> 0.01138486
  68585   46421 -> 0.01165798
  68585   43860 -> 0.00841031
  68585   42720 -> 0.00857883
  68585   43363 -> 0.00959553
  68585   41468 -> 0.01045333
  68585   44892 -> 0.00818136
  68585   44706 -> 0.00980128
  68585   43613 -> 0.00820510
  68585   42677 -> 0.00749735
  68585   41571 -> 0.00918972
  68585   45345 -> 0.01196482
  68585   43030 -> 0.00765376
  68585   43353 -> 0.00765638
  68585   44559 -> 0.00906988
  68585   43290 -> 0.00760443
  68585   43455 -> 0.00743613
  68585   43212 -> 0.00904131
  68585   42041 -> 0.00941817
  68585   44128 -> 0.00735368
  68585   43374 -> 0.00727942
  68585   43181 -> 0.00867432
  68585   41654 -> 0.00815863
  68585   42501 -> 0.00733386
  68585   43220 -> 0.00818809
  68585   43271 -> 0.00717987
  68585   43428 -> 0.00754398
  68585   43228 -> 0.00752574
  68585   43005 -> 0.00751789
  68585   43155 -> 0.00769459
  68585   43222 -> 0.00715360
  68585   43417 -> 0.00749090
  68585   44029 -> 0.00768569
  68585   43011 -> 0.00715437
  68585   43093 -> 0.00744036
  68585   43200 -> 0.00714386
  68585   43004 -> 0.00736141
  68585   43131 -> 0.00711206
  68585   42070 -> 0.00828996
  68585   43634 -> 0.00703998
  68585   44024 -> 0.00710456
  68585   43294 -> 0.00735386
  68585   43361 -> 0.00709029
  68585   43470 -> 0.00715103
  68585   43853 -> 0.00715626
  68585   43230 -> 0.00706344
  68585   43670 -> 0.00717533
  68585   43334 -> 0.00705797
  68585   43357 -> 0.00715993
  68585   43441 -> 0.00705939
  68585   43656 -> 0.00703383
  68585   43908 -> 0.00719680
  68585   43915 -> 0.00706166
  68585   42989 -> 0.00711946
  68585   43768 -> 0.00703073
  68585   43775 -> 0.00702044
  68585   43992 -> 0.00713077
  68585   44070 -> 0.00704274
done with simplex after 123 iterations
0 0.00702:-3.26179 -7.98336  1.21758 -27.44834  0.23507  6.20269 55.20771 
1 0.00706:-3.18287 -6.94856  1.49708 -27.13616  0.99231  5.91618 54.60922 
2 0.00706:-3.28112 -8.49981  1.19606 -27.61402  1.32738  6.44029 55.14758 
3 0.00706:-3.08105 -6.97084  1.28134 -25.89606  0.93355  6.43253 54.84112 
4 0.00704:-3.02134 -7.82743  0.75192 -27.16538 -0.44895  5.90331 55.07715 
5 0.00703:-2.98165 -7.77120  1.45853 -27.04343  0.56183  6.39452 55.13751 
6 0.00703:-2.95288 -7.79729  1.56522 -27.58658 -0.00321  7.42976 55.04872 
7 0.00704:-3.11242 -8.54815  1.86952 -26.85614  0.11145  6.58603 55.21870 
after parameter optimization
-center         3.42060    3.23720  -20.48226
-translation   -3.26179   -7.98336    1.21758
-rotation     -27.44834    0.23507    6.20269
-scale          1.10415    1.10415    1.10415
-shear          0.00000    0.00000    0.00000
  68585   43775 -> 0.00702044
Initial objective function val = 0.05257604
Final objective function value = 0.00702044
successful write

8mm intensity lsq7 fit, no masks: making /tmp/mritotal_16215/nu_8tmp1a.xfm
[mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FK/FKsurf/mri] [2006-01-10 16:49:49] /Applications/freesurfer/lib/mni/bin/minctracc -clobber -debug /tmp/mritotal_16215/nu_8_blur.mnc /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_blur.mnc /tmp/mritotal_16215/nu_8tmp1a.xfm -transformation /tmp/mritotal_16215/nu_16.xfm -lsq7 -xcorr -center 3.420597 3.237205 -20.482256 -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  159.178
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    =    1.0977   -0.1079   -0.0510   -4.2910 
                         0.1193    0.9739    0.5064    2.0656 
                        -0.0045   -0.5090    0.9798    2.4679 

Transform center   =    3.421    3.237  -20.482
Transform rotations  =   -0.479    0.004    0.108
Transform trans    =   -3.262   -7.983    1.218
Transform scale    =    1.104    1.104    1.104
Transform shear    =    0.000   -0.000   -0.000

