[christip@varda:/home/christip/FM/FMsurf/mri] [2006-01-11 14:09:45] 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/FM/FMsurf/mri] [2006-01-11 14:09:45] /home/christip/sw/freesurfer/lib/mni/bin/autocrop -clobber nu.mnc /tmp/mritotal_2613/nu_crop.mnc -step 2 2 2 -extend 0,0 0,0 -25%,0
[autocrop] [christip@varda:/home/christip/FM/FMsurf/mri] [2006-01-11 14:09:45] /home/christip/sw/freesurfer/lib/mni/bin/mincresample -clobber nu.mnc /tmp/mritotal_2613/nu_crop.mnc -start -132.3 -128 -64 -step 2 2 2 -nelements 128 128 96
Transforming slices:................................................................................................................................Done
[mritotal] [christip@varda:/home/christip/FM/FMsurf/mri] [2006-01-11 14:09:45] /home/christip/sw/freesurfer/lib/mni/bin/volume_cog /tmp/mritotal_2613/nu_crop.mnc | tail -1
Centroid of input volume: 3.291864 10.920820 -22.100143

Zero-padding data:
[mritotal] [christip@varda:/home/christip/FM/FMsurf/mri] [2006-01-11 14:09:46] /home/christip/sw/freesurfer/lib/mni/bin/autocrop -clobber /tmp/mritotal_2613/nu_crop.mnc /tmp/mritotal_2613/nu_pad.mnc -expand 22 22 22
[autocrop] [christip@varda:/home/christip/FM/FMsurf/mri] [2006-01-11 14:09:46] /home/christip/sw/freesurfer/lib/mni/bin/mincreshape -clobber /tmp/mritotal_2613/nu_crop.mnc /tmp/mritotal_2613/nu_pad.mnc -start -11,-11,-11 -count 150,150,118
Copying chunks:......................................................................................................................................................Done.

Intensity blurring data:
[mritotal] [christip@varda:/home/christip/FM/FMsurf/mri] [2006-01-11 14:09:47] /home/christip/sw/freesurfer/lib/mni/bin/mincblur -clobber -debug /tmp/mritotal_2613/nu_pad.mnc /tmp/mritotal_2613/tmp_16 -fwhm 16
===== Debugging information from /home/christip/sw/freesurfer/lib/mni/bin/mincblur =====
Data filename     = /tmp/mritotal_2613/nu_pad.mnc
Output basename   = /tmp/mritotal_2613/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  251.999
Apodizing data at 16.000000
Volume def min and max: = 0.000000 251.998740
before blur min/max = 0.000000 251.998734
after  blur min/max = -0.000003 137.780609
Making byte volume...
[mritotal] [christip@varda:/home/christip/FM/FMsurf/mri] [2006-01-11 14:09:53] /home/christip/sw/freesurfer/lib/mni/bin/autocrop -clobber /tmp/mritotal_2613/tmp_16_blur.mnc /tmp/mritotal_2613/nu_16_blur.mnc -expand -44 -44 -44
[autocrop] [christip@varda:/home/christip/FM/FMsurf/mri] [2006-01-11 14:09:53] /home/christip/sw/freesurfer/lib/mni/bin/mincreshape -clobber /tmp/mritotal_2613/tmp_16_blur.mnc /tmp/mritotal_2613/nu_16_blur.mnc -start 22,22,22 -count 106,106,74
Copying chunks:..........................................................................................................Done.

Gradient blurring data:
[mritotal] [christip@varda:/home/christip/FM/FMsurf/mri] [2006-01-11 14:09:53] /home/christip/sw/freesurfer/lib/mni/bin/mincblur -clobber -debug /tmp/mritotal_2613/nu_pad.mnc /tmp/mritotal_2613/tmp_8 -fwhm 8 -gradient
Transforming slices:......................................................................................................................................................Done
===== Debugging information from /home/christip/sw/freesurfer/lib/mni/bin/mincblur =====
Data filename     = /tmp/mritotal_2613/nu_pad.mnc
Output basename   = /tmp/mritotal_2613/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  251.999
Apodizing data at 8.000000
Volume def min and max: = 0.000000 251.998740
before blur min/max = 0.000000 251.998734
after  blur min/max = -0.000015 171.775986
Making byte volume...
Making byte volume dx...dx: min = -15.772635, max = 15.837479
Making byte volume dy...dy: min = -15.589806, max = 16.665554
Making byte volume dz...dz: min = -16.159241, max = 16.349195
[mritotal] [christip@varda:/home/christip/FM/FMsurf/mri] [2006-01-11 14:10:01] /home/christip/sw/freesurfer/lib/mni/bin/autocrop -clobber /tmp/mritotal_2613/tmp_8_blur.mnc /tmp/mritotal_2613/nu_8_blur.mnc -expand -34 -34 -34
[autocrop] [christip@varda:/home/christip/FM/FMsurf/mri] [2006-01-11 14:10:02] /home/christip/sw/freesurfer/lib/mni/bin/mincreshape -clobber /tmp/mritotal_2613/tmp_8_blur.mnc /tmp/mritotal_2613/nu_8_blur.mnc -start 17,17,17 -count 116,116,84
Copying chunks:....................................................................................................................Done.
[mritotal] [christip@varda:/home/christip/FM/FMsurf/mri] [2006-01-11 14:10:02] /home/christip/sw/freesurfer/lib/mni/bin/autocrop -clobber /tmp/mritotal_2613/tmp_8_dxyz.mnc /tmp/mritotal_2613/nu_8_dxyz.mnc -expand -34 -34 -34
[autocrop] [christip@varda:/home/christip/FM/FMsurf/mri] [2006-01-11 14:10:02] /home/christip/sw/freesurfer/lib/mni/bin/mincreshape -clobber /tmp/mritotal_2613/tmp_8_dxyz.mnc /tmp/mritotal_2613/nu_8_dxyz.mnc -start 17,17,17 -count 116,116,84
Copying chunks:....................................................................................................................Done.

