[christip@varda:/home/christip/EE/EEsurf/mri] [2006-01-19 15:12:14] 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/EE/EEsurf/mri] [2006-01-19 15:12:14] /home/christip/sw/freesurfer/lib/mni/bin/autocrop -clobber nu.mnc /tmp/mritotal_26388/nu_crop.mnc -step 2 2 2 -extend 0,0 0,0 -25%,0
[autocrop] [christip@varda:/home/christip/EE/EEsurf/mri] [2006-01-19 15:12:14] /home/christip/sw/freesurfer/lib/mni/bin/mincresample -clobber nu.mnc /tmp/mritotal_26388/nu_crop.mnc -start -127.1 -128 -64 -step 2 2 2 -nelements 128 128 96
Transforming slices:................................................................................................................................Done
[mritotal] [christip@varda:/home/christip/EE/EEsurf/mri] [2006-01-19 15:12:15] /home/christip/sw/freesurfer/lib/mni/bin/volume_cog /tmp/mritotal_26388/nu_crop.mnc | tail -1
Centroid of input volume: -2.527718 7.708347 -23.107967

Zero-padding data:
[mritotal] [christip@varda:/home/christip/EE/EEsurf/mri] [2006-01-19 15:12:16] /home/christip/sw/freesurfer/lib/mni/bin/autocrop -clobber /tmp/mritotal_26388/nu_crop.mnc /tmp/mritotal_26388/nu_pad.mnc -expand 22 22 22
[autocrop] [christip@varda:/home/christip/EE/EEsurf/mri] [2006-01-19 15:12:16] /home/christip/sw/freesurfer/lib/mni/bin/mincreshape -clobber /tmp/mritotal_26388/nu_crop.mnc /tmp/mritotal_26388/nu_pad.mnc -start -11,-11,-11 -count 150,150,118
Copying chunks:......................................................................................................................................................Done.

Intensity blurring data:
[mritotal] [christip@varda:/home/christip/EE/EEsurf/mri] [2006-01-19 15:12:16] /home/christip/sw/freesurfer/lib/mni/bin/mincblur -clobber -debug /tmp/mritotal_26388/nu_pad.mnc /tmp/mritotal_26388/tmp_16 -fwhm 16
===== Debugging information from /home/christip/sw/freesurfer/lib/mni/bin/mincblur =====
Data filename     = /tmp/mritotal_26388/nu_pad.mnc
Output basename   = /tmp/mritotal_26388/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  254.994
Apodizing data at 16.000000
Volume def min and max: = 0.000000 254.993864
before blur min/max = 0.000000 254.993866
after  blur min/max = -0.000006 145.910492
Making byte volume...
[mritotal] [christip@varda:/home/christip/EE/EEsurf/mri] [2006-01-19 15:12:20] /home/christip/sw/freesurfer/lib/mni/bin/autocrop -clobber /tmp/mritotal_26388/tmp_16_blur.mnc /tmp/mritotal_26388/nu_16_blur.mnc -expand -44 -44 -44
[autocrop] [christip@varda:/home/christip/EE/EEsurf/mri] [2006-01-19 15:12:20] /home/christip/sw/freesurfer/lib/mni/bin/mincreshape -clobber /tmp/mritotal_26388/tmp_16_blur.mnc /tmp/mritotal_26388/nu_16_blur.mnc -start 22,22,22 -count 106,106,74
Copying chunks:..........................................................................................................Done.

Gradient blurring data:
[mritotal] [christip@varda:/home/christip/EE/EEsurf/mri] [2006-01-19 15:12:20] /home/christip/sw/freesurfer/lib/mni/bin/mincblur -clobber -debug /tmp/mritotal_26388/nu_pad.mnc /tmp/mritotal_26388/tmp_8 -fwhm 8 -gradient
Transforming slices:......................................................................................................................................................Done
===== Debugging information from /home/christip/sw/freesurfer/lib/mni/bin/mincblur =====
Data filename     = /tmp/mritotal_26388/nu_pad.mnc
Output basename   = /tmp/mritotal_26388/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  254.994
Apodizing data at 8.000000
Volume def min and max: = 0.000000 254.993864
before blur min/max = 0.000000 254.993866
after  blur min/max = -0.000017 191.743500
Making byte volume...
Making byte volume dx...dx: min = -18.493130, max = 17.584578
Making byte volume dy...dy: min = -17.661434, max = 15.489302
Making byte volume dz...dz: min = -17.854713, max = 17.001926
[mritotal] [christip@varda:/home/christip/EE/EEsurf/mri] [2006-01-19 15:12:28] /home/christip/sw/freesurfer/lib/mni/bin/autocrop -clobber /tmp/mritotal_26388/tmp_8_blur.mnc /tmp/mritotal_26388/nu_8_blur.mnc -expand -34 -34 -34
[autocrop] [christip@varda:/home/christip/EE/EEsurf/mri] [2006-01-19 15:12:28] /home/christip/sw/freesurfer/lib/mni/bin/mincreshape -clobber /tmp/mritotal_26388/tmp_8_blur.mnc /tmp/mritotal_26388/nu_8_blur.mnc -start 17,17,17 -count 116,116,84
Copying chunks:....................................................................................................................Done.
[mritotal] [christip@varda:/home/christip/EE/EEsurf/mri] [2006-01-19 15:12:28] /home/christip/sw/freesurfer/lib/mni/bin/autocrop -clobber /tmp/mritotal_26388/tmp_8_dxyz.mnc /tmp/mritotal_26388/nu_8_dxyz.mnc -expand -34 -34 -34
[autocrop] [christip@varda:/home/christip/EE/EEsurf/mri] [2006-01-19 15:12:28] /home/christip/sw/freesurfer/lib/mni/bin/mincreshape -clobber /tmp/mritotal_26388/tmp_8_dxyz.mnc /tmp/mritotal_26388/nu_8_dxyz.mnc -start 17,17,17 -count 116,116,84
Copying chunks:....................................................................................................................Done.