Target volume is smallest
Lattice step size  =    4.000    4.000    4.000
Lattice start      =  -85.095 -125.510  -57.250
Lattice count      =       43       55       34

===== Debugging information from /Applications/freesurfer/lib/mni/bin/minctracc =====
Data filename       = /tmp/mritotal_16215/nu_8_blur.mnc
Model filename      = /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_blur.mnc
Data mask filename  = 
Model mask filename = 
Input xform name    = /tmp/mritotal_16215/nu_16.xfm
Output filename     = /tmp/mritotal_16215/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    =    1.0977   -0.1079   -0.0510   -4.2910 
                         0.1193    0.9739    0.5064    2.0656 
                        -0.0045   -0.5090    0.9798    2.4679 
Transform center   =    3.421    3.237  -20.482
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: 3.420597 3.237205 -20.482256
  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   55003 -> 0.02297819
  80410   55003 -> 0.02297819
  80410   55374 -> 0.03130254
  80410   53323 -> 0.02697778
  80410   55915 -> 0.02825865
  80410   55140 -> 0.02162351
  80410   55303 -> 0.02483366
  80410   54419 -> 0.02371182
  80410   58054 -> 0.03802253
  80410   50080 -> 0.03856910
  80410   56628 -> 0.02919233
  80410   54426 -> 0.02922796
  80410   54847 -> 0.02504918
  80410   52723 -> 0.02480533
  80410   53052 -> 0.02112086
  80410   51740 -> 0.02575327
  80410   55382 -> 0.02453536
  80410   53908 -> 0.02586178
  80410   54684 -> 0.02260512
  80410   53194 -> 0.02252828
  80410   55911 -> 0.02259787
  80410   53480 -> 0.02601728
  80410   54971 -> 0.02175260
  80410   54800 -> 0.02091076
  80410   55136 -> 0.02418389
  80410   54224 -> 0.02109443
  80410   54477 -> 0.02142958
  80410   52479 -> 0.02362240
  80410   55110 -> 0.02084549
  80410   55624 -> 0.02274183
  80410   53878 -> 0.02080211
  80410   53843 -> 0.02113288
  80410   53231 -> 0.02261755
  80410   54652 -> 0.02043622
  80410   54094 -> 0.02145691
  80410   54364 -> 0.02043927
  80410   54808 -> 0.02166842
  80410   54062 -> 0.02032160
  80410   55740 -> 0.02330508
  80410   53784 -> 0.02021406
  80410   54543 -> 0.02085713
  80410   53891 -> 0.02088268
  80410   54148 -> 0.02034277
  80410   54023 -> 0.02125874
  80410   54387 -> 0.02028371
  80410   53288 -> 0.02036812
  80410   54263 -> 0.02061224
  80410   54182 -> 0.02019613
  80410   53806 -> 0.02040982
  80410   53224 -> 0.02031520
  80410   53960 -> 0.02055016
  80410   53821 -> 0.02013333
  80410   54612 -> 0.02087258
  80410   53625 -> 0.02006859
  80410   53646 -> 0.02033303
  80410   53757 -> 0.02012588
  80410   53580 -> 0.02025508
  80410   54540 -> 0.02035706
  80410   53544 -> 0.02010823
  80410   53099 -> 0.02048899
  80410   54054 -> 0.02007727
  80410   54058 -> 0.02029430
  80410   53697 -> 0.02009190
  80410   53827 -> 0.02023683
  80410   53801 -> 0.02007199
  80410   53348 -> 0.02016805
  80410   53550 -> 0.02007413
  80410   53598 -> 0.02009186
  80410   53657 -> 0.02014119
  80410   53720 -> 0.02005584
done with simplex after 61 iterations
0 0.02008:-3.85237 -7.21609 -1.77247 -23.51362  0.09952  7.14971 55.05574 
1 0.02009:-4.15286 -6.85416 -2.67673 -23.34764  0.46427  7.34569 54.76134 
2 0.02009:-3.86829 -6.70787 -2.05890 -23.87973  0.60676  7.37253 54.81108 
3 0.02007:-4.13186 -6.86301 -2.19702 -23.48691  0.77426  7.65097 54.94646 
4 0.02011:-4.03142 -6.53712 -2.63885 -23.41623  0.22836  7.67107 54.88848 
5 0.02007:-4.10790 -6.56687 -1.94413 -23.75174  0.27903  7.44397 54.73623 
6 0.02006:-4.11177 -6.66419 -2.31637 -23.12389  0.43344  7.06426 54.88087 
7 0.02007:-4.04547 -6.74326 -1.96436 -22.58856 -0.05079  7.50214 54.68172 
after parameter optimization
-center         3.42060    3.23720  -20.48226
-translation   -4.11177   -6.66419   -2.31637
-rotation     -23.12389    0.43344    7.06426
-scale          1.09762    1.09762    1.09762
-shear          0.00000    0.00000    0.00000
  80410   53720 -> 0.02005584
Initial objective function val = 0.02297819
Final objective function value = 0.02005584
successful write