16mm intensity lsq7 fit, no masks: making /tmp/mritotal_2613/nu_16.xfm
[mritotal] [christip@varda:/home/christip/FM/FMsurf/mri] [2006-01-11 14:10:02] /home/christip/sw/freesurfer/lib/mni/bin/minctracc -clobber -debug /tmp/mritotal_2613/nu_16_blur.mnc /home/christip/sw/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_16_blur.mnc /tmp/mritotal_2613/nu_16.xfm -est_translations -lsq7 -xcorr -center 3.291864 10.920820 -22.100143 -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  137.781
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   -2.9638 
                         0.0000    1.0000    0.0000  -28.5121 
                         0.0000    0.0000    1.0000   31.5548 

Transform center   =    3.292   10.921  -22.100
Transform rotations  =    0.000    0.000    0.000
Transform trans    =   -2.964  -28.512   31.555
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_2613/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_2613/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   =    3.292   10.921  -22.100
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: 3.291864 10.920820 -22.100143
  using PAT to get initial parameters:
  will try to get: [trans]
COG of v1 forced: 3.291864 10.920820 -22.100143
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] = -2.963769 -28.512150 31.554770
Only center & trans required, now returning from init_transformation
Transform center   =    3.292   10.921  -22.100
Transform rots    =    0.000    0.000    0.000
Transform trans    =   -2.964  -28.512   31.555
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   46052 -> 0.04235287
  68585   46052 -> 0.04235287
  68585   41092 -> 0.09016167
  68585   44834 -> 0.04234985
  68585   46089 -> 0.05597873
  68585   47898 -> 0.04720662
  68585   45052 -> 0.05191008
  68585   43871 -> 0.04862075
  68585   57362 -> 0.09412297
  68585   15002 -> 0.15078782
  68585   53755 -> 0.05707831
  68585   44872 -> 0.09519189
  68585   44141 -> 0.05674326
  68585   30419 -> 0.09001708
  68585   50259 -> 0.04256386
  68585   44780 -> 0.05932344
  68585   45638 -> 0.04616783
  68585   47005 -> 0.03381118
  68585   47174 -> 0.06344806
  68585   47347 -> 0.03963723
  68585   46544 -> 0.04129072
  68585   47611 -> 0.03281141
  68585   46587 -> 0.04990166
  68585   47891 -> 0.02789089
  68585   46276 -> 0.03560155
  68585   43967 -> 0.02953524
  68585   44610 -> 0.03520500
  68585   49724 -> 0.02679784
  68585   52627 -> 0.03911117
  68585   44422 -> 0.02428621
  68585   42086 -> 0.03668519
  68585   43671 -> 0.02269828
  68585   38678 -> 0.04964969
  68585   47085 -> 0.02426128
  68585   44228 -> 0.02816871
  68585   45932 -> 0.03934456
  68585   47134 -> 0.02251730
  68585   49110 -> 0.01852081
  68585   51555 -> 0.02777131
  68585   49058 -> 0.03128808
  68585   46012 -> 0.01878275
  68585   46589 -> 0.02096871
  68585   44059 -> 0.02336091
  68585   46888 -> 0.01787608
  68585   46870 -> 0.03012466
  68585   42736 -> 0.03901149
  68585   47704 -> 0.01505086
  68585   49476 -> 0.02437905
  68585   45633 -> 0.01640624
  68585   49695 -> 0.02076877
  68585   48116 -> 0.01318229
  68585   48338 -> 0.02194128
  68585   48965 -> 0.02257388
  68585   47309 -> 0.01465552
  68585   44139 -> 0.02204499
  68585   48693 -> 0.01506578
  68585   49569 -> 0.02114330
  68585   46978 -> 0.01407004
  68585   45418 -> 0.01529802
  68585   45139 -> 0.01904669
  68585   47423 -> 0.01373558
  68585   49077 -> 0.01430342
  68585   50110 -> 0.01761752
  68585   46906 -> 0.01265497
  68585   46601 -> 0.01519038
  68585   48245 -> 0.01297896
  68585   47505 -> 0.01262845
  68585   47047 -> 0.01712354
  68585   48325 -> 0.01092767
  68585   48924 -> 0.01231511
  68585   46025 -> 0.01548809
  68585   48445 -> 0.01200562
  68585   48818 -> 0.01529598
  68585   47439 -> 0.01196195
  68585   48104 -> 0.01116801
  68585   47592 -> 0.01480848
  68585   48028 -> 0.01140873
  68585   47402 -> 0.01033450
  68585   46818 -> 0.01155249
  68585   48855 -> 0.01219523
  68585   48595 -> 0.01103637
  68585   47112 -> 0.01320960
  68585   48495 -> 0.01082828
  68585   47699 -> 0.00997392
  68585   47244 -> 0.01094936
  68585   48838 -> 0.01056101
  68585   48514 -> 0.00947069
  68585   48755 -> 0.01007975
  68585   48288 -> 0.01010063
  68585   47663 -> 0.01117933
  68585   48443 -> 0.00998969
  68585   48110 -> 0.01054194
  68585   47895 -> 0.00884049
  68585   47589 -> 0.00909089
  68585   47300 -> 0.00940354
  68585   47722 -> 0.01083247
  68585   48041 -> 0.00949650
  68585   48634 -> 0.00973916
  68585   47653 -> 0.01006264
  68585   47939 -> 0.00934299
  68585   47534 -> 0.00870879
  68585   47015 -> 0.00913636
  68585   48255 -> 0.00891525
  68585   47206 -> 0.00939226
  68585   47624 -> 0.00851845
  68585   47372 -> 0.00905434
  68585   46841 -> 0.00836482
  68585   45959 -> 0.00901227
  68585   47939 -> 0.00915714
  68585   48237 -> 0.00883202
  68585   47579 -> 0.00817965
  68585   47270 -> 0.00897734
  68585   47476 -> 0.00911464
  68585   47608 -> 0.00844891
  68585   46936 -> 0.00824044
  68585   47073 -> 0.00853805
  68585   46301 -> 0.00870918
  68585   46817 -> 0.00819677
  68585   46885 -> 0.00833667
  68585   47298 -> 0.00896556
  68585   47136 -> 0.00811542
  68585   46664 -> 0.00827976
  68585   46368 -> 0.00820663
  68585   46995 -> 0.00802417
  68585   47116 -> 0.00862694
  68585   46899 -> 0.00856686
  68585   46903 -> 0.00799263
  68585   47305 -> 0.00799555
  68585   47061 -> 0.00828578
  68585   46966 -> 0.00797515
  68585   47841 -> 0.00870830
  68585   46711 -> 0.00789709
  68585   47344 -> 0.00803176
  68585   46504 -> 0.00818343
  68585   47318 -> 0.00792666
  68585   47035 -> 0.00809389
  68585   47065 -> 0.00791412
  68585   46736 -> 0.00817870
  68585   47192 -> 0.00787973
  68585   47162 -> 0.00801023
  68585   47134 -> 0.00790966
  68585   46750 -> 0.00816561
  68585   47176 -> 0.00788247
  68585   47177 -> 0.00780890
  68585   47448 -> 0.00800012
  68585   47259 -> 0.00801107
  68585   47042 -> 0.00786160
  68585   46785 -> 0.00784865
  68585   47054 -> 0.00789867
  68585   46964 -> 0.00781669
  68585   47023 -> 0.00789145
  68585   47418 -> 0.00793539
  68585   46896 -> 0.00785072
  68585   47109 -> 0.00790643
  68585   47024 -> 0.00783793
  68585   46870 -> 0.00786813
  68585   46786 -> 0.00800797
  68585   47085 -> 0.00782560
done with simplex after 149 iterations
0 0.00781:-2.73393 -17.60162  5.10090 -19.02479 -2.00936  0.58810 53.96749 
1 0.00787:-3.13085 -16.66623  4.74789 -19.39459 -0.92098  0.32495 53.80349 
2 0.00786:-2.76028 -16.73210  5.39656 -18.09968 -1.37979  0.41202 53.84755 
3 0.00785:-2.76393 -16.47425  5.10069 -18.34199 -1.33645  0.02945 53.73416 
4 0.00782:-2.93291 -16.58880  5.43274 -18.89332 -1.67164  0.14705 53.84262 
5 0.00783:-3.02233 -17.07068  5.60464 -18.49275 -1.27522 -0.32482 53.73759 
6 0.00785:-2.69162 -16.32632  5.42987 -18.54640 -1.57504  0.70582 53.64406 
7 0.00784:-2.94258 -16.98759  5.44937 -18.79510 -1.13631 -0.46139 53.72208 
after parameter optimization
-center         3.29186   10.92082  -22.10014
-translation   -2.73393  -17.60162    5.10090
-rotation     -19.02479   -2.00936    0.58810
-scale          1.07935    1.07935    1.07935
-shear          0.00000    0.00000    0.00000
  68585   47177 -> 0.00780890
Initial objective function val = 0.04235287
Final objective function value = 0.00780890
successful write

