cortical-surfaces-freesurfer/sub-06/mri/transforms/T2raw.dat.log

Logfile for bbregister
Thu Aug  8 23:20:09 CEST 2013

setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
/opt/freesurfer/5.3.0/bin/bbregister --s sub006 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.lta --init-fsl --T2

$Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $
Linux snake5 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
FREESURFER_HOME /opt/freesurfer/5.3.0
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998757, 0.0408089, 0.02861)
j_ras = (0.0441177, 0.99097, 0.126615)
k_ras = (0.0231846, -0.12772, 0.991539)
writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii...
fslregister --s sub006 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister --dof 6 --fsvol brainmask.mgz

Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat.fslregister.log

Thu Aug  8 23:20:14 CEST 2013
--s sub006 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister --dof 6 --fsvol brainmask.mgz
$Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $
snake5
Linux snake5 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
nIters 1
--------------------------------------
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/refvol.fslregister.nii
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/refvol.fslregister.nii 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/brainmask.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -1.16415e-09, 1.86265e-09)
j_ras = (-1.86265e-09, 1.49012e-08, -1)
k_ras = (9.31323e-10, 1, -1.49012e-08)
writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/refvol.fslregister.nii...
--------------------------------------
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/movvol.fslregister.nii --frame 0
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/movvol.fslregister.nii --frame 0 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998757, 0.0408089, 0.02861)
j_ras = (0.0441177, 0.99097, 0.126615)
k_ras = (0.0231846, -0.12772, 0.991539)
keeping frame 0
writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/movvol.fslregister.nii...
Mov determinant is -0.311076
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/movvol.fslregister.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/reg0.19186.dat --regheader --fslregout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat.fsl.mat0 --s sub006 --noedit
tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl
INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/movvol.fslregister.nii
reg file       /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/reg0.19186.dat
LoadVol        0
ZeroCRAS       0
$Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
Diagnostic Level -1
INFO: loading target /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig.mgz
Ttarg: --------------------
-1.000   0.000   0.000   128.000;
 0.000   0.000   1.000  -128.000;
 0.000  -1.000   0.000   128.000;
 0.000   0.000   0.000   1.000;
INFO: loading movable /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/movvol.fslregister.nii
Tmov: --------------------
-0.700   0.000   0.000   95.889;
 0.000   0.000   0.667  -128.000;
 0.000  -0.667   0.000   128.000;
 0.000   0.000   0.000   1.000;
mkheaderreg = 1, float2int = 0
Computing reg from header (and possibly input matrix)
---- Input registration matrix (computed) --------
 0.999  -0.041  -0.029  -0.000;
 0.023  -0.128   0.992  -0.000;
-0.044  -0.991  -0.127   0.000;
 0.000   0.000   0.000   1.000;
---------------------------------------
---- Input registration matrix --------
 0.999  -0.041  -0.029  -0.000;
 0.023  -0.128   0.992  -0.000;
-0.044  -0.991  -0.127   0.000;
 0.000   0.000   0.000   1.000;
Determinant 1
subject = sub006
RegMat ---------------------------
 0.999  -0.041  -0.029  -0.000;
 0.023  -0.128   0.992  -0.000;
-0.044  -0.991  -0.127   0.000;
 0.000   0.000   0.000   1.000;
FSLOUTPUTTYPE NIFTI 
tkreg2FSL: mov det = -0.311076, ref det = -1
Thu Aug  8 23:20:22 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat.fsl.mat0
Thu Aug  8 23:24:44 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat.fsl.mat -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/fslmat0.trans.mat -schedule /opt/freesurfer/5.3.0/bin/flirt.newdefault.20080811.sch
tkregister2_cmdl --s sub006 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat --fslreg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat.fsl.mat --noedit
tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl
---- FSL registration matrix --------
 0.999  -0.042  -0.020   40.136;
-0.025  -0.120  -0.992   274.192;
 0.039   0.992  -0.121   12.050;
 0.000   0.000   0.000   1.000;
---------------------------------------
INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii
reg file       /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat
LoadVol        0
ZeroCRAS       0
$Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
Diagnostic Level -1
INFO: loading target /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig.mgz
Ttarg: --------------------
-1.000   0.000   0.000   128.000;
 0.000   0.000   1.000  -128.000;
 0.000  -1.000   0.000   128.000;
 0.000   0.000   0.000   1.000;
INFO: loading movable /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii
Tmov: --------------------
-0.700   0.000   0.000   95.889;
 0.000   0.000   0.667  -128.000;
 0.000  -0.667   0.000   128.000;
 0.000   0.000   0.000   1.000;
mkheaderreg = 0, float2int = 0
FSLOUTPUTTYPE NIFTI 
fsl2TkReg: mov det = -0.311076, ref det = -1
---- Input registration matrix (computed) --------
 0.999  -0.039  -0.025   0.009;
 0.020  -0.121   0.992   1.308;
-0.042  -0.992  -0.120  -0.930;
 0.000   0.000   0.000   1.000;
---------------------------------------
---- Input registration matrix --------
 0.999  -0.039  -0.025   0.009;
 0.020  -0.121   0.992   1.308;
-0.042  -0.992  -0.120  -0.930;
 0.000   0.000   0.000   1.000;
Determinant 1
subject = sub006
RegMat ---------------------------
 0.999  -0.039  -0.025   0.009;
 0.020  -0.121   0.992   1.308;
-0.042  -0.992  -0.120  -0.930;
 0.000   0.000   0.000   1.000;
 