8mm gradient lsq7 fit, target masked: making /tmp/mritotal_16215/nu_8tmp1b.xfm
[mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FK/FKsurf/mri] [2006-01-10 16:50:00] /Applications/freesurfer/lib/mni/bin/minctracc -clobber -debug /tmp/mritotal_16215/nu_8_dxyz.mnc /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc /tmp/mritotal_16215/nu_8tmp1b.xfm -transformation /tmp/mritotal_16215/nu_8tmp1a.xfm -lsq7 -xcorr -model_mask /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc -center 3.420597 3.237205 -20.482256 -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=    0.060   19.533
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    =    1.0893   -0.1274   -0.0454   -4.9353 
                         0.1350    1.0014    0.4287    1.6509 
                        -0.0083   -0.4310    1.0094   -0.7000 

Transform center   =    3.421    3.237  -20.482
Transform rotations  =   -0.404    0.008    0.123
Transform trans    =   -4.112   -6.664   -2.316
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 /Applications/freesurfer/lib/mni/bin/minctracc =====
Data filename       = /tmp/mritotal_16215/nu_8_dxyz.mnc
Model filename      = /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc
Data mask filename  = 
Model mask filename = /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc
Input xform name    = /tmp/mritotal_16215/nu_8tmp1a.xfm
Output filename     = /tmp/mritotal_16215/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    =    1.0893   -0.1274   -0.0454   -4.9353 
                         0.1350    1.0014    0.4287    1.6509 
                        -0.0083   -0.4310    1.0094   -0.7000 
Transform center   =    3.421    3.237  -20.482
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: 3.420597 3.237205 -20.482256
  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   22928 -> 0.11104101
  29440   22928 -> 0.11104101
  29440   22984 -> 0.12367633
  29440   22470 -> 0.11496137
  29440   23117 -> 0.12159138
  29440   23037 -> 0.10336389
  29440   22925 -> 0.12018242
  29440   22938 -> 0.10978162
  29440   23471 -> 0.13529260
  29440   22346 -> 0.11729383
  29440   22657 -> 0.10264905
  29440   22476 -> 0.10606475
  29440   22403 -> 0.10439893
  29440   22434 -> 0.09557685
  29440   22180 -> 0.09649879
  29440   23046 -> 0.11583386
  29440   22871 -> 0.10717940
  29440   23029 -> 0.10090297
  29440   22610 -> 0.09503618
  29440   22449 -> 0.09489775
  29440   22470 -> 0.09063897
  29440   22249 -> 0.09414630
  29440   22414 -> 0.10031323
  29440   22871 -> 0.09686866
  29440   22184 -> 0.10198124
  29440   22464 -> 0.10205100
  29440   22506 -> 0.09582084
  29440   23005 -> 0.09807829
  29440   22141 -> 0.08959159
  29440   21686 -> 0.09213882
  29440   22698 -> 0.09369433
  29440   22000 -> 0.10196362
  29440   22760 -> 0.09236408
  29440   22109 -> 0.09429436
  29440   22366 -> 0.09460177
  29440   22433 -> 0.09010656
  29440   22397 -> 0.08964836
  29440   22495 -> 0.09198833
  29440   22853 -> 0.09051206
  29440   22325 -> 0.09471180
  29440   22608 -> 0.08933637
  29440   22222 -> 0.08969413
  29440   22394 -> 0.09027555
  29440   22399 -> 0.08758043
  29440   22362 -> 0.09168504
  29440   21877 -> 0.09173762
  29440   22614 -> 0.08767438
  29440   22409 -> 0.08989070
  29440   22363 -> 0.08901105
  29440   22382 -> 0.09173605
  29440   22401 -> 0.08760114
  29440   22623 -> 0.09010707
  29440   22318 -> 0.08760057
  29440   22408 -> 0.09373982
  29440   22397 -> 0.08703411
  29440   22738 -> 0.09002845
  29440   22291 -> 0.08764639
  29440   22197 -> 0.08698684
  29440   21986 -> 0.08984104
  29440   22389 -> 0.08818407
  29440   22381 -> 0.08695973
  29440   22066 -> 0.08734630
  29440   22330 -> 0.08685176
  29440   22347 -> 0.08836851
  29440   22198 -> 0.08712637
  29440   22244 -> 0.08617574
  29440   22206 -> 0.08723321
  29440   22139 -> 0.08701829
  29440   22468 -> 0.08661021
  29440   22414 -> 0.08648510
  29440   22210 -> 0.08729329
  29440   22356 -> 0.08617644
  29440   22559 -> 0.08688340
  29440   22591 -> 0.08781455
  29440   22294 -> 0.08613034
  29440   22378 -> 0.08660624
  29440   22146 -> 0.08670999
  29440   22330 -> 0.08599323
  29440   22334 -> 0.08737258
  29440   22558 -> 0.08647726
  29440   22278 -> 0.08574031
  29440   22173 -> 0.08671957
  29440   22326 -> 0.08669620
  29440   22366 -> 0.08582509
  29440   22283 -> 0.08717465
  29440   22388 -> 0.08578967
  29440   22077 -> 0.08681832
  29440   22441 -> 0.08584214
  29440   22307 -> 0.08557495
  29440   22283 -> 0.08591031
  29440   22431 -> 0.08653088
  29440   22293 -> 0.08572730
  29440   22367 -> 0.08572418
  29440   22370 -> 0.08600948
  29440   22352 -> 0.08563921
  29440   22228 -> 0.08563460
  29440   22269 -> 0.08549174
  29440   22221 -> 0.08605400
done with simplex after 89 iterations
0 0.08557:-5.31696 -3.89046 -2.02330 -17.70703 -1.41987  6.77874 53.86845 
1 0.08579:-5.46585 -4.43482 -2.54119 -18.34256 -0.90321  6.98499 53.96648 
2 0.08564:-5.24761 -4.20268 -2.23863 -18.41013 -1.11550  6.59783 53.92757 
3 0.08574:-5.10550 -4.07787 -2.42628 -18.32233 -1.44030  7.25734 53.80453 
4 0.08573:-5.39167 -3.84808 -2.33457 -18.00424 -1.18193  6.89637 54.00949 
5 0.08549:-5.01327 -4.05660 -2.38047 -18.25481 -1.28408  7.14181 53.77005 
6 0.08563:-4.96254 -3.85424 -2.42839 -18.17402 -1.48286  6.60526 53.79797 
7 0.08572:-4.90080 -4.20436 -2.22626 -18.39064 -1.38739  6.72215 54.05846 
after parameter optimization
-center         3.42060    3.23720  -20.48226
-translation   -5.01327   -4.05660   -2.38047
-rotation     -18.25481   -1.28408    7.14181
-scale          1.07540    1.07540    1.07540
-shear          0.00000    0.00000    0.00000
  29440   22269 -> 0.08549174
Initial objective function val = 0.11104101
Final objective function value = 0.08549174
successful write