16mm intensity lsq7 fit, no masks: making /tmp/mritotal_26388/nu_16.xfm
[mritotal] [christip@varda:/home/christip/EE/EEsurf/mri] [2006-01-19 15:12:28] /home/christip/sw/freesurfer/lib/mni/bin/minctracc -clobber -debug /tmp/mritotal_26388/nu_16_blur.mnc /home/christip/sw/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_16_blur.mnc /tmp/mritotal_26388/nu_16.xfm -est_translations -lsq7 -xcorr -center -2.527718 7.708347 -23.107967 -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  145.910
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    2.8558 
                         0.0000    1.0000    0.0000  -25.2997 
                         0.0000    0.0000    1.0000   32.5626 

Transform center   =   -2.528    7.708  -23.108
Transform rotations  =    0.000    0.000    0.000
Transform trans    =    2.856  -25.300   32.563
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_26388/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_26388/nu_16.xfm
Step size           = 4.000000 4.000000 4.000000
Sub-lattice dia     = 24.000000 24.000000 24.000000
Objective function  = cross correlation (threshold = 0.000000 0.000000)
Transform linear    = TRUE
Transform inverted? = FALSE
Transform type      = 4
Transform matrix    =    1.0000    0.0000    0.0000    0.0000 
                         0.0000    1.0000    0.0000    0.0000 
                         0.0000    0.0000    1.0000    0.0000 
Transform center   =   -2.528    7.708  -23.108
Transform rotation   =    0.000    0.000    0.000 

Transform trans    =    0.000    0.000    0.000
Transform scale    =    1.000    1.000    1.000

Center of rot/scale forced: -2.527718 7.708347 -23.107967
  using PAT to get initial parameters:
  will try to get: [trans]
COG of v1 forced: -2.527718 7.708347 -23.107967
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] = 2.855813 -25.299677 32.562594
Only center & trans required, now returning from init_transformation
Transform center   =   -2.528    7.708  -23.108
Transform rots    =    0.000    0.000    0.000
Transform trans    =    2.856  -25.300   32.563
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   45835 -> 0.03318377
  68585   45835 -> 0.03318377
  68585   40705 -> 0.07693741
  68585   43399 -> 0.04063487
  68585   45861 -> 0.04911242
  68585   47331 -> 0.03770052
  68585   45101 -> 0.04330375
  68585   43826 -> 0.03977548
  68585   56115 -> 0.08982270
  68585   14921 -> 0.14558914
  68585   52557 -> 0.05354805
  68585   44763 -> 0.08374336
  68585   44194 -> 0.04769279
  68585   30535 -> 0.08196643
  68585   50175 -> 0.03717650
  68585   46972 -> 0.02687185
  68585   46843 -> 0.05393219
  68585   45747 -> 0.03963635
  68585   46715 -> 0.03287039
  68585   49010 -> 0.04865520
  68585   46415 -> 0.03050782
  68585   47739 -> 0.03422063
  68585   46749 -> 0.04258976
  68585   46940 -> 0.03015077
  68585   47027 -> 0.02502886
  68585   45027 -> 0.04260212
  68585   44157 -> 0.02823733
  68585   42708 -> 0.02958093
  68585   44532 -> 0.03050488
  68585   44449 -> 0.02404937
  68585   41898 -> 0.04094152
  68585   45027 -> 0.02223452
  68585   44414 -> 0.04026018
  68585   44832 -> 0.02917645
  68585   43371 -> 0.02440460
  68585   45378 -> 0.02174202
  68585   45170 -> 0.04093954
  68585   44402 -> 0.03248966
  68585   45949 -> 0.01987914
  68585   47244 -> 0.03019104
  68585   45646 -> 0.01965998
  68585   43644 -> 0.01642373
  68585   41087 -> 0.02882634
  68585   41332 -> 0.05412649
  68585   46493 -> 0.01648688
  68585   47152 -> 0.02376571
  68585   47428 -> 0.01636638
  68585   48083 -> 0.02676347
  68585   44385 -> 0.01962654
  68585   44541 -> 0.01396405
  68585   42910 -> 0.02152348
  68585   43881 -> 0.02130052
  68585   44987 -> 0.01587304
  68585   43485 -> 0.01980766
  68585   44740 -> 0.01477201
  68585   45051 -> 0.01285939
  68585   44586 -> 0.01986318
  68585   45855 -> 0.02642827
  68585   45265 -> 0.01337515
  68585   44295 -> 0.01332497
  68585   47183 -> 0.01306569
  68585   43829 -> 0.01459500
  68585   43528 -> 0.01304356
  68585   44415 -> 0.00993944
  68585   43810 -> 0.01317258
  68585   46636 -> 0.01318149
  68585   44866 -> 0.01494951
  68585   44985 -> 0.01111330
  68585   44662 -> 0.01370165
  68585   45646 -> 0.01087390
  68585   46338 -> 0.01273325
  68585   44572 -> 0.01474493
  68585   45967 -> 0.01066616
  68585   43308 -> 0.01437525
  68585   46178 -> 0.01071476
  68585   47302 -> 0.01141883
  68585   45511 -> 0.01520203
  68585   45656 -> 0.01035230
  68585   44988 -> 0.01209661
  68585   45392 -> 0.01024139
  68585   43312 -> 0.01273897
  68585   46420 -> 0.01010809
  68585   46183 -> 0.00936130
  68585   46221 -> 0.01031462
  68585   45926 -> 0.00932873
  68585   46124 -> 0.01034747
  68585   45388 -> 0.00882190
  68585   45069 -> 0.00956200
  68585   45669 -> 0.01045633
  68585   45521 -> 0.00942314
  68585   45550 -> 0.00928253
  68585   45961 -> 0.00923704
  68585   44799 -> 0.00902190
  68585   46672 -> 0.00863069
  68585   47199 -> 0.01021839
  68585   46077 -> 0.00827729
  68585   46342 -> 0.00892355
  68585   45321 -> 0.00926928
  68585   45452 -> 0.00869567
  68585   45756 -> 0.00903284
  68585   45965 -> 0.00927369
  68585   45535 -> 0.00851320
  68585   45426 -> 0.00831986
  68585   45524 -> 0.00912969
  68585   45681 -> 0.00834792
  68585   46790 -> 0.00826900
  68585   47414 -> 0.00955959
  68585   46543 -> 0.00787872
  68585   47125 -> 0.00856420
  68585   46739 -> 0.00900975
  68585   45817 -> 0.00806983
  68585   45135 -> 0.00861164
  68585   45566 -> 0.00807717
  68585   46407 -> 0.00813659
  68585   46463 -> 0.00816687
  68585   47034 -> 0.00824147
  68585   46725 -> 0.00781195
  68585   46817 -> 0.00839388
  68585   45954 -> 0.00846575
  68585   46497 -> 0.00785855
  68585   45452 -> 0.00836315
  68585   46666 -> 0.00785224
  68585   46245 -> 0.00815767
  68585   46278 -> 0.00784545
  68585   46170 -> 0.00831421
  68585   46313 -> 0.00781638
  68585   47120 -> 0.00815382
  68585   45951 -> 0.00782119
  68585   47042 -> 0.00778757
  68585   47598 -> 0.00828025
  68585   46416 -> 0.00794324
  68585   46523 -> 0.00774850
  68585   46458 -> 0.00779866
  68585   46229 -> 0.00779554
  68585   46680 -> 0.00777550
  68585   47066 -> 0.00796635
  68585   46299 -> 0.00770717
  68585   46760 -> 0.00764235
  68585   46999 -> 0.00772528
  68585   46488 -> 0.00792713
  68585   46589 -> 0.00768902
  68585   46753 -> 0.00774731
  68585   47069 -> 0.00788018
  68585   46433 -> 0.00769133
  68585   46142 -> 0.00780652
  68585   46800 -> 0.00769207
  68585   46515 -> 0.00771930
  68585   46653 -> 0.00768049
  68585   46469 -> 0.00775885
  68585   46642 -> 0.00767167
  68585   46700 -> 0.00776059
  68585   46541 -> 0.00766222
  68585   47059 -> 0.00773680
  68585   46454 -> 0.00765754
  68585   46366 -> 0.00771519
  68585   46681 -> 0.00765408
done with simplex after 147 iterations
0 0.00766: 3.38617 -16.41435  8.28611 -15.39232 -0.61240 -2.74114 52.71370 
1 0.00765: 3.22759 -16.75826  8.24669 -15.00833 -0.92920 -2.46800 52.86540 
2 0.00764: 3.47477 -17.45249  8.40294 -15.98340 -1.03637 -2.85557 52.88659 
3 0.00768: 2.74049 -16.70367  8.31179 -15.92185 -0.09552 -2.03294 52.81671 
4 0.00769: 3.25487 -16.35699  8.00601 -15.99716 -0.72462 -2.44413 52.75512 
5 0.00769: 3.21882 -16.67069  8.30867 -15.50821 -0.64041 -1.90176 52.68834 
6 0.00767: 2.97706 -16.56805  8.42824 -15.00837 -0.72298 -2.29068 52.78880 
7 0.00766: 3.37579 -16.57351  8.67691 -15.58779 -0.55415 -2.59588 52.77811 
after parameter optimization
-center        -2.52772    7.70835  -23.10797
-translation    3.47477  -17.45249    8.40294
-rotation     -15.98340   -1.03637   -2.85557
-scale          1.05773    1.05773    1.05773
-shear          0.00000    0.00000    0.00000
  68585   46760 -> 0.00764235
Initial objective function val = 0.03318377
Final objective function value = 0.00764235
successful write