8mm intensity lsq7 fit, no masks: making /tmp/mritotal_2613/nu_8tmp1a.xfm
[mritotal] [christip@varda:/home/christip/FM/FMsurf/mri] [2006-01-11 14:10:15] /home/christip/sw/freesurfer/lib/mni/bin/minctracc -clobber -debug /tmp/mritotal_2613/nu_8_blur.mnc /home/christip/sw/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_blur.mnc /tmp/mritotal_2613/nu_8tmp1a.xfm -transformation /tmp/mritotal_2613/nu_16.xfm -lsq7 -xcorr -center 3.291864 10.920820 -22.100143 -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  171.776
min/max voxel=    0.000  255.000

Target volume size:  68  by 110  by 86 
Target voxel =    2.000    2.000    2.000
min/max value=   -0.000  144.070
min/max voxel=    0.000  255.000


AFTER init_params()
Transform matrix    =    1.0786    0.0019   -0.0394   -3.8836 
                         0.0111    1.0205    0.3515  -10.0943 
                         0.0378   -0.3516    1.0198    9.2532 

Transform center   =    3.292   10.921  -22.100
Transform rotations  =   -0.332   -0.035    0.010
Transform trans    =   -2.734  -17.602    5.101
Transform scale    =    1.079    1.079    1.079
Transform shear    =    0.000    0.000    0.000

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

===== Debugging information from /home/christip/sw/freesurfer/lib/mni/bin/minctracc =====
Data filename       = /tmp/mritotal_2613/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_2613/nu_16.xfm
Output filename     = /tmp/mritotal_2613/nu_8tmp1a.xfm
Step size           = 4.000000 4.000000 4.000000
Sub-lattice dia     = 24.000000 24.000000 24.000000
Objective function  = cross correlation (threshold = 0.000000 0.000000)
Transform linear    = TRUE
Transform inverted? = FALSE
Transform type      = 4
Transform matrix    =    1.0786    0.0019   -0.0394   -3.8836 
                         0.0111    1.0205    0.3515  -10.0943 
                         0.0378   -0.3516    1.0198    9.2532 
Transform center   =    3.292   10.921  -22.100
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: 3.291864 10.920820 -22.100143
  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   59300 -> 0.02239882
  80410   59300 -> 0.02239882
  80410   57675 -> 0.03137075
  80410   57565 -> 0.02292038
  80410   59896 -> 0.02814468
  80410   59659 -> 0.02465564
  80410   58771 -> 0.02606062
  80410   58536 -> 0.02424214
  80410   61786 -> 0.03981150
  80410   52051 -> 0.04477083
  80410   60547 -> 0.02838055
  80410   58809 -> 0.02947970
  80410   59234 -> 0.02454418
  80410   56193 -> 0.02898209
  80410   59921 -> 0.02451388
  80410   58577 -> 0.02387644
  80410   58148 -> 0.02375264
  80410   58193 -> 0.02432392
  80410   57993 -> 0.02310885
  80410   56407 -> 0.02281673
  80410   57926 -> 0.02471775
  80410   58172 -> 0.02232506
  80410   57164 -> 0.02241955
  80410   57136 -> 0.02466718
  80410   58275 -> 0.02197787
  80410   56806 -> 0.02451511
  80410   58032 -> 0.02192448
  80410   57799 -> 0.02283099
  80410   58195 -> 0.02288257
  80410   58038 -> 0.02168073
  80410   58112 -> 0.02316195
  80410   57846 -> 0.02162086
  80410   59386 -> 0.02309588
  80410   57334 -> 0.02165845
  80410   58749 -> 0.02408220
  80410   57757 -> 0.02145856
  80410   56480 -> 0.02402353
  80410   58695 -> 0.02149429
  80410   57817 -> 0.02214649
  80410   57920 -> 0.02158247
  80410   57739 -> 0.02184416
  80410   57758 -> 0.02157712
  80410   58206 -> 0.02217512
  80410   57841 -> 0.02137547
  80410   57603 -> 0.02136014
  80410   57143 -> 0.02196867
  80410   58322 -> 0.02170406
  80410   57609 -> 0.02134901
  80410   57826 -> 0.02131076
  80410   57668 -> 0.02185335
  80410   57864 -> 0.02127693
  80410   57847 -> 0.02180057
  80410   58035 -> 0.02163213
  80410   57783 -> 0.02129345
  80410   56904 -> 0.02174245
  80410   58240 -> 0.02116731
  80410   57883 -> 0.02158487
  80410   57707 -> 0.02117383
  80410   57891 -> 0.02137629
  80410   57789 -> 0.02122156
  80410   58039 -> 0.02137853
  80410   57693 -> 0.02116030
  80410   57994 -> 0.02115216
  80410   58015 -> 0.02138228
  80410   57895 -> 0.02153070
  80410   57856 -> 0.02118590
  80410   57990 -> 0.02119756
  80410   58001 -> 0.02126222
  80410   57983 -> 0.02116459
  80410   58065 -> 0.02116568
  80410   57946 -> 0.02116472
done with simplex after 62 iterations
0 0.02117:-3.11493 -15.31854  3.50053 -18.95267 -2.75734  1.28336 54.01255 
1 0.02119:-2.88554 -14.85073  2.82798 -19.03586 -3.09315  1.01979 53.92015 
2 0.02116:-3.17559 -14.30953  3.34626 -18.91834 -2.80652  0.85563 53.85556 
3 0.02117:-2.71355 -14.70832  3.22656 -19.01582 -2.69438  0.40415 54.04594 
4 0.02116:-3.04011 -14.76881  3.10196 -18.47111 -3.20854  0.87828 54.02463 
5 0.02116:-3.21274 -14.86034  2.63736 -18.70551 -2.55472  0.72593 53.90900 
6 0.02117:-3.15810 -14.24190  2.77948 -18.85097 -3.08601  1.02171 54.09094 
7 0.02115:-2.95401 -14.85947  3.34477 -19.38608 -2.80915  0.11592 53.96378 
after parameter optimization
-center         3.29186   10.92082  -22.10014
-translation   -2.95401  -14.85947    3.34477
-rotation     -19.38608   -2.80915    0.11592
-scale          1.07928    1.07928    1.07928
-shear          0.00000    0.00000    0.00000
  80410   57994 -> 0.02115216
Initial objective function val = 0.02239882
Final objective function value = 0.02115216
successful write