8mm gradient lsq9 fit, target masked: making /tmp/mritotal_16215/nu_8tmp2a.xfm
[mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FK/FKsurf/mri] [2006-01-10 16:50:11] /Applications/freesurfer/lib/mni/bin/minctracc -clobber -debug /tmp/mritotal_16215/nu_8_dxyz.mnc /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc /tmp/mritotal_16215/nu_8tmp2a.xfm -transformation /tmp/mritotal_16215/nu_8tmp1b.xfm -lsq9 -xcorr -model_mask /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc -center 3.420597 3.237205 -20.482256 -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=    0.060   19.533
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    =    1.0668   -0.1195   -0.0646   -6.1779 
                         0.1337    1.0143    0.3314    2.2278 
                         0.0241   -0.3368    1.0210   -0.9421 

Transform center   =    3.421    3.237  -20.482
Transform rotations  =   -0.319   -0.022    0.125
Transform trans    =   -5.013   -4.057   -2.380
Transform scale    =    1.075    1.075    1.075
Transform shear    =   -0.000    0.000   -0.000

Target volume is smallest
Lattice step size  =    4.000    4.000    4.000
Lattice start      =  -65.095 -105.510  -57.250
Lattice count      =       35       46       34

===== Debugging information from /Applications/freesurfer/lib/mni/bin/minctracc =====
Data filename       = /tmp/mritotal_16215/nu_8_dxyz.mnc
Model filename      = /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc
Data mask filename  = 
Model mask filename = /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc
Input xform name    = /tmp/mritotal_16215/nu_8tmp1b.xfm
Output filename     = /tmp/mritotal_16215/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    =    1.0668   -0.1195   -0.0646   -6.1779 
                         0.1337    1.0143    0.3314    2.2278 
                         0.0241   -0.3368    1.0210   -0.9421 
Transform center   =    3.421    3.237  -20.482
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: 3.420597 3.237205 -20.482256
  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   22269 -> 0.08549175
  29440   22269 -> 0.08549175
  29440   22319 -> 0.09469447
  29440   21786 -> 0.09029014
  29440   22422 -> 0.08995100
  29440   22397 -> 0.08672000
  29440   22269 -> 0.09035797
  29440   22275 -> 0.08813181
  29440   22260 -> 0.09745582
  29440   22721 -> 0.08205552
  29440   22360 -> 0.08612380
  29440   22356 -> 0.08106098
  29440   22395 -> 0.09390329
  29440   22304 -> 0.08867414
  29440   22376 -> 0.08923078
  29440   22970 -> 0.08330320
  29440   22482 -> 0.08307400
  29440   22541 -> 0.08712645
  29440   22662 -> 0.09078545
  29440   22394 -> 0.08319610
  29440   22737 -> 0.07902069
  29440   22979 -> 0.08206235
  29440   22500 -> 0.08575517
  29440   22670 -> 0.08054191
  29440   22766 -> 0.07903332
  29440   22690 -> 0.08193779
  29440   23015 -> 0.07436036
  29440   23378 -> 0.07363179
  29440   22402 -> 0.07747941
  29440   22980 -> 0.07463951
  29440   23016 -> 0.07816994
  29440   22830 -> 0.07835069
  29440   22903 -> 0.07530907
  29440   23351 -> 0.07607876
  29440   23209 -> 0.07954206
  29440   23065 -> 0.07433598