8mm intensity lsq7 fit, no masks: making /tmp/mritotal_26388/nu_8tmp1a.xfm
[mritotal] [christip@varda:/home/christip/EE/EEsurf/mri] [2006-01-19 15:12:39] /home/christip/sw/freesurfer/lib/mni/bin/minctracc -clobber -debug /tmp/mritotal_26388/nu_8_blur.mnc /home/christip/sw/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_blur.mnc /tmp/mritotal_26388/nu_8tmp1a.xfm -transformation /tmp/mritotal_26388/nu_16.xfm -lsq7 -xcorr -center -2.527718 7.708347 -23.107967 -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  191.743
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    =    1.0562    0.0559   -0.0039    3.0967 
                        -0.0527    1.0153    0.2918  -10.9606 
                         0.0191   -0.2912    1.0167   11.0814 

Transform center   =   -2.528    7.708  -23.108
Transform rotations  =   -0.279   -0.018   -0.050
Transform trans    =    3.475  -17.452    8.403
Transform scale    =    1.058    1.058    1.058
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_26388/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_26388/nu_16.xfm
Output filename     = /tmp/mritotal_26388/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    =    1.0562    0.0559   -0.0039    3.0967 
                        -0.0527    1.0153    0.2918  -10.9606 
                         0.0191   -0.2912    1.0167   11.0814 
Transform center   =   -2.528    7.708  -23.108
Transform rotation   =    0.000    0.000    0.000 

Transform trans    =    0.000    0.000    0.000
Transform scale    =    1.000    1.000    1.000