8mm gradient lsq7 fit, target masked: making /tmp/mritotal_2613/nu_8tmp1b.xfm
[mritotal] [christip@varda:/home/christip/FM/FMsurf/mri] [2006-01-11 14:10:23] /home/christip/sw/freesurfer/lib/mni/bin/minctracc -clobber -debug /tmp/mritotal_2613/nu_8_dxyz.mnc /home/christip/sw/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc /tmp/mritotal_2613/nu_8tmp1b.xfm -transformation /tmp/mritotal_2613/nu_8tmp1a.xfm -lsq7 -xcorr -model_mask /home/christip/sw/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc -center 3.291864 10.920820 -22.100143 -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=    0.053   18.113
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    =    1.0780    0.0155   -0.0506   -4.4987 
                         0.0022    1.0181    0.3581   -7.1495 
                         0.0529   -0.3578    1.0169    7.4509 

Transform center   =    3.292   10.921  -22.100
Transform rotations  =   -0.338   -0.049    0.002
Transform trans    =   -2.954  -14.859    3.345
Transform scale    =    1.079    1.079    1.079
Transform shear    =    0.000   -0.000    0.000

Target volume is smallest
Lattice step size  =    4.000    4.000    4.000
Lattice start      =  -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_2613/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_2613/nu_8tmp1a.xfm
Output filename     = /tmp/mritotal_2613/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    =    1.0780    0.0155   -0.0506   -4.4987 
                         0.0022    1.0181    0.3581   -7.1495 
                         0.0529   -0.3578    1.0169    7.4509 
Transform center   =    3.292   10.921  -22.100
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: 3.291864 10.920820 -22.100143
  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   25219 -> 0.11368034
  29440   25219 -> 0.11368034
  29440   25214 -> 0.12940784
  29440   24817 -> 0.10854817
  29440   25359 -> 0.12171631
  29440   25308 -> 0.11418853
  29440   25211 -> 0.12200065
  29440   25216 -> 0.11339055
  29440   25742 -> 0.13762286
  29440   24633 -> 0.13444075
  29440   24912 -> 0.11898461
  29440   25010 -> 0.11225516
  29440   25006 -> 0.10815623
  29440   24940 -> 0.11392061
  29440   24760 -> 0.10957061
  29440   25265 -> 0.11124807
  29440   24813 -> 0.10754451
  29440   24563 -> 0.11346406
  29440   24778 -> 0.10536598
  29440   24528 -> 0.10788945
  29440   24641 -> 0.11121146
  29440   24679 -> 0.10125677
  29440   24465 -> 0.10179678
  29440   24331 -> 0.10450093
  29440   24855 -> 0.11211082
  29440   24707 -> 0.10542374
  29440   24687 -> 0.11269104
  29440   24713 -> 0.10452563
  29440   24629 -> 0.11129635
  29440   24788 -> 0.10428544
  29440   24332 -> 0.10278321
  29440   24450 -> 0.10014607
  29440   24257 -> 0.10198141
  29440   24476 -> 0.10285225
  29440   24311 -> 0.10477908
  29440   24422 -> 0.10199763
  29440   24224 -> 0.09932339
  29440   23933 -> 0.10008587
  29440   24650 -> 0.10327774
  29440   24148 -> 0.10173036
  29440   24165 -> 0.10357859
  29440   24466 -> 0.10064031
  29440   24305 -> 0.10031866
  29440   24437 -> 0.09869158
  29440   24481 -> 0.10021944
  29440   24381 -> 0.09906613
  29440   24689 -> 0.10117166
  29440   24171 -> 0.09815463
  29440   23906 -> 0.10024589
  29440   23929 -> 0.10203879
  29440   24534 -> 0.09918404
  29440   24192 -> 0.09826612
  29440   24354 -> 0.09788330
  29440   24381 -> 0.10037104
  29440   24208 -> 0.09738389
  29440   24078 -> 0.09944462
  29440   24423 -> 0.09828258
  29440   24078 -> 0.09788812
  29440   24178 -> 0.09897833
  29440   24225 -> 0.09756317
  29440   24028 -> 0.09683525
  29440   23821 -> 0.09821183
  29440   23934 -> 0.09879629
  29440   24301 -> 0.09729844
  29440   24190 -> 0.09713157
  29440   24227 -> 0.09703883
  29440   24363 -> 0.09702051
  29440   24073 -> 0.09691670
  29440   24178 -> 0.09658702
  29440   24149 -> 0.09808640
  29440   24187 -> 0.09661501
  29440   24054 -> 0.09576113
  29440   23927 -> 0.09632584
  29440   24122 -> 0.09688209
  29440   24061 -> 0.09697575
  29440   23849 -> 0.09807922
  29440   24230 -> 0.09613656
  29440   24188 -> 0.09703223
  29440   24090 -> 0.09626251
  29440   24173 -> 0.09575898
  29440   24225 -> 0.09654698
  29440   24148 -> 0.09634800
  29440   24274 -> 0.09593344
  29440   24138 -> 0.09688016
  29440   24174 -> 0.09584520
  29440   24155 -> 0.09625509
  29440   24181 -> 0.09610938
  29440   24265 -> 0.09629329
  29440   24132 -> 0.09581364
  29440   24195 -> 0.09671061
  29440   24163 -> 0.09571487
  29440   24100 -> 0.09531000
  29440   24043 -> 0.09535202
  29440   24127 -> 0.09603661
  29440   24137 -> 0.09565193
  29440   24001 -> 0.09645418
  29440   24206 -> 0.09556918
  29440   24106 -> 0.09544890
  29440   24133 -> 0.09559238
  29440   24238 -> 0.09547743
  29440   24135 -> 0.09577505
  29440   24161 -> 0.09546906
  29440   24144 -> 0.09532069
  29440   24171 -> 0.09535714
  29440   24191 -> 0.09534886
done with simplex after 96 iterations
0 0.09532:-2.36142 -9.67914  2.73745 -16.83871 -5.48575  1.15023 53.76339 
1 0.09535:-2.59474 -9.86531  2.88145 -16.86278 -5.34334  0.71631 53.73428 
2 0.09531:-2.22010 -9.53464  2.76013 -16.61850 -5.71408  0.72973 53.68191 
3 0.09548:-2.66161 -10.17603  2.98968 -16.52432 -4.94718  0.84999 53.59920 
4 0.09545:-2.33911 -9.65460  2.84746 -17.27360 -5.33412  0.81465 53.67496 
5 0.09557:-2.19530 -9.97060  2.59664 -17.05961 -5.56064  0.73228 53.80461 
6 0.09547:-2.52852 -9.94990  2.83590 -16.93856 -5.22713  0.80901 53.61488 
7 0.09536:-2.32807 -9.79850  3.17110 -16.73014 -5.59721  0.92129 53.64777 
after parameter optimization
-center         3.29186   10.92082  -22.10014
-translation   -2.22010   -9.53464    2.76013
-rotation     -16.61850   -5.71408    0.72973
-scale          1.07364    1.07364    1.07364
-shear          0.00000    0.00000    0.00000
  29440   24100 -> 0.09531000
Initial objective function val = 0.11368034
Final objective function value = 0.09531000
successful write

8mm gradient lsq9 fit, target masked: making /tmp/mritotal_2613/nu_8tmp2a.xfm
[mritotal] [christip@varda:/home/christip/FM/FMsurf/mri] [2006-01-11 14:10:29] /home/christip/sw/freesurfer/lib/mni/bin/minctracc -clobber -debug /tmp/mritotal_2613/nu_8_dxyz.mnc /home/christip/sw/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc /tmp/mritotal_2613/nu_8tmp2a.xfm -transformation /tmp/mritotal_2613/nu_8tmp1b.xfm -lsq9 -xcorr -model_mask /home/christip/sw/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc -center 3.291864 10.920820 -22.100143 -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=    0.053   18.113
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    =    1.0682    0.0175   -0.1063   -4.9854 
                         0.0136    1.0291    0.3057   -3.1406 
                         0.1069   -0.3055    1.0237    6.2683 