  29440   23157 -> 0.07681510
  29440   23265 -> 0.07926381
  29440   22874 -> 0.07473214
  29440   23205 -> 0.07595330
  29440   23065 -> 0.07679471
  29440   23800 -> 0.07660277
  29440   23207 -> 0.07933044
  29440   23170 -> 0.07350875
  29440   23332 -> 0.07794560
  29440   23127 -> 0.07357046
  29440   22417 -> 0.07747807
  29440   23462 -> 0.07357516
  29440   22910 -> 0.07498264
  29440   22991 -> 0.08002492
  29440   23150 -> 0.07319438
  29440   23346 -> 0.07707531
  29440   23012 -> 0.07310047
  29440   23362 -> 0.07569292
  29440   23023 -> 0.07306372
  29440   23426 -> 0.07301760
  29440   23697 -> 0.07776916
  29440   23420 -> 0.07596309
  29440   23092 -> 0.07278549
  29440   23341 -> 0.07318126
  29440   23017 -> 0.07369367
  29440   23291 -> 0.07269776
  29440   22900 -> 0.07271597
  29440   23190 -> 0.07369158
  29440   23141 -> 0.07254285
  29440   23140 -> 0.07263480
  29440   23157 -> 0.07388051
  29440   23152 -> 0.07233696
  29440   22920 -> 0.07434148
  29440   23233 -> 0.07233758
  29440   23296 -> 0.07263238
  29440   23342 -> 0.07264338
  29440   22928 -> 0.07413667
  29440   23303 -> 0.07208231
  29440   23309 -> 0.07288344
  29440   23151 -> 0.07220961
  29440   23554 -> 0.07337894
  29440   23068 -> 0.07212240
  29440   23121 -> 0.07217395
  29440   23005 -> 0.07283654
  29440   23263 -> 0.07214054
  29440   23244 -> 0.07256342
  29440   23074 -> 0.07287797
  29440   23243 -> 0.07211737
  29440   23126 -> 0.07264227
  29440   23214 -> 0.07218723
  29440   23239 -> 0.07191171
  29440   23296 -> 0.07230829
  29440   23151 -> 0.07238768
  29440   23213 -> 0.07207783
  29440   23250 -> 0.07229500
  29440   23225 -> 0.07194797
  29440   23278 -> 0.07193974
  29440   23220 -> 0.07202992
  29440   23338 -> 0.07242738
  29440   23171 -> 0.07196748
done with simplex after 85 iterations
0 0.07197:-5.19668 -4.04528 -3.22892 -17.43446 -1.25152  7.30884 51.17415 57.56364 55.25576 
1 0.07194:-5.36620 -4.08314 -3.27640 -17.41061 -1.14653  7.47866 50.97838 57.94982 55.57899 
2 0.07212:-5.33606 -3.97565 -3.04678 -17.40965 -0.96163  7.31347 51.16305 57.11306 55.25806 
3 0.07191:-5.16200 -4.24171 -3.00056 -17.60314 -1.05987  7.50079 51.13256 57.67199 55.21517 
4 0.07208:-5.34660 -4.26759 -2.95051 -17.39575 -1.11901  7.22189 51.11013 57.39606 55.50221 
5 0.07212:-5.36814 -4.36260 -3.19756 -17.29445 -0.86842  7.41241 51.17377 57.50483 55.34946 
6 0.07208:-5.41157 -4.32140 -2.96658 -17.19741 -1.01111  7.34751 50.75075 57.73051 55.32374 
7 0.07214:-5.49953 -4.30909 -3.15169 -17.40377 -1.12478  7.44510 51.11043 57.69549 55.34227 
8 0.07195:-5.30688 -4.24705 -3.26334 -17.43120 -1.02163  7.50010 50.97666 57.60453 55.40312 
9 0.07203:-5.21199 -4.11336 -3.06920 -17.34513 -1.41477  7.76514 51.07878 57.65223 55.16825 
after parameter optimization
-center         3.42060    3.23720  -20.48226
-translation   -5.16200   -4.24171   -3.00056
-rotation     -17.60314   -1.05987    7.50079
-scale          1.02265    1.15344    1.10430
-shear          0.00000    0.00000    0.00000
  29440   23239 -> 0.07191171
Initial objective function val = 0.08549175
Final objective function value = 0.07191171
successful write