Started at Thu Aug 8 23:20:14 CEST 2013 
Ended   at Thu Aug  8 23:31:25 CEST 2013
 
fslregister Done
 
To check results, run:
tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat --surf orig
 
mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5
$Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $
setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 
sysname  Linux
hostname snake5
machine  x86_64
user     fkaule
movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii
regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat
subject sub006
dof 6
outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/bbr.pass1.dat
UseMask 0
UseLH 1
UseRH 1
nsubsamp 100
PenaltySign  -1
PenaltySlope 0.500000
PenaltyCenter 0.000000
surfname white
GMProjFrac 0.500000
WMProjAbs 2.000000
lhcostfile (null)
rhcostfile (null)
interp  trilinear (1)
frame  0
TolPowell 0.000100
nMaxItersPowell 36
n1dmin  3
Profile   0
Gdiag_no  -1
AddNoise  0 (0)
SynthSeed 1376052073
TransRandMax 0.000000
RotRandMax 0.000000
Translations 0.000000 0.000000 0.000000
Rotations   0.000000 0.000000 0.000000
Input reg
 0.999  -0.039  -0.025   0.009;
 0.020  -0.121   0.992   1.308;
-0.042  -0.992  -0.120  -0.930;
 0.000   0.000   0.000   1.000;

Loading mov
Projecting LH Surfs
Loading lh.white surf
Loading lh.thickness for GM
GM Proj: 1 0.500000 2.000000
WM Proj: 0 0.500000 2.000000
Projecting RH Surfs
Loading rh.white surf
Loading rh.thickness
Projecting RH Surfs
Computing relative cost
 0  -25.0 -25.0 -25.0   0.990036
 1  -25.0 -25.0  25.0   1.013869
 2  -25.0  25.0 -25.0   1.045360
 3  -25.0  25.0  25.0   1.003149
 4   25.0 -25.0 -25.0   1.023281
 5   25.0 -25.0  25.0   1.006686
 6   25.0  25.0 -25.0   1.010024
 7   25.0  25.0  25.0   1.048604
REL:  8  0.322576    8.141011  1.017626 rel = 0.316989 
Initial costs ----------------
Number of surface hits 3238
WM  Intensity    61.7561 +/-  11.7398
Ctx Intensity    77.7046 +/-  15.1309
Pct Contrast     22.3549 +/-  23.0208
Cost   0.3226
RelCost   0.3170

------------------------------------
Brute force preopt -4 4 4, n = 729
     0  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000      0.9854   0.9854  0.0
     1  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000   0.0000      0.9791   0.9791  0.0
     3  -4.0000  -4.0000  -4.0000  -4.0000   0.0000  -4.0000      0.9606   0.9606  0.0
     6  -4.0000  -4.0000  -4.0000  -4.0000   4.0000  -4.0000      0.9556   0.9556  0.0
    15  -4.0000  -4.0000  -4.0000   0.0000   4.0000  -4.0000      0.8671   0.8671  0.0
    21  -4.0000  -4.0000  -4.0000   4.0000   0.0000  -4.0000      0.8189   0.8189  0.0
    39  -4.0000  -4.0000   0.0000   0.0000   0.0000  -4.0000      0.7643   0.7643  0.0
   120  -4.0000   0.0000   0.0000   0.0000   0.0000  -4.0000      0.6566   0.6566  0.0
   283   0.0000  -4.0000   0.0000   0.0000   0.0000   0.0000      0.6078   0.6078  0.0
   364   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000      0.3226   0.3226  0.0
Brute Force --------------------------
Min cost was 0.322576
Number of iterations   729
Search time 2.528000 sec
Parameters at best (transmm, rotdeg)
  0.000   0.000   0.000  0.000  0.000  0.000 
--------------------------------------------