Center of rot/scale forced: -2.527718 7.708347 -23.107967
  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   57632 -> 0.02382966
  80410   57632 -> 0.02382966
  80410   55831 -> 0.03194711
  80410   56019 -> 0.02605494
  80410   58109 -> 0.02988552
  80410   57857 -> 0.02406544
  80410   57005 -> 0.02553477
  80410   57932 -> 0.02588916
  80410   61164 -> 0.04142720
  80410   50596 -> 0.04905168
  80410   59519 -> 0.02908143
  80410   58762 -> 0.03190378
  80410   58544 -> 0.02618718
  80410   57682 -> 0.02211577
  80410   57417 -> 0.02696586
  80410   54847 -> 0.03073228
  80410   58534 -> 0.02461475
  80410   56258 -> 0.02449449
  80410   59235 -> 0.02627049
  80410   56894 -> 0.02359977
  80410   56587 -> 0.02302297
  80410   57690 -> 0.02330568
  80410   55861 -> 0.02362641
  80410   57603 -> 0.02373121
  80410   56409 -> 0.02334902
  80410   56475 -> 0.02384006
  80410   57326 -> 0.02231475
  80410   55802 -> 0.02492897
  80410   57321 -> 0.02212517
  80410   58151 -> 0.02575039
  80410   56524 -> 0.02200086
  80410   57391 -> 0.02196576
  80410   57731 -> 0.02473735
  80410   58038 -> 0.02271400
  80410   56689 -> 0.02287867
  80410   57890 -> 0.02311295
  80410   56972 -> 0.02182262
  80410   57739 -> 0.02334169
  80410   56980 -> 0.02170182
  80410   56229 -> 0.02293237
  80410   57597 -> 0.02167974
  80410   57120 -> 0.02204942
  80410   56975 -> 0.02262468
  80410   57242 -> 0.02149548
  80410   56621 -> 0.02350063
  80410   57436 -> 0.02141429
  80410   57182 -> 0.02224351
  80410   57117 -> 0.02151331
  80410   57880 -> 0.02148885
  80410   57240 -> 0.02231177
  80410   57328 -> 0.02142905
  80410   57858 -> 0.02157236
  80410   57992 -> 0.02180406
  80410   57206 -> 0.02136688
  80410   57281 -> 0.02187615
  80410   57509 -> 0.02135052
  80410   57016 -> 0.02172128
  80410   57679 -> 0.02134093
  80410   57837 -> 0.02129030
  80410   58150 -> 0.02154206
  80410   57846 -> 0.02143133
  80410   57236 -> 0.02164838
  80410   57677 -> 0.02127826
  80410   57185 -> 0.02153096
  80410   57669 -> 0.02126395
  80410   57849 -> 0.02143635
  80410   57418 -> 0.02128091
  80410   57740 -> 0.02150964
  80410   57530 -> 0.02127503
  80410   57997 -> 0.02128089
  80410   57858 -> 0.02137888
  80410   57587 -> 0.02125264
  80410   57683 -> 0.02123968
  80410   57719 -> 0.02139201
  80410   57489 -> 0.02145340
  80410   57749 -> 0.02122051
  80410   58004 -> 0.02123280
done with simplex after 68 iterations
0 0.02122: 2.89032 -16.38407  4.88938 -13.02484  0.18009 -3.52885 53.71243 
1 0.02126: 2.96971 -16.48033  4.25035 -12.69150  0.63681 -3.60470 53.75635 
2 0.02123: 2.82019 -16.58236  4.78773 -12.79933  0.52595 -3.18722 53.85460 
3 0.02128: 3.03398 -16.00190  4.53470 -13.08579  0.38534 -3.15487 53.61159 
4 0.02125: 3.05426 -16.27821  4.85114 -12.56054  0.06291 -3.60239 53.60993 
5 0.02128: 2.89779 -16.34790  4.24551 -12.49993 -0.27516 -3.23979 53.91860 
6 0.02124: 3.08515 -16.47011  4.87749 -13.10018  0.38598 -3.85423 53.82901 
7 0.02128: 2.80891 -16.39352  4.49628 -12.56543  0.71496 -4.07124 53.85368 
after parameter optimization
-center        -2.52772    7.70835  -23.10797
-translation    2.89032  -16.38407    4.88938
-rotation     -13.02484    0.18009   -3.52885
-scale          1.07425    1.07425    1.07425
-shear          0.00000    0.00000    0.00000
  80410   57749 -> 0.02122051
Initial objective function val = 0.02382966
Final objective function value = 0.02122051
successful write

8mm gradient lsq7 fit, target masked: making /tmp/mritotal_26388/nu_8tmp1b.xfm
[mritotal] [christip@varda:/home/christip/EE/EEsurf/mri] [2006-01-19 15:12:46] /home/christip/sw/freesurfer/lib/mni/bin/minctracc -clobber -debug /tmp/mritotal_26388/nu_8_dxyz.mnc /home/christip/sw/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc /tmp/mritotal_26388/nu_8tmp1b.xfm -transformation /tmp/mritotal_26388/nu_8tmp1a.xfm -lsq7 -xcorr -model_mask /home/christip/sw/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc -center -2.527718 7.708347 -23.107967 -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=    0.069   19.657
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    =    1.0722    0.0637    0.0182    3.0023 
                        -0.0661    1.0447    0.2414  -11.3162 
                        -0.0034   -0.2421    1.0466    7.8240 

Transform center   =   -2.528    7.708  -23.108
Transform rotations  =   -0.227    0.003   -0.062
Transform trans    =    2.890  -16.384    4.889
Transform scale    =    1.074    1.074    1.074
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_26388/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_26388/nu_8tmp1a.xfm
Output filename     = /tmp/mritotal_26388/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    =    1.0722    0.0637    0.0182    3.0023 
                        -0.0661    1.0447    0.2414  -11.3162 
                        -0.0034   -0.2421    1.0466    7.8240 
Transform center   =   -2.528    7.708  -23.108
Transform rotation   =    0.000    0.000    0.000 

Transform trans    =    0.000    0.000    0.000
Transform scale    =    1.000    1.000    1.000