Transform center   =    3.292   10.921  -22.100
Transform rotations  =   -0.290   -0.100    0.013
Transform trans    =   -2.220   -9.535    2.760
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_2613/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_2613/nu_8tmp1b.xfm
Output filename     = /tmp/mritotal_2613/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    =    1.0682    0.0175   -0.1063   -4.9854 
                         0.0136    1.0291    0.3057   -3.1406 
                         0.1069   -0.3055    1.0237    6.2683 
Transform center   =    3.292   10.921  -22.100
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: 3.291864 10.920820 -22.100143
  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   24100 -> 0.09531000
  29440   24100 -> 0.09531000
  29440   24092 -> 0.10945361
  29440   23660 -> 0.09645367
  29440   24231 -> 0.09952427
  29440   24209 -> 0.09764934
  29440   24096 -> 0.09980637
  29440   24102 -> 0.10006689
  29440   24100 -> 0.10466649
  29440   24609 -> 0.10497524
  29440   24174 -> 0.08955940
  29440   24181 -> 0.10285824
  29440   23561 -> 0.08694224
  29440   22993 -> 0.08484342
  29440   23847 -> 0.09811381
  29440   23693 -> 0.10381692
  29440   24070 -> 0.09433958
  29440   23770 -> 0.09204932
  29440   23687 -> 0.09432147
  29440   23439 -> 0.08905613
  29440   23743 -> 0.09770928
  29440   23769 -> 0.09137166
  29440   23293 -> 0.09094235
  29440   23733 -> 0.08535656
  29440   23194 -> 0.08885115
  29440   23046 -> 0.08398246
  29440   22501 -> 0.08726810
  29440   23300 -> 0.08384909
  29440   23108 -> 0.09099320
  29440   23106 -> 0.08387386
  29440   22946 -> 0.08161349
  29440   22532 -> 0.08644938
  29440   23376 -> 0.08081957
  29440   23439 -> 0.08707955
  29440   22246 -> 0.08710521
  29440   22770 -> 0.08972584
  29440   23279 -> 0.08306101
  29440   22973 -> 0.07783238
  29440   22978 -> 0.08137145
  29440   24111 -> 0.08777902
  29440   22733 -> 0.08209035
  29440   22463 -> 0.08471167
  29440   23072 -> 0.07995605
  29440   23754 -> 0.08484790
  29440   22703 -> 0.08111665
  29440   23101 -> 0.08032214
  29440   23029 -> 0.08175508
  29440   22779 -> 0.08204197
  29440   22690 -> 0.07915790
  29440   23233 -> 0.07921546
  29440   23286 -> 0.08265372
  29440   22906 -> 0.07928994
  29440   23010 -> 0.08151765
  29440   23091 -> 0.08457041
  29440   22946 -> 0.07862268
  29440   23038 -> 0.08186275
  29440   23013 -> 0.07909054
  29440   23322 -> 0.07783280
  29440   22698 -> 0.07678959
  29440   22375 -> 0.07881834
  29440   22890 -> 0.07814662
  29440   22881 -> 0.07967106
  29440   22929 -> 0.07756275
  29440   23050 -> 0.07643154
  29440   23130 -> 0.07785092
  29440   22690 -> 0.07823972
  29440   23241 -> 0.07754985
  29440   22946 -> 0.07531898
  29440   22946 -> 0.07648726
  29440   22972 -> 0.07558780
  29440   23410 -> 0.07906609
  29440   22858 -> 0.07632101
  29440   23131 -> 0.07788484
  29440   23069 -> 0.07629994
  29440   22641 -> 0.07699643
  29440   22821 -> 0.07649252
  29440   22920 -> 0.07471959
  29440   22916 -> 0.07541358
  29440   22552 -> 0.07815710
  29440   23061 -> 0.07580452
  29440   23237 -> 0.07705479
  29440   22790 -> 0.07559902
  29440   23187 -> 0.07531739
  29440   23175 -> 0.07686353
  29440   22917 -> 0.07531731
  29440   22900 -> 0.07449395
  29440   22780 -> 0.07509648
  29440   23089 -> 0.07472456
  29440   22879 -> 0.07464934
  29440   22881 -> 0.07448051
  29440   22703 -> 0.07653702
  29440   23187 -> 0.07456521
  29440   22982 -> 0.07520575
  29440   23000 -> 0.07388873