Starting Powell Minimization
Init Powel Params dof = 6
0 0
1 0
2 0
3 0
4 0
5 0
  10 -0.006  0.000  0.000  0.000  0.000  0.000   0.3225513539
  11 -0.005  0.000  0.000  0.000  0.000  0.000   0.3225499366
  15 -0.005 -1.618  0.000  0.000  0.000  0.000   0.1223710691
  20 -0.005 -1.431  0.000  0.000  0.000  0.000   0.1196453081
  21 -0.005 -1.460  0.000  0.000  0.000  0.000   0.1190840389
  22 -0.005 -1.491  0.000  0.000  0.000  0.000   0.1184857389
  24 -0.005 -1.500  0.000  0.000  0.000  0.000   0.1184697786
  25 -0.005 -1.498  0.000  0.000  0.000  0.000   0.1184583008
  26 -0.005 -1.496  0.000  0.000  0.000  0.000   0.1184563610
  29 -0.005 -1.496  1.000  0.000  0.000  0.000   0.1170204377
  33 -0.005 -1.496  0.618  0.000  0.000  0.000   0.0877717013
  35 -0.005 -1.496  0.524  0.000  0.000  0.000   0.0860064007
  36 -0.005 -1.496  0.509  0.000  0.000  0.000   0.0859274583
  38 -0.005 -1.496  0.507  0.000  0.000  0.000   0.0859264095
  48 -0.005 -1.496  0.507 -0.064  0.000  0.000   0.0855856668
  49 -0.005 -1.496  0.507 -0.038  0.000  0.000   0.0849571324
  59 -0.005 -1.496  0.507 -0.038 -0.082  0.000   0.0845974589
  60 -0.005 -1.496  0.507 -0.038 -0.052  0.000   0.0843965611
  61 -0.005 -1.496  0.507 -0.038 -0.051  0.000   0.0843894536
  62 -0.005 -1.496  0.507 -0.038 -0.032  0.000   0.0843761775
  63 -0.005 -1.496  0.507 -0.038 -0.040  0.000   0.0843609554
  64 -0.005 -1.496  0.507 -0.038 -0.039  0.000   0.0843584762
  65 -0.005 -1.496  0.507 -0.038 -0.037  0.000   0.0843576955
  74 -0.005 -1.496  0.507 -0.038 -0.037  0.119   0.0818356881
  76 -0.005 -1.496  0.507 -0.038 -0.037  0.104   0.0817269000
  79 -0.005 -1.496  0.507 -0.038 -0.037  0.098   0.0817165227
  89  0.062 -1.496  0.507 -0.038 -0.037  0.098   0.0784200867
  91  0.079 -1.496  0.507 -0.038 -0.037  0.098   0.0783580601
  92  0.076 -1.496  0.507 -0.038 -0.037  0.098   0.0783375078
  93  0.074 -1.496  0.507 -0.038 -0.037  0.098   0.0783332821
 102  0.074 -1.500  0.507 -0.038 -0.037  0.098   0.0782613848
 104  0.074 -1.532  0.507 -0.038 -0.037  0.098   0.0782124181
 105  0.074 -1.518  0.507 -0.038 -0.037  0.098   0.0781260750
 106  0.074 -1.519  0.507 -0.038 -0.037  0.098   0.0781256759
 114  0.074 -1.519  0.518 -0.038 -0.037  0.098   0.0780031421
 116  0.074 -1.519  0.528 -0.038 -0.037  0.098   0.0779685306
 117  0.074 -1.519  0.530 -0.038 -0.037  0.098   0.0779660198
 128  0.074 -1.519  0.530 -0.079 -0.037  0.098   0.0775032375
 129  0.074 -1.519  0.530 -0.070 -0.037  0.098   0.0773934281
 130  0.074 -1.519  0.530 -0.066 -0.037  0.098   0.0773850494
 140  0.074 -1.519  0.530 -0.066 -0.045  0.098   0.0772513331
 142  0.074 -1.519  0.530 -0.066 -0.049  0.098   0.0772355263
 151  0.074 -1.519  0.530 -0.066 -0.049  0.153   0.0768815185
 152  0.074 -1.519  0.530 -0.066 -0.049  0.144   0.0767667536
 153  0.074 -1.519  0.530 -0.066 -0.049  0.133   0.0767352155