Center of rot/scale forced: -2.527718 7.708347 -23.107967
  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   25745 -> 0.10994571
  29440   25745 -> 0.10994571
  29440   25713 -> 0.11402741
  29440   25338 -> 0.10248990
  29440   25831 -> 0.12051868
  29440   25855 -> 0.10730385
  29440   25738 -> 0.11262799
  29440   25728 -> 0.10989367
  29440   26232 -> 0.13630928
  29440   25163 -> 0.12042518
  29440   25394 -> 0.10889640
  29440   26108 -> 0.12523417
  29440   25407 -> 0.10959350
  29440   25476 -> 0.10986906
  29440   25390 -> 0.10421706
  29440   25281 -> 0.10186206
  29440   25052 -> 0.10359649
  29440   25172 -> 0.10524040
  29440   25327 -> 0.10249475
  29440   25388 -> 0.09591171
  29440   25387 -> 0.09628090
  29440   25389 -> 0.10263354
  29440   24773 -> 0.09731220
  29440   25376 -> 0.09989034
  29440   25146 -> 0.09524322
  29440   25019 -> 0.10088287
  29440   25076 -> 0.10245928
  29440   25055 -> 0.10127093
  29440   24995 -> 0.09638183
  29440   25213 -> 0.10376851
  29440   25110 -> 0.09684502
  29440   24954 -> 0.09681410
  29440   25147 -> 0.09659482
  29440   24769 -> 0.09913101
  29440   24923 -> 0.09503227
  29440   25409 -> 0.09604614
  29440   25165 -> 0.09109894
  29440   25189 -> 0.09161973
  29440   25384 -> 0.10231845
  29440   25059 -> 0.09302926
  29440   25162 -> 0.09605785
  29440   25370 -> 0.10027216
  29440   25091 -> 0.09346284
  29440   25167 -> 0.09626269
  29440   25168 -> 0.09368939
  29440   24853 -> 0.09632102
  29440   25274 -> 0.09369110
  29440   24839 -> 0.09411883
  29440   25010 -> 0.09514186
  29440   25042 -> 0.09298839
  29440   25255 -> 0.09357223
  29440   25451 -> 0.09546585
  29440   24997 -> 0.09257907
  29440   24947 -> 0.09220293
  29440   24991 -> 0.09130335
  29440   24822 -> 0.09420455
  29440   25151 -> 0.09214702
  29440   25009 -> 0.09328511
  29440   25030 -> 0.09208349
  29440   25029 -> 0.09112766
  29440   25049 -> 0.09161655
  29440   25107 -> 0.09129106
  29440   25199 -> 0.09150166
  29440   25016 -> 0.09087511
  29440   24950 -> 0.09208518
  29440   25129 -> 0.09029248
  29440   25180 -> 0.09069079
  29440   25137 -> 0.09236215
  29440   25071 -> 0.09080081
  29440   24941 -> 0.09123216
  29440   25141 -> 0.09084823
  29440   25033 -> 0.09061554
  29440   25220 -> 0.09141466
  29440   25013 -> 0.09053625
  29440   25131 -> 0.09054711
  29440   24988 -> 0.09034835
  29440   25128 -> 0.08996958
  29440   25183 -> 0.09014471
  29440   25003 -> 0.09061477
  29440   25052 -> 0.09060591
  29440   25090 -> 0.09022546
  29440   25156 -> 0.09102438
  29440   25033 -> 0.09009250
  29440   25095 -> 0.09085790
  29440   25061 -> 0.09019154
  29440   24998 -> 0.09046719
  29440   25109 -> 0.08991037
  29440   25160 -> 0.09028835
  29440   25153 -> 0.09053672
  29440   25034 -> 0.09008472
  29440   25180 -> 0.09020304
  29440   25055 -> 0.08977733
  29440   25020 -> 0.08979517
  29440   25084 -> 0.09014669
  29440   24966 -> 0.09006278
  29440   25054 -> 0.08968421
  29440   25053 -> 0.08967919
  29440   25027 -> 0.09017291
  29440   25068 -> 0.08985212
  29440   25086 -> 0.08947488
  29440   25110 -> 0.08958974
  29440   25095 -> 0.08954457
  29440   25211 -> 0.08975325
  29440   25068 -> 0.08945850
  29440   25037 -> 0.08979641
  29440   25068 -> 0.08959979
  29440   25105 -> 0.08947816
  29440   25137 -> 0.08945200
  29440   25181 -> 0.08979246
  29440   24969 -> 0.08951264
done with simplex after 101 iterations
0 0.08954: 4.54063 -12.69676  3.79136 -9.53691 -2.18049 -3.32800 53.58261 
1 0.08947: 4.50344 -12.59417  3.54460 -9.28431 -2.37241 -3.03003 53.59171 
2 0.08945: 4.51569 -12.74751  3.86086 -9.40675 -2.04639 -2.70411 53.67634 
3 0.08951: 4.73629 -12.17084  3.73954 -9.41279 -2.37710 -2.91469 53.52156 
4 0.08960: 4.12335 -12.69531  3.71171 -9.85813 -1.69428 -2.87633 53.56900 
5 0.08968: 4.60030 -12.62080  3.62333 -9.87392 -2.18748 -2.74384 53.60830 
6 0.08946: 4.97899 -12.64626  3.76490 -9.41574 -2.75614 -2.89592 53.50767 
7 0.08948: 4.44931 -12.68790  3.94215 -9.51171 -2.39651 -2.85491 53.62288 
after parameter optimization
-center        -2.52772    7.70835  -23.10797
-translation    4.51569  -12.74751    3.86086
-rotation      -9.40675   -2.04639   -2.70411
-scale          1.07353    1.07353    1.07353
-shear          0.00000    0.00000    0.00000
  29440   25137 -> 0.08945200
Initial objective function val = 0.10994571
Final objective function value = 0.08945200
successful write

8mm gradient lsq9 fit, target masked: making /tmp/mritotal_26388/nu_8tmp2a.xfm
[mritotal] [christip@varda:/home/christip/EE/EEsurf/mri] [2006-01-19 15:12:52] /home/christip/sw/freesurfer/lib/mni/bin/minctracc -clobber -debug /tmp/mritotal_26388/nu_8_dxyz.mnc /home/christip/sw/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc /tmp/mritotal_26388/nu_8tmp2a.xfm -transformation /tmp/mritotal_26388/nu_8tmp1b.xfm -lsq9 -xcorr -model_mask /home/christip/sw/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc -center -2.527718 7.708347 -23.107967 -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=    0.069   19.657
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    =    1.0716    0.0562   -0.0295    3.5817 
                        -0.0506    1.0576    0.1770   -9.2283 
                         0.0383   -0.1753    1.0584    6.6593 

Transform center   =   -2.528    7.708  -23.108
Transform rotations  =   -0.164   -0.036   -0.047
Transform trans    =    4.516  -12.748    3.861
Transform scale    =    1.074    1.074    1.074
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_26388/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_26388/nu_8tmp1b.xfm
Output filename     = /tmp/mritotal_26388/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    =    1.0716    0.0562   -0.0295    3.5817 
                        -0.0506    1.0576    0.1770   -9.2283 
                         0.0383   -0.1753    1.0584    6.6593 
Transform center   =   -2.528    7.708  -23.108
Transform rotation   =    0.000    0.000    0.000 

Transform trans    =    0.000    0.000    0.000
Transform scale    =    1.000    1.000    1.000