checking z-scale: making /tmp/mritotal_16215/nu_8tmp2b.xfm
[mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FK/FKsurf/mri] [2006-01-10 16:50:22] /Applications/freesurfer/lib/mni/bin/check_scale /tmp/mritotal_16215/nu_8tmp2a.xfm /tmp/mritotal_16215/nu_8tmp2b.xfm

8mm gradient lsq9 fit, target masked: making /tmp/mritotal_16215/nu_8tmp2c.xfm
[mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FK/FKsurf/mri] [2006-01-10 16:50:22] /Applications/freesurfer/lib/mni/bin/minctracc -clobber -debug /tmp/mritotal_16215/nu_8_dxyz.mnc /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc /tmp/mritotal_16215/nu_8tmp2c.xfm -transformation /tmp/mritotal_16215/nu_8tmp2b.xfm -lsq9 -xcorr -model_mask /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc -center 3.420597 3.237205 -20.482256 -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=    0.060   19.533
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    =    1.0137   -0.1216   -0.0582   -6.0085 
                         0.1505    1.0909    0.3432    1.9784 
                         0.0204   -0.3339    1.0524   -0.9160 

Transform center   =    3.421    3.237  -20.482
Transform rotations  =   -0.307   -0.018    0.131
Transform trans    =   -5.162   -4.242   -3.001
Transform scale    =    1.023    1.153    1.104
Transform shear    =    0.000    0.000    0.000

Target volume is smallest
Lattice step size  =    4.000    4.000    4.000
Lattice start      =  -65.095 -105.510  -57.250
Lattice count      =       35       46       34