 154  0.074 -1.519  0.530 -0.066 -0.049  0.136   0.0767350124
 156  0.074 -1.519  0.530 -0.066 -0.049  0.135   0.0767345098
 157  0.153 -1.542  0.554 -0.094 -0.061  0.171   0.0757315281
 165  0.156 -1.543  0.555 -0.096 -0.062  0.173   0.0757278872
 166  0.160 -1.544  0.556 -0.097 -0.062  0.175   0.0757259927
 169  0.160 -1.544  0.556 -0.097 -0.062  0.175   0.0757256658
 177  0.160 -1.544  0.556 -0.097 -0.062  0.204   0.0755171844
 179  0.160 -1.544  0.556 -0.097 -0.062  0.196   0.0755028243
 181  0.160 -1.544  0.556 -0.097 -0.062  0.199   0.0754996383
 190  0.160 -1.513  0.556 -0.097 -0.062  0.199   0.0746624075
 191  0.160 -1.464  0.556 -0.097 -0.062  0.199   0.0746055559
 193  0.160 -1.487  0.556 -0.097 -0.062  0.199   0.0744588357
 195  0.160 -1.489  0.556 -0.097 -0.062  0.199   0.0744576947
 206  0.160 -1.489  0.566 -0.097 -0.062  0.199   0.0743555643
 207  0.160 -1.489  0.571 -0.097 -0.062  0.199   0.0743416053
 219  0.160 -1.489  0.571 -0.102 -0.062  0.199   0.0743244867
 229  0.160 -1.489  0.571 -0.102 -0.054  0.199   0.0742840259
 232  0.160 -1.489  0.571 -0.102 -0.055  0.199   0.0742834399
 239  0.190 -1.498  0.580 -0.112 -0.059  0.213   0.0741403009
 242  0.209 -1.503  0.586 -0.119 -0.062  0.221   0.0741398050
 244  0.209 -1.503  0.586 -0.119 -0.062  0.221   0.0741395840
 247  0.211 -1.504  0.586 -0.120 -0.063  0.222   0.0741395027
 248  0.210 -1.503  0.586 -0.120 -0.062  0.222   0.0741393948
 249  0.210 -1.503  0.586 -0.120 -0.062  0.222   0.0741393463
 259  0.210 -1.503  0.586 -0.120 -0.062  0.233   0.0738855742
 261  0.210 -1.503  0.586 -0.120 -0.062  0.248   0.0737759217
 262  0.210 -1.503  0.586 -0.120 -0.062  0.246   0.0737721810
 273  0.210 -1.490  0.586 -0.120 -0.062  0.246   0.0736963995
 285  0.210 -1.490  0.587 -0.120 -0.062  0.246   0.0736915133
 286  0.210 -1.490  0.592 -0.120 -0.062  0.246   0.0736834938
 288  0.210 -1.490  0.591 -0.120 -0.062  0.246   0.0736833623
 298  0.210 -1.490  0.591 -0.111 -0.062  0.246   0.0735968226
 300  0.210 -1.490  0.591 -0.107 -0.062  0.246   0.0735963327
 302  0.210 -1.490  0.591 -0.108 -0.062  0.246   0.0735944569
 303  0.210 -1.490  0.591 -0.109 -0.062  0.246   0.0735940538
 311  0.210 -1.490  0.591 -0.109 -0.070  0.246   0.0735228430
 312  0.210 -1.490  0.591 -0.109 -0.074  0.246   0.0735080376
 315  0.210 -1.490  0.591 -0.109 -0.075  0.246   0.0735077031
 321  0.240 -1.498  0.599 -0.120 -0.080  0.260   0.0734949468
 322  0.226 -1.494  0.595 -0.115 -0.078  0.254   0.0734300529
 324  0.228 -1.495  0.596 -0.116 -0.078  0.255   0.0734286940
 327  0.228 -1.495  0.596 -0.116 -0.078  0.255   0.0734286205
 338  0.228 -1.495  0.596 -0.116 -0.078  0.253   0.0734281123
 348  0.228 -1.479  0.596 -0.116 -0.078  0.253   0.0734006223
 349  0.228 -1.482  0.596 -0.116 -0.078  0.253   0.0733844990
 350  0.228 -1.486  0.596 -0.116 -0.078  0.253   0.0733790100