Center of rot/scale forced: -2.527718 7.708347 -23.107967
  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   25137 -> 0.08945202
  29440   25137 -> 0.08945202
  29440   25117 -> 0.10015152
  29440   24705 -> 0.09474880
  29440   25211 -> 0.09738322
  29440   25271 -> 0.09093136
  29440   25139 -> 0.09358287
  29440   25136 -> 0.09191758
  29440   25139 -> 0.10750107
  29440   25614 -> 0.09456722
  29440   25179 -> 0.08842473
  29440   25196 -> 0.08199119
  29440   25228 -> 0.09810343
  29440   25235 -> 0.09412598
  29440   25158 -> 0.08770584
  29440   25739 -> 0.08546464
  29440   24860 -> 0.08316875
  29440   25172 -> 0.09758083
  29440   25218 -> 0.08623959
  29440   25276 -> 0.08331347
  29440   25326 -> 0.07913805
  29440   25418 -> 0.08321082
  29440   25200 -> 0.07705605
  29440   25170 -> 0.08091783
  29440   25330 -> 0.07555611
  29440   25429 -> 0.07890634
  29440   25337 -> 0.08801006
  29440   25297 -> 0.08114746
  29440   25378 -> 0.08580788
  29440   25363 -> 0.07837494
  29440   25194 -> 0.08403820
  29440   24697 -> 0.07743363
  29440   25153 -> 0.08452838
  29440   25183 -> 0.07831363
  29440   25043 -> 0.07993762
  29440   25502 -> 0.07731175
  29440   25237 -> 0.07602262
  29440   25127 -> 0.07476952
  29440   25036 -> 0.08042705
  29440   25392 -> 0.08019396
  29440   25137 -> 0.07581904
  29440   25076 -> 0.07801991
  29440   24967 -> 0.07713027
  29440   25106 -> 0.07937925
  29440   25165 -> 0.07492462
  29440   25232 -> 0.07926321
  29440   25114 -> 0.07457550
  29440   25674 -> 0.07644661
  29440   24922 -> 0.07836506
  29440   25358 -> 0.07468204
  29440   25547 -> 0.07833430
  29440   25116 -> 0.07467895
  29440   25311 -> 0.07526375
  29440   24726 -> 0.07763287
  29440   25444 -> 0.07434251
  29440   25225 -> 0.07763733
  29440   25236 -> 0.07418483
  29440   25356 -> 0.07484342
  29440   25162 -> 0.07396529
  29440   25063 -> 0.07642436
  29440   25154 -> 0.07622250
  29440   25270 -> 0.07381359
  29440   25323 -> 0.07559748
  29440   25205 -> 0.07372623
  29440   25093 -> 0.07549617
  29440   25293 -> 0.07382634
  29440   25362 -> 0.07673109
  29440   25187 -> 0.07368943
  29440   25085 -> 0.07345722
  29440   24951 -> 0.07454447
  29440   25321 -> 0.07388353
  29440   25376 -> 0.07426221
  29440   25026 -> 0.07368873
  29440   25020 -> 0.07471547
  29440   25289 -> 0.07340769
  29440   25174 -> 0.07353932
  29440   25245 -> 0.07414304
  29440   25185 -> 0.07333495
  29440   25053 -> 0.07443143
  29440   25261 -> 0.07325523
  29440   25081 -> 0.07361287
  29440   25063 -> 0.07309441
  29440   24950 -> 0.07346415
  29440   25094 -> 0.07390390
  29440   25177 -> 0.07321915
  29440   25115 -> 0.07324843
  29440   25286 -> 0.07339998
  29440   25281 -> 0.07343927
  29440   25215 -> 0.07382873
  29440   25186 -> 0.07310745
  29440   25315 -> 0.07346359
  29440   25146 -> 0.07307682
  29440   25098 -> 0.07358874
  29440   25238 -> 0.07307064
  29440   25076 -> 0.07330745
  29440   25028 -> 0.07357840
  29440   25224 -> 0.07304145
  29440   25144 -> 0.07286566
  29440   25122 -> 0.07310611
  29440   25266 -> 0.07334670
  29440   25124 -> 0.07306219
  29440   25051 -> 0.07324480
  29440   25186 -> 0.07385456
  29440   25133 -> 0.07293743
  29440   25262 -> 0.07328564
  29440   25107 -> 0.07306587
  29440   25127 -> 0.07298627
  29440   25103 -> 0.07305112
  29440   25237 -> 0.07311689
  29440   25104 -> 0.07299819
done with simplex after 99 iterations
0 0.07287: 4.14494 -12.51831  2.15003 -8.86850 -1.30267 -2.22800 51.72174 53.77397 56.54650 
1 0.07307: 4.13899 -12.26677  2.05747 -9.10498 -1.27449 -2.45735 51.68678 53.90848 56.49770 
2 0.07304: 4.14978 -12.56642  2.20827 -9.06809 -1.10219 -2.48775 51.59774 54.10733 56.46284 
3 0.07299: 4.16202 -12.39258  1.80506 -9.17582 -1.23038 -2.45539 51.59832 53.90209 56.87840 
4 0.07300: 4.18611 -12.34994  2.09795 -9.10937 -1.34785 -2.52808 51.64289 53.82201 56.58076 
5 0.07307: 4.05286 -12.51219  2.15543 -8.97679 -1.32119 -2.38364 51.61024 54.17687 56.53880 
6 0.07306: 4.22579 -12.33540  2.12083 -9.08599 -1.30974 -2.33129 51.50253 53.91848 56.49882 
7 0.07305: 4.02034 -12.48942  1.99895 -9.13323 -1.22191 -2.27895 51.80813 53.71805 56.56207 
8 0.07308: 3.98401 -12.43063  2.11674 -8.87378 -1.13884 -2.35449 51.65997 53.85337 56.58650 
9 0.07294: 4.13348 -12.31486  1.91141 -8.82404 -1.27229 -2.50553 51.56261 53.91030 56.56640 
after parameter optimization
-center        -2.52772    7.70835  -23.10797
-translation    4.14494  -12.51831    2.15003
-rotation      -8.86850   -1.30267   -2.22800
-scale          1.03443    1.07548    1.13093
-shear          0.00000    0.00000    0.00000
  29440   25144 -> 0.07286566
Initial objective function val = 0.08945202
Final objective function value = 0.07286566
successful write

checking z-scale: making /tmp/mritotal_26388/nu_8tmp2b.xfm
[mritotal] [christip@varda:/home/christip/EE/EEsurf/mri] [2006-01-19 15:12:58] /home/christip/sw/freesurfer/lib/mni/bin/check_scale /tmp/mritotal_26388/nu_8tmp2a.xfm /tmp/mritotal_26388/nu_8tmp2b.xfm

8mm gradient lsq9 fit, target masked: making /tmp/mritotal_26388/nu_8tmp2c.xfm
[mritotal] [christip@varda:/home/christip/EE/EEsurf/mri] [2006-01-19 15:12:58] /home/christip/sw/freesurfer/lib/mni/bin/minctracc -clobber -debug /tmp/mritotal_26388/nu_8_dxyz.mnc /home/christip/sw/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc /tmp/mritotal_26388/nu_8tmp2c.xfm -transformation /tmp/mritotal_26388/nu_8tmp2b.xfm -lsq9 -xcorr -model_mask /home/christip/sw/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc -center -2.527718 7.708347 -23.107967 -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=    0.069   19.657
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    =    1.0334    0.0434   -0.0170    3.5019 
                        -0.0418    1.0617    0.1666   -9.2492 
                         0.0257   -0.1743    1.1171    6.2651 