===== Debugging information from /Applications/freesurfer/lib/mni/bin/minctracc =====
Data filename       = /tmp/mritotal_16215/nu_8_dxyz.mnc
Model filename      = /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc
Data mask filename  = 
Model mask filename = /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc
Input xform name    = /tmp/mritotal_16215/nu_8tmp2b.xfm
Output filename     = /tmp/mritotal_16215/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    =    1.0137   -0.1216   -0.0582   -6.0085 
                         0.1505    1.0909    0.3432    1.9784 
                         0.0204   -0.3339    1.0524   -0.9160 
Transform center   =    3.421    3.237  -20.482
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: 3.420597 3.237205 -20.482256
  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   23239 -> 0.07191171
  29440   23239 -> 0.07191171
  29440   23316 -> 0.08639084
  29440   22786 -> 0.07523159
  29440   23397 -> 0.07732443
  29440   23390 -> 0.07442107
  29440   23237 -> 0.07870151
  29440   23237 -> 0.07570345
  29440   23252 -> 0.07879837
  29440   23678 -> 0.07316095
  29440   23333 -> 0.07486451
  29440   23256 -> 0.08078719
  29440   23270 -> 0.07458864
  29440   23318 -> 0.08162890
  29440   23272 -> 0.07466962
  29440   23341 -> 0.07914396
  29440   23264 -> 0.07383337
  29440   23160 -> 0.07750657
  29440   23333 -> 0.07371693
  29440   23342 -> 0.07539827
  29440   23314 -> 0.07317010
  29440   23896 -> 0.07593136
  29440   23063 -> 0.07318730
  29440   23290 -> 0.07398966
  29440   23366 -> 0.07261131
  29440   23387 -> 0.07503302
  29440   23298 -> 0.07268113
  29440   23249 -> 0.07567507
  29440   23351 -> 0.07238518
  29440   23355 -> 0.07455897
  29440   23310 -> 0.07223979
  29440   23399 -> 0.07303100
  29440   23345 -> 0.07319839
  29440   23342 -> 0.07219268
  29440   23668 -> 0.07305287
  29440   23500 -> 0.07331952
  29440   23363 -> 0.07228222
  29440   23052 -> 0.07288796
  29440   22933 -> 0.07309626
  29440   23487 -> 0.07217703
  29440   23230 -> 0.07330793
  29440   23356 -> 0.07210201
  29440   23629 -> 0.07298540
  29440   23198 -> 0.07214952
  29440   23372 -> 0.07242975
  29440   23303 -> 0.07321652
  29440   23351 -> 0.07192952
  29440   23294 -> 0.07280885
  29440   23355 -> 0.07193082
  29440   23314 -> 0.07209458
  29440   23296 -> 0.07228083
  29440   23313 -> 0.07196662
  29440   23346 -> 0.07226358
  29440   23320 -> 0.07193001
  29440   23312 -> 0.07201432
  29440   23126 -> 0.07191288
done with simplex after 45 iterations
0 0.07191:-5.16200 -4.24171 -3.00056 -17.60315 -1.05987  7.50079 51.13258 57.67198 55.21517 
1 0.07193:-5.23180 -3.96666 -2.84807 -16.81837 -1.02648  7.12093 50.94672 58.21527 54.85895 
2 0.07191:-5.30501 -3.63568 -2.72568 -17.28533 -1.04291  7.32255 50.96481 57.67249 54.83057 
3 0.07201:-5.38071 -4.19013 -2.37080 -17.09934 -1.03361  7.32590 50.93835 57.78547 54.76205 
4 0.07209:-5.52383 -3.82362 -2.76189 -17.52828 -1.00804  7.03437 50.98969 58.44335 54.79538 
5 0.07210:-5.44424 -3.82648 -2.67225 -16.93020 -1.30256  7.24077 51.07675 58.34330 55.03616 
6 0.07197:-5.41663 -3.95456 -2.82480 -17.00555 -1.01705  7.37946 50.95422 58.16567 54.70277 
7 0.07193:-5.41927 -3.87669 -2.71936 -16.88386 -0.83647  7.27731 50.74561 58.29506 54.98507 
8 0.07215:-5.54786 -3.84486 -2.68111 -16.68302 -0.89896  7.22932 51.05291 57.58675 54.96373 
9 0.07193:-5.40215 -3.89382 -2.73534 -17.03887 -0.86364  7.34510 51.16927 58.24221 54.68066 
after parameter optimization
-center         3.42060    3.23720  -20.48226
-translation   -5.16200   -4.24171   -3.00056
-rotation     -17.60315   -1.05987    7.50079
-scale          1.02265    1.15344    1.10430
-shear          0.00000    0.00000    0.00000
  29440   23239 -> 0.07191171
Initial objective function val = 0.07191171
Final objective function value = 0.07191171
successful write

final linear fit: 8mm gradient lsq9 fit, target masked: making transforms/talairach.xfm
[mritotal] [dglen@gollum.local:/Users/dglen/freesurfer/subjects/FK/FKsurf/mri] [2006-01-10 16:50:29] /Applications/freesurfer/lib/mni/bin/minctracc -clobber -debug /tmp/mritotal_16215/nu_8_dxyz.mnc /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc transforms/talairach.xfm -transformation /tmp/mritotal_16215/nu_8tmp2c.xfm -lsq9 -xcorr -model_mask /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc -center 3.420597 3.237205 -20.482256 -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=    0.060   19.533
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    =    1.0137   -0.1216   -0.0582   -6.0085 
                         0.1505    1.0909    0.3432    1.9784 
                         0.0204   -0.3339    1.0524   -0.9160 

Transform center   =    3.421    3.237  -20.482
Transform rotations  =   -0.307   -0.018    0.131
Transform trans    =   -5.162   -4.242   -3.001
Transform scale    =    1.023    1.153    1.104
Transform shear    =    0.000    0.000    0.000

Target volume is smallest
Lattice step size  =    4.000    4.000    4.000
Lattice start      =  -65.095 -105.510  -57.250
Lattice count      =       35       46       34