  29440   23022 -> 0.07442715
  29440   22738 -> 0.07463885
  29440   22973 -> 0.07306341
  29440   23009 -> 0.07313152
  29440   22927 -> 0.07417677
  29440   22730 -> 0.07399826
  29440   22946 -> 0.07456924
  29440   22912 -> 0.07352375
  29440   23187 -> 0.07497969
  29440   22825 -> 0.07372877
  29440   22950 -> 0.07426335
  29440   22660 -> 0.07402046
  29440   22869 -> 0.07363259
  29440   22868 -> 0.07374397
  29440   22788 -> 0.07329807
  29440   22808 -> 0.07362244
  29440   23078 -> 0.07377684
  29440   23057 -> 0.07362143
  29440   22819 -> 0.07298925
  29440   22727 -> 0.07396273
  29440   22690 -> 0.07362717
  29440   22821 -> 0.07413549
  29440   22887 -> 0.07303552
  29440   22894 -> 0.07238684
  29440   22942 -> 0.07265575
  29440   22868 -> 0.07312655
  29440   23096 -> 0.07339067
  29440   23056 -> 0.07392536
  29440   22865 -> 0.07288849
  29440   22742 -> 0.07336057
  29440   22847 -> 0.07358747
  29440   22893 -> 0.07288785
  29440   22626 -> 0.07340784
  29440   22977 -> 0.07280406
  29440   23024 -> 0.07352102
  29440   22813 -> 0.07277650
  29440   23003 -> 0.07319354
  29440   22944 -> 0.07268146
  29440   22917 -> 0.07329830
  29440   22895 -> 0.07274343
  29440   22809 -> 0.07294798
  29440   22888 -> 0.07269633
  29440   22948 -> 0.07282464
  29440   23001 -> 0.07299718
  29440   22852 -> 0.07263309
  29440   22942 -> 0.07262081
  29440   22908 -> 0.07239777
  29440   22852 -> 0.07294555
  29440   22926 -> 0.07258791
  29440   22815 -> 0.07230749
  29440   22730 -> 0.07278384
  29440   22970 -> 0.07259158
  29440   22916 -> 0.07220417
  29440   22937 -> 0.07232730
  29440   22937 -> 0.07288472
  29440   22898 -> 0.07242805
  29440   22862 -> 0.07236298
  29440   22959 -> 0.07220978
  29440   22877 -> 0.07239951
  29440   22813 -> 0.07224837
  29440   22845 -> 0.07225075
  29440   22860 -> 0.07223667
  29440   22879 -> 0.07233267
done with simplex after 146 iterations
0 0.07221:-2.59977 -10.67533  0.84838 -17.97049 -4.88477  1.15148 53.73857 48.65559 56.67912 
1 0.07240:-2.69260 -10.39982  0.89836 -17.92615 -5.03482  1.10196 53.59891 48.66132 56.98209 
2 0.07231:-2.82108 -10.25738  0.79461 -17.85931 -4.80165  1.32934 53.76317 48.47948 56.74917 
3 0.07224:-2.54094 -10.55870  0.56602 -18.37245 -4.99304  1.21714 53.84210 48.48237 56.91304 
4 0.07239:-2.57559 -10.52382  0.58280 -18.05193 -4.80980  1.28647 53.79058 48.60000 57.11656 
5 0.07220:-2.71294 -10.67816  0.65127 -17.95253 -4.77899  1.19342 53.73833 48.51352 57.09511 
6 0.07225:-2.58853 -10.62309  0.50175 -18.31186 -4.82298  1.06097 53.70841 48.35834 56.99043 
7 0.07233:-2.63351 -10.62899  0.70617 -17.66175 -4.93848  1.19483 53.72480 48.36962 56.92489 
8 0.07236:-2.64575 -10.73477  0.62734 -17.97568 -4.98330  1.37558 53.72710 48.27265 56.98976 
9 0.07225:-2.61624 -10.43057  0.89551 -17.82358 -5.01527  1.11442 53.72700 48.27750 57.06947 
after parameter optimization
-center         3.29186   10.92082  -22.10014
-translation   -2.71294  -10.67816    0.65127
-rotation     -17.95253   -4.77899    1.19342
-scale          1.07477    0.97027    1.14190
-shear          0.00000    0.00000    0.00000
  29440   22916 -> 0.07220417
Initial objective function val = 0.09531000
Final objective function value = 0.07220417
successful write

checking z-scale: making /tmp/mritotal_2613/nu_8tmp2b.xfm
[mritotal] [christip@varda:/home/christip/FM/FMsurf/mri] [2006-01-11 14:10:38] /home/christip/sw/freesurfer/lib/mni/bin/check_scale /tmp/mritotal_2613/nu_8tmp2a.xfm /tmp/mritotal_2613/nu_8tmp2b.xfm