Transform center   =   -2.528    7.708  -23.108
Transform rotations  =   -0.155   -0.023   -0.039
Transform trans    =    4.145  -12.518    2.150
Transform scale    =    1.034    1.075    1.131
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_26388/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_26388/nu_8tmp2b.xfm
Output filename     = /tmp/mritotal_26388/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    =    1.0334    0.0434   -0.0170    3.5019 
                        -0.0418    1.0617    0.1666   -9.2492 
                         0.0257   -0.1743    1.1171    6.2651 
Transform center   =   -2.528    7.708  -23.108
Transform rotation   =    0.000    0.000    0.000 

Transform trans    =    0.000    0.000    0.000
Transform scale    =    1.000    1.000    1.000

Center of rot/scale forced: -2.527718 7.708347 -23.107967
  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   25144 -> 0.07286566
  29440   25144 -> 0.07286566
  29440   25126 -> 0.08694077
  29440   24709 -> 0.07765677
  29440   25209 -> 0.08144642
  29440   25279 -> 0.07556362
  29440   25143 -> 0.07780708
  29440   25138 -> 0.07666756
  29440   25143 -> 0.08532723
  29440   25622 -> 0.07572625
  29440   25174 -> 0.08083782
  29440   25216 -> 0.08945946
  29440   25153 -> 0.07700001
  29440   25202 -> 0.08593056
  29440   25161 -> 0.07748231
  29440   25136 -> 0.07933112
  29440   25157 -> 0.08566415
  29440   25170 -> 0.07548083
  29440   25209 -> 0.08016443
  29440   25154 -> 0.07475952
  29440   25197 -> 0.07655344
  29440   25728 -> 0.07767713
  29440   24973 -> 0.07448059
  29440   25237 -> 0.07552260
  29440   25272 -> 0.07809418
  29440   25183 -> 0.07393152
  29440   25304 -> 0.07482776
  29440   25264 -> 0.07687638
  29440   25214 -> 0.07394736
  29440   24740 -> 0.07538958
  29440   24971 -> 0.07584932
  29440   25194 -> 0.07339133
  29440   24988 -> 0.07689939
  29440   25180 -> 0.07332641
  29440   25075 -> 0.07592171
  29440   25144 -> 0.07359808
  29440   25585 -> 0.07588717
  29440   24954 -> 0.07337546
  29440   24963 -> 0.07702534
  29440   25217 -> 0.07327510
  29440   25114 -> 0.07451826
  29440   25122 -> 0.07331543
  29440   25329 -> 0.07344911
  29440   25110 -> 0.07428859
  29440   25187 -> 0.07312274
  29440   25144 -> 0.07407171
  29440   25173 -> 0.07305098
  29440   25187 -> 0.07342754
  29440   24971 -> 0.07398477
  29440   25237 -> 0.07292517
  29440   25124 -> 0.07366997
  29440   25170 -> 0.07292948
  29440   25112 -> 0.07309116
  29440   25388 -> 0.07331383
  29440   25212 -> 0.07328124
  29440   25285 -> 0.07272746
  29440   25360 -> 0.07335944
  29440   24996 -> 0.07312530
  29440   25134 -> 0.07339460
  29440   25191 -> 0.07282008
  29440   25118 -> 0.07324111
  29440   25138 -> 0.07279606
  29440   25367 -> 0.07313363
  29440   25091 -> 0.07266437
  29440   25154 -> 0.07287904
  29440   25242 -> 0.07347107
  29440   25143 -> 0.07265876
  29440   25178 -> 0.07279302
  29440   25173 -> 0.07275996
  29440   25093 -> 0.07289876
  29440   25129 -> 0.07266437
done with simplex after 60 iterations
0 0.07287: 4.14494 -12.51831  2.15003 -8.86850 -1.30267 -2.22799 51.72174 53.77398 56.54650 
1 0.07279: 4.28697 -12.56957  1.92389 -8.54827 -1.68052 -2.53082 51.67716 53.78920 56.68852 
2 0.07266: 4.34343 -12.44080  1.98683 -8.92562 -1.46390 -2.38242 51.79647 53.81561 56.64806 
3 0.07273: 4.43376 -12.55204  1.74131 -8.60956 -1.51542 -2.41381 51.75985 54.30705 56.73838 
4 0.07266: 4.47608 -12.27569  1.98449 -8.67262 -1.68849 -2.30146 51.63111 53.94659 56.83597 
5 0.07288: 4.46000 -12.59025  2.00432 -8.66524 -1.32479 -2.47534 51.63540 53.72206 56.67667 
6 0.07280: 4.42470 -12.48622  2.03507 -8.56059 -1.64197 -1.99461 51.70427 53.73286 56.72597 
7 0.07282: 4.41426 -12.36553  2.11317 -8.46309 -1.68536 -2.53082 51.82387 53.98141 56.76324 
8 0.07266: 4.43789 -12.24625  1.87497 -8.32242 -1.56907 -2.31285 51.77594 53.66151 56.85813 
9 0.07276: 4.35456 -12.66747  1.94715 -8.99720 -1.41758 -2.38985 51.82192 53.81499 56.83458 
after parameter optimization
-center        -2.52772    7.70835  -23.10797
-translation    4.47608  -12.27569    1.98449
-rotation      -8.67262   -1.68849   -2.30146
-scale          1.03262    1.07893    1.13672
-shear          0.00000    0.00000    0.00000
  29440   25143 -> 0.07265876
Initial objective function val = 0.07286566
Final objective function value = 0.07265876
successful write

final linear fit: 8mm gradient lsq9 fit, target masked: making transforms/talairach.xfm
[mritotal] [christip@varda:/home/christip/EE/EEsurf/mri] [2006-01-19 15:13:02] /home/christip/sw/freesurfer/lib/mni/bin/minctracc -clobber -debug /tmp/mritotal_26388/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_26388/nu_8tmp2c.xfm -lsq9 -xcorr -model_mask /home/christip/sw/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc -center -2.527718 7.708347 -23.107967 -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=    0.069   19.657
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    =    1.0313    0.0456   -0.0238    3.6540 
                        -0.0433    1.0655    0.1638   -9.1048 
                         0.0335   -0.1713    1.1232    6.2375 