===== Debugging information from /Applications/freesurfer/lib/mni/bin/minctracc =====
Data filename       = /tmp/mritotal_16215/nu_8_dxyz.mnc
Model filename      = /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc
Data mask filename  = 
Model mask filename = /Applications/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc
Input xform name    = /tmp/mritotal_16215/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    =    1.0137   -0.1216   -0.0582   -6.0085 
                         0.1505    1.0909    0.3432    1.9784 
                         0.0204   -0.3339    1.0524   -0.9160 
Transform center   =    3.421    3.237  -20.482
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: 3.420597 3.237205 -20.482256
  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   23239 -> 0.07191171
  29440   23239 -> 0.07191171
  29440   23316 -> 0.08639082
  29440   22786 -> 0.07523160
  29440   23397 -> 0.07732444
  29440   23390 -> 0.07442106
  29440   23237 -> 0.07870150
  29440   23237 -> 0.07570346
  29440   23252 -> 0.07879841
  29440   23678 -> 0.07316096
  29440   23333 -> 0.07486452
  29440   23256 -> 0.08078721
  29440   23270 -> 0.07458866
  29440   23318 -> 0.08162885
  29440   23272 -> 0.07466964
  29440   23341 -> 0.07914399
  29440   23264 -> 0.07383337
  29440   23160 -> 0.07750659
  29440   23333 -> 0.07371694
  29440   23342 -> 0.07539829
  29440   23314 -> 0.07317013
  29440   23896 -> 0.07593136
  29440   23063 -> 0.07318731
  29440   23290 -> 0.07398967
  29440   23366 -> 0.07261130
  29440   23387 -> 0.07503300
  29440   23298 -> 0.07268114
  29440   23249 -> 0.07567509
  29440   23351 -> 0.07238518
  29440   23355 -> 0.07455896
  29440   23310 -> 0.07223979
  29440   23399 -> 0.07303102
  29440   23345 -> 0.07319839
  29440   23342 -> 0.07219268
  29440   23668 -> 0.07305287
  29440   23500 -> 0.07331950
  29440   23363 -> 0.07228223
  29440   23052 -> 0.07288795
  29440   22933 -> 0.07309628
  29440   23487 -> 0.07217703
  29440   23230 -> 0.07330792
  29440   23356 -> 0.07210201
  29440   23629 -> 0.07298542
  29440   23198 -> 0.07214952
  29440   23372 -> 0.07242974
  29440   23303 -> 0.07321655
  29440   23351 -> 0.07192952
  29440   23294 -> 0.07280886
  29440   23355 -> 0.07193081
  29440   23314 -> 0.07209459
  29440   23296 -> 0.07228082
  29440   23313 -> 0.07196662
  29440   23346 -> 0.07226357
  29440   23320 -> 0.07193002
  29440   23312 -> 0.07201432
  29440   23126 -> 0.07191287
done with simplex after 45 iterations
0 0.07191:-5.16200 -4.24171 -3.00056 -17.60315 -1.05987  7.50079 51.13258 57.67198 55.21517 
1 0.07193:-5.23180 -3.96666 -2.84807 -16.81837 -1.02648  7.12093 50.94673 58.21527 54.85895 
2 0.07191:-5.30501 -3.63568 -2.72568 -17.28533 -1.04291  7.32255 50.96482 57.67249 54.83057 
3 0.07201:-5.38071 -4.19013 -2.37080 -17.09934 -1.03361  7.32590 50.93836 57.78547 54.76205 
4 0.07209:-5.52383 -3.82362 -2.76189 -17.52829 -1.00804  7.03437 50.98969 58.44335 54.79538 
5 0.07210:-5.44424 -3.82648 -2.67225 -16.93020 -1.30256  7.24077 51.07676 58.34330 55.03616 
6 0.07197:-5.41663 -3.95456 -2.82480 -17.00555 -1.01705  7.37946 50.95423 58.16567 54.70277 
7 0.07193:-5.41927 -3.87669 -2.71936 -16.88386 -0.83647  7.27731 50.74562 58.29506 54.98507 
8 0.07215:-5.54786 -3.84486 -2.68111 -16.68302 -0.89896  7.22932 51.05292 57.58675 54.96373 
9 0.07193:-5.40215 -3.89382 -2.73534 -17.03887 -0.86364  7.34510 51.16927 58.24221 54.68066 
after parameter optimization
-center         3.42060    3.23720  -20.48226
-translation   -5.16200   -4.24171   -3.00056
-rotation     -17.60315   -1.05987    7.50079
-scale          1.02265    1.15344    1.10430
-shear          0.00000    0.00000    0.00000
  29440   23239 -> 0.07191171
Initial objective function val = 0.07191171
Final objective function value = 0.07191171
successful write