8mm gradient lsq9 fit, target masked: making /tmp/mritotal_2613/nu_8tmp2c.xfm
[mritotal] [christip@varda:/home/christip/FM/FMsurf/mri] [2006-01-11 14:10:38] /home/christip/sw/freesurfer/lib/mni/bin/minctracc -clobber -debug /tmp/mritotal_2613/nu_8_dxyz.mnc /home/christip/sw/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc /tmp/mritotal_2613/nu_8tmp2c.xfm -transformation /tmp/mritotal_2613/nu_8tmp2b.xfm -lsq9 -xcorr -model_mask /home/christip/sw/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc -center 3.291864 10.920820 -22.100143 -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=    0.053   18.113
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    =    1.0708    0.0063   -0.0921   -5.0494 
                         0.0201    0.9233    0.2974   -3.3348 
                         0.0951   -0.3507    1.0825    5.9924 

Transform center   =    3.292   10.921  -22.100
Transform rotations  =   -0.313   -0.083    0.021
Transform trans    =   -2.713  -10.678    0.651
Transform scale    =    1.075    0.970    1.142
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_2613/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_2613/nu_8tmp2b.xfm
Output filename     = /tmp/mritotal_2613/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    =    1.0708    0.0063   -0.0921   -5.0494 
                         0.0201    0.9233    0.2974   -3.3348 
                         0.0951   -0.3507    1.0825    5.9924 
Transform center   =    3.292   10.921  -22.100
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: 3.291864 10.920820 -22.100143
  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   22916 -> 0.07220416
  29440   22916 -> 0.07220416
  29440   22914 -> 0.08799569
  29440   22444 -> 0.07665604
  29440   23050 -> 0.07820609
  29440   22990 -> 0.07561637
  29440   22910 -> 0.07876095
  29440   22919 -> 0.07858142
  29440   22916 -> 0.08132968
  29440   23465 -> 0.07569560
  29440   22986 -> 0.07658417
  29440   22987 -> 0.08242738
  29440   22967 -> 0.07534352
  29440   23000 -> 0.08549294
  29440   22944 -> 0.07516322
  29440   23014 -> 0.07930858
  29440   22948 -> 0.07454113
  29440   23029 -> 0.07888763
  29440   22942 -> 0.07434810
  29440   22868 -> 0.07880999
  29440   22997 -> 0.07422905
  29440   23575 -> 0.07749635
  29440   22731 -> 0.07384235
  29440   22998 -> 0.07614353
  29440   22986 -> 0.07341786
  29440   22425 -> 0.07648306
  29440   23194 -> 0.07378187
  29440   22942 -> 0.07824370
  29440   22968 -> 0.07312411
  29440   22945 -> 0.07619616
  29440   22950 -> 0.07348631
  29440   22977 -> 0.07553100
  29440   22948 -> 0.07345254
  29440   22982 -> 0.07410705
  29440   23002 -> 0.07379060
  29440   22941 -> 0.07498708
  29440   22980 -> 0.07303903
  29440   22950 -> 0.07390850
  29440   22961 -> 0.07295979
  29440   23246 -> 0.07327269
  29440   23048 -> 0.07435386
  29440   23009 -> 0.07286250
  29440   22805 -> 0.07295638
  29440   22995 -> 0.07277453
  29440   23022 -> 0.07295131
  29440   22991 -> 0.07307979
  29440   22665 -> 0.07318688
  29440   22813 -> 0.07254957
  29440   22919 -> 0.07257361
  29440   22883 -> 0.07307598
  29440   22908 -> 0.07253855
  29440   22874 -> 0.07294005
  29440   22880 -> 0.07242176
  29440   23054 -> 0.07302534
  29440   22866 -> 0.07239099
  29440   22801 -> 0.07263076
  29440   22931 -> 0.07287141
  29440   22920 -> 0.07235646
  29440   22768 -> 0.07262056
  29440   22738 -> 0.07272989
  29440   22800 -> 0.07227343
  29440   22937 -> 0.07275727
  29440   22832 -> 0.07225959
  29440   22976 -> 0.07291271
  29440   22822 -> 0.07218840
  29440   22811 -> 0.07272974
  29440   22890 -> 0.07224183
  29440   22921 -> 0.07217529
  29440   22967 -> 0.07275287
  29440   22832 -> 0.07245018
  29440   22853 -> 0.07220874
  29440   22855 -> 0.07281757
  29440   22877 -> 0.07213089
  29440   22879 -> 0.07220288
done with simplex after 63 iterations
0 0.07220:-2.71294 -10.67816  0.65127 -17.95253 -4.77899  1.19342 53.73834 48.51352 57.09512 
1 0.07227:-2.84212 -10.38961  0.95172 -17.96549 -4.71320  1.09164 53.85737 48.26403 56.98311 
2 0.07218:-2.80682 -10.77055  1.01231 -18.06676 -4.76726  1.11530 54.01350 48.43735 56.58115 
3 0.07236:-2.73415 -10.46714  1.09562 -17.76388 -4.79937  1.11505 53.94775 48.57032 56.96194 
4 0.07224:-2.76349 -10.54235  1.04608 -17.92228 -4.61650  0.93348 53.88563 48.45234 56.86440 
5 0.07213:-2.73701 -10.62357  0.99417 -17.65976 -4.82893  0.99781 53.87606 48.32183 56.70472 
6 0.07219:-2.64376 -10.56773  0.94068 -17.82801 -4.68810  1.10767 53.85350 48.20197 56.81171 
7 0.07226:-2.69541 -10.43908  0.87701 -17.89348 -4.70038  1.02959 54.01825 48.35268 56.92665 
8 0.07220:-2.60203 -10.58970  0.88633 -18.32485 -4.94012  1.03921 53.81454 48.42941 56.95051 
9 0.07221:-2.71763 -10.68002  0.93663 -17.88386 -4.82716  0.99968 53.89744 48.20597 56.95707 
after parameter optimization
-center         3.29186   10.92082  -22.10014
-translation   -2.73701  -10.62357    0.99417
-rotation     -17.65976   -4.82893    0.99781
-scale          1.07752    0.96644    1.13409
-shear          0.00000    0.00000    0.00000
  29440   22877 -> 0.07213089
Initial objective function val = 0.07220416
Final objective function value = 0.07213089
successful write