Transform center   =   -2.528    7.708  -23.108
Transform rotations  =   -0.151   -0.029   -0.040
Transform trans    =    4.476  -12.276    1.984
Transform scale    =    1.033    1.079    1.137
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_26388/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_26388/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    =    1.0313    0.0456   -0.0238    3.6540 
                        -0.0433    1.0655    0.1638   -9.1048 
                         0.0335   -0.1713    1.1232    6.2375 
Transform center   =   -2.528    7.708  -23.108
Transform rotation   =    0.000    0.000    0.000 

Transform trans    =    0.000    0.000    0.000
Transform scale    =    1.000    1.000    1.000

Center of rot/scale forced: -2.527718 7.708347 -23.107967
  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   25143 -> 0.07265876
  29440   25143 -> 0.07265876
  29440   25125 -> 0.08916658
  29440   24710 -> 0.07837671
  29440   25206 -> 0.08136570
  29440   25279 -> 0.07511073
  29440   25144 -> 0.07814416
  29440   25142 -> 0.07675523
  29440   25147 -> 0.08562628
  29440   25624 -> 0.07587282
  29440   25179 -> 0.08140330
  29440   25217 -> 0.08835313
  29440   25197 -> 0.07827768
  29440   25212 -> 0.08564782
  29440   25164 -> 0.07771532
  29440   25184 -> 0.07938802
  29440   25152 -> 0.08261659
  29440   25190 -> 0.07577337
  29440   25170 -> 0.08046731
  29440   25181 -> 0.07491868
  29440   25736 -> 0.07722070
  29440   25376 -> 0.07947052
  29440   25241 -> 0.07474182
  29440   25455 -> 0.07909215
  29440   25220 -> 0.07464530
  29440   25448 -> 0.07665313
  29440   24809 -> 0.07743698
  29440   25500 -> 0.07443049
  29440   25495 -> 0.07584435
  29440   25194 -> 0.07808719
  29440   25383 -> 0.07403751
  29440   24949 -> 0.07586599
  29440   25121 -> 0.07368115
  29440   25020 -> 0.07689688
  29440   25371 -> 0.07395491
  29440   25356 -> 0.07599387
  29440   25230 -> 0.07395007
  29440   25267 -> 0.07573485
  29440   25264 -> 0.07358336
  29440   25371 -> 0.07526200
  29440   25228 -> 0.07368193
  29440   25306 -> 0.07505795
  29440   25257 -> 0.07356693
  29440   25338 -> 0.07430567
  29440   25016 -> 0.07403240
  29440   25112 -> 0.07435726
  29440   25281 -> 0.07350025
  29440   25042 -> 0.07388908
  29440   25412 -> 0.07418646
  29440   25116 -> 0.07334310
  29440   25010 -> 0.07364631
  29440   25097 -> 0.07344010
  29440   25291 -> 0.07400621
  29440   25105 -> 0.07325081
  29440   25081 -> 0.07352030
  29440   25180 -> 0.07343115
  29440   25337 -> 0.07371022
  29440   25089 -> 0.07309950
  29440   25026 -> 0.07364710
  29440   25206 -> 0.07313779
  29440   25034 -> 0.07337414
  29440   25195 -> 0.07342532
  29440   24978 -> 0.07311230
  29440   25136 -> 0.07337629
  29440   25044 -> 0.07330249
  29440   24993 -> 0.07353597
  29440   25142 -> 0.07305342
  29440   25055 -> 0.07365222
  29440   25117 -> 0.07299568
  29440   25182 -> 0.07365025
  29440   25069 -> 0.07301945
  29440   25080 -> 0.07283168
  29440   25163 -> 0.07322019
  29440   25112 -> 0.07288075
  29440   25055 -> 0.07318669
  29440   25062 -> 0.07286853
  29440   24968 -> 0.07295915
  29440   25200 -> 0.07297815
  29440   25117 -> 0.07265780
  29440   25129 -> 0.07293994
  29440   25052 -> 0.07277885
  29440   25124 -> 0.07300705
  29440   25110 -> 0.07281870
  29440   25075 -> 0.07279139
  29440   24962 -> 0.07290781
  29440   25193 -> 0.07276444
  29440   25250 -> 0.07296653
  29440   25035 -> 0.07266381
  29440   25084 -> 0.07273225
done with simplex after 78 iterations
0 0.07266: 4.47608 -12.27569  1.98449 -8.67263 -1.68849 -2.30146 51.63110 53.94657 56.83597 
1 0.07282: 4.57469 -12.21267  1.95476 -8.70487 -1.78133 -2.12862 51.65249 53.88923 56.79533 
2 0.07283: 4.51193 -12.23574  1.93281 -8.31511 -1.73099 -2.09279 51.83863 53.65116 56.76838 
3 0.07279: 4.62856 -12.34744  1.74342 -8.76759 -1.85903 -2.06690 51.62624 53.67468 56.79060 
4 0.07276: 4.56654 -12.45033  1.84361 -8.34037 -1.69923 -2.21677 51.60410 53.93031 56.88680 
5 0.07266: 4.61408 -12.09517  1.72993 -8.63096 -1.78852 -2.26316 51.68725 53.68421 56.84595 
6 0.07266: 4.64738 -12.12226  1.90751 -8.60400 -1.85095 -2.48738 51.60997 53.96994 56.69522 
7 0.07273: 4.57407 -12.36160  2.02388 -8.67968 -1.58668 -2.40656 51.74818 53.62459 56.75858 
8 0.07287: 4.46883 -12.08271  2.14494 -8.19060 -1.55512 -2.25951 51.67428 53.70191 56.62706 
9 0.07278: 4.62353 -12.23779  1.90764 -8.61158 -1.91357 -2.21514 51.61365 53.59791 56.92274 
after parameter optimization
-center        -2.52772    7.70835  -23.10797
-translation    4.64738  -12.12226    1.90751
-rotation      -8.60400   -1.85095   -2.48738
-scale          1.03220    1.07940    1.13390
-shear          0.00000    0.00000    0.00000
  29440   25117 -> 0.07265780
Initial objective function val = 0.07265876
Final objective function value = 0.07265780
successful write