final linear fit: 8mm gradient lsq9 fit, target masked: making transforms/talairach.xfm
[mritotal] [christip@varda:/home/christip/FM/FMsurf/mri] [2006-01-11 14:10:42] /home/christip/sw/freesurfer/lib/mni/bin/minctracc -clobber -debug /tmp/mritotal_2613/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_2613/nu_8tmp2c.xfm -lsq9 -xcorr -model_mask /home/christip/sw/freesurfer/lib/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc -center 3.291864 10.920820 -22.100143 -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=    0.053   18.113
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    =    1.0735    0.0096   -0.0921   -5.1200 
                         0.0168    0.9212    0.2918   -3.3695 
                         0.0955   -0.3428    1.0768    6.1214 

Transform center   =    3.292   10.921  -22.100
Transform rotations  =   -0.308   -0.084    0.017
Transform trans    =   -2.737  -10.624    0.994
Transform scale    =    1.078    0.966    1.134
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_2613/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_2613/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    =    1.0735    0.0096   -0.0921   -5.1200 
                         0.0168    0.9212    0.2918   -3.3695 
                         0.0955   -0.3428    1.0768    6.1214 
Transform center   =    3.292   10.921  -22.100
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: 3.291864 10.920820 -22.100143
  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   22877 -> 0.07213088
  29440   22877 -> 0.07213088
  29440   22873 -> 0.08657942
  29440   22393 -> 0.07655723
  29440   22998 -> 0.07857048
  29440   22941 -> 0.07635332
  29440   22868 -> 0.07797226
  29440   22873 -> 0.07746956
  29440   22877 -> 0.08178327
  29440   23416 -> 0.07515375
  29440   22934 -> 0.07587685
  29440   22949 -> 0.08298025
  29440   22924 -> 0.07546623
  29440   22961 -> 0.08415747
  29440   22900 -> 0.07532544
  29440   22810 -> 0.07857127
  29440   22951 -> 0.07412571
  29440   22955 -> 0.07940904
  29440   22901 -> 0.07382468
  29440   22973 -> 0.07926980
  29440   22897 -> 0.07366799
  29440   23532 -> 0.07757181
  29440   22685 -> 0.07371647
  29440   22954 -> 0.07863712
  29440   22946 -> 0.07322194
  29440   22941 -> 0.07664730
  29440   22940 -> 0.07358199
  29440   22957 -> 0.07534314
  29440   22951 -> 0.07324535
  29440   23002 -> 0.07539573
  29440   22926 -> 0.07344998
  29440   22366 -> 0.07726547
  29440   23153 -> 0.07334828
  29440   22884 -> 0.07384980
  29440   22899 -> 0.07293420
  29440   22946 -> 0.07347092
  29440   23211 -> 0.07360689
  29440   23074 -> 0.07342327
  29440   22722 -> 0.07385519
  29440   23089 -> 0.07271746
  29440   23020 -> 0.07354943
  29440   23000 -> 0.07271692
  29440   23029 -> 0.07413255
  29440   22967 -> 0.07276463
  29440   23069 -> 0.07295565
  29440   22921 -> 0.07372475
  29440   23032 -> 0.07265917
  29440   22799 -> 0.07313745
  29440   22981 -> 0.07356380
  29440   22958 -> 0.07263659
  29440   22992 -> 0.07225939
  29440   23164 -> 0.07340766
  29440   22889 -> 0.07257427
  29440   22872 -> 0.07308257
  29440   23016 -> 0.07242213
  29440   23061 -> 0.07242154
  29440   23013 -> 0.07263659
  29440   22878 -> 0.07241418
  29440   22936 -> 0.07234298
  29440   22883 -> 0.07242285
  29440   22943 -> 0.07236215
  29440   22869 -> 0.07225247
  29440   22982 -> 0.07237410
  29440   23019 -> 0.07256979
  29440   22918 -> 0.07212632
  29440   22867 -> 0.07227112
  29440   22776 -> 0.07237601
  29440   22933 -> 0.07232226
  29440   23071 -> 0.07249807
  29440   22848 -> 0.07207643
  29440   22827 -> 0.07221413
  29440   22847 -> 0.07217523
  29440   22838 -> 0.07222560
done with simplex after 62 iterations
0 0.07213:-2.73701 -10.62357  0.99417 -17.65977 -4.82893  0.99781 53.87607 48.32183 56.70472 
1 0.07218:-2.51921 -10.50486  0.90817 -17.99575 -5.00564  1.14009 53.90561 48.35226 57.01218 
2 0.07232:-2.55235 -10.91194  0.84406 -18.24287 -5.16958  1.04890 53.75909 48.34735 57.02482 
3 0.07208:-2.49725 -10.57869  0.73226 -18.05879 -5.00755  0.86081 53.74636 48.36028 56.79943 
4 0.07226:-2.37959 -10.67830  0.69971 -17.99895 -5.07770  0.97829 53.96304 48.79123 56.89375 
5 0.07225:-2.52211 -10.46578  0.90119 -17.68388 -5.35298  0.97122 53.82039 48.44348 56.86918 
6 0.07213:-2.43747 -10.70579  0.90026 -17.73381 -5.05486  0.96058 53.78096 48.43942 56.71111 
7 0.07227:-2.40651 -10.73031  0.99363 -18.19886 -5.24988  0.69257 53.83878 48.24962 56.65884 
8 0.07221:-2.55962 -10.67557  0.75905 -17.69300 -5.00198  1.03536 53.93595 48.14756 56.98903 
9 0.07223:-2.58655 -10.53840  0.81637 -18.12646 -5.19931  1.19202 53.94609 48.36880 56.60337 
after parameter optimization
-center         3.29186   10.92082  -22.10014
-translation   -2.49725  -10.57869    0.73226
-rotation     -18.05879   -5.00755    0.86081
-scale          1.07493    0.96721    1.13599
-shear          0.00000    0.00000    0.00000
  29440   22848 -> 0.07207643
Initial objective function val = 0.07213088
Final objective function value = 0.07207643
successful write