 362  0.228 -1.486  0.592 -0.116 -0.078  0.253   0.0733697099
 364  0.228 -1.486  0.593 -0.116 -0.078  0.253   0.0733696556
 374  0.228 -1.486  0.593 -0.110 -0.078  0.253   0.0733206040
 376  0.228 -1.486  0.593 -0.105 -0.078  0.253   0.0733125478
 377  0.228 -1.486  0.593 -0.107 -0.078  0.253   0.0733110118
 387  0.228 -1.486  0.593 -0.107 -0.083  0.253   0.0732951888
 396  0.232 -1.487  0.595 -0.108 -0.083  0.255   0.0732732502
 397  0.237 -1.488  0.596 -0.110 -0.084  0.257   0.0732630673
 398  0.238 -1.488  0.596 -0.110 -0.084  0.258   0.0732627839
 399  0.238 -1.488  0.596 -0.110 -0.084  0.257   0.0732624241
 403  0.247 -1.482  0.597 -0.104 -0.090  0.260   0.0732474931
 437  0.238 -1.483  0.592 -0.110 -0.084  0.259   0.0732438122
 439  0.238 -1.483  0.590 -0.110 -0.084  0.259   0.0732404503
 449  0.238 -1.483  0.590 -0.108 -0.084  0.259   0.0732309201
 451  0.238 -1.483  0.590 -0.105 -0.084  0.259   0.0732277520
 452  0.238 -1.483  0.590 -0.106 -0.084  0.259   0.0732268628
 462  0.238 -1.483  0.590 -0.106 -0.083  0.259   0.0732261879
 471  0.241 -1.484  0.590 -0.107 -0.084  0.260   0.0732203038
 472  0.242 -1.484  0.591 -0.108 -0.084  0.260   0.0732202274
 481  0.245 -1.480  0.585 -0.105 -0.083  0.263   0.0732121668
 527  0.242 -1.483  0.588 -0.105 -0.084  0.260   0.0732108126
 547  0.243 -1.483  0.589 -0.106 -0.084  0.261   0.0732097022
 549  0.243 -1.483  0.589 -0.106 -0.084  0.261   0.0732096414
 551  0.244 -1.482  0.587 -0.104 -0.084  0.262   0.0732042478
 556  0.245 -1.481  0.586 -0.103 -0.084  0.262   0.0732030385
 559  0.245 -1.481  0.585 -0.103 -0.084  0.262   0.0732029930
 561  0.245 -1.481  0.585 -0.103 -0.084  0.262   0.0732029320
 562  0.245 -1.481  0.585 -0.103 -0.084  0.262   0.0732029164
 564  0.245 -1.481  0.585 -0.103 -0.084  0.262   0.0732028100
 577  0.245 -1.481  0.585 -0.103 -0.084  0.264   0.0732018670
Powell done niters = 7
Computing relative cost
 0  -25.0 -25.0 -25.0   1.013482
 1  -25.0 -25.0  25.0   1.015559
 2  -25.0  25.0 -25.0   1.034208
 3  -25.0  25.0  25.0   1.000666
 4   25.0 -25.0 -25.0   1.034182
 5   25.0 -25.0  25.0   0.991798
 6   25.0  25.0 -25.0   1.006023
 7   25.0  25.0  25.0   1.034180
REL:  8  0.073202    8.130098  1.016262 rel = 0.0720305 
Number of iterations     7
Min cost was 0.073202
Number of FunctionCalls   641
TolPowell 0.000100
nMaxItersPowell 36
OptimizationTime 2.591000 sec
Parameters at optimum (transmm)  0.24532 -1.48124  0.58539
Parameters at optimum (rotdeg) -0.10298 -0.08425  0.26413 
Final costs ----------------
Number of surface hits 3238
WM  Intensity    60.0746 +/-  10.5131
Ctx Intensity    78.1624 +/-  10.7433
Pct Contrast     26.4330 +/-  15.2985
Cost   0.0732
RelCost   0.3170
Reg at min cost was 
 0.999  -0.037  -0.029   0.250;
 0.024  -0.123   0.992  -0.175;
-0.040  -0.992  -0.122  -0.347;
 0.000   0.000   0.000   1.000;

Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/bbr.pass1.dat, type = 14 
Original Reg 
 0.999  -0.039  -0.025   0.009;
 0.020  -0.121   0.992   1.308;
-0.042  -0.992  -0.120  -0.930;
 0.000   0.000   0.000   1.000;

Original Reg - Optimal Reg
 0.000  -0.002   0.004  -0.241;
-0.005   0.002   0.000   1.483;
-0.001  -0.000   0.002  -0.583;
 0.000   0.000   0.000   0.000;

Computing change in lh position
LH rmsDiffMean 1.655014
Computing change in rh position
Surface RMS Diff (mm) 1.549561 1.872015
mri_segreg done
mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5
$Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $
setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 
sysname  Linux
hostname snake5
machine  x86_64
user     fkaule
movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii
regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/bbr.pass1.dat
subject sub006
dof 6
outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.dat
UseMask 0
UseLH 1
UseRH 1
nsubsamp 1
PenaltySign  -1
PenaltySlope 0.500000
PenaltyCenter 0.000000
surfname white
GMProjFrac 0.500000
WMProjAbs 2.000000
lhcostfile (null)
rhcostfile (null)
interp  trilinear (1)
frame  0
TolPowell 0.000000
nMaxItersPowell 36
n1dmin  3
Profile   0
Gdiag_no  -1
AddNoise  0 (0)
SynthSeed 1376539157
TransRandMax 0.000000
RotRandMax 0.000000
Translations 0.000000 0.000000 0.000000
Rotations   0.000000 0.000000 0.000000
Input reg
 0.999  -0.037  -0.029   0.250;
 0.024  -0.123   0.992  -0.175;
-0.040  -0.992  -0.122  -0.347;
 0.000   0.000   0.000   1.000;

Loading mov
Projecting LH Surfs
Loading lh.white surf
Loading lh.thickness for GM
GM Proj: 1 0.500000 2.000000
WM Proj: 0 0.500000 2.000000
Projecting RH Surfs
Loading rh.white surf
Loading rh.thickness
Projecting RH Surfs
Computing relative cost
 0  -25.0 -25.0 -25.0   1.000144
 1  -25.0 -25.0  25.0   1.011963
 2  -25.0  25.0 -25.0   1.028762
 3  -25.0  25.0  25.0   1.017444
 4   25.0 -25.0 -25.0   1.023030
 5   25.0 -25.0  25.0   1.003200
 6   25.0  25.0 -25.0   1.006099
 7   25.0  25.0  25.0   1.018704
REL:  8  0.074000    8.109344  1.013668 rel = 0.0730019 
Initial costs ----------------
Number of surface hits 323295
WM  Intensity    60.0945 +/-  10.4129
Ctx Intensity    78.3960 +/-  10.7337
Pct Contrast     26.6644 +/-  15.2882
Cost   0.0740
RelCost   0.0730

------------------------------------
Brute force preopt -0.1 0.1 0.1, n = 729
     0  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000      0.0884   0.0884  0.0
     3  -0.1000  -0.1000  -0.1000  -0.1000   0.0000  -0.1000      0.0860   0.0860  0.0
     9  -0.1000  -0.1000  -0.1000   0.0000  -0.1000  -0.1000      0.0824   0.0824  0.0
    12  -0.1000  -0.1000  -0.1000   0.0000   0.0000  -0.1000      0.0789   0.0789  0.0
    21  -0.1000  -0.1000  -0.1000   0.1000   0.0000  -0.1000      0.0775   0.0775  0.0
    39  -0.1000  -0.1000   0.0000   0.0000   0.0000  -0.1000      0.0762   0.0762  0.0
   120  -0.1000   0.0000   0.0000   0.0000   0.0000  -0.1000      0.0755   0.0755  0.0
   121  -0.1000   0.0000   0.0000   0.0000   0.0000   0.0000      0.0755   0.0755  0.0
   364   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000      0.0732   0.0732  0.0
Brute Force --------------------------
Min cost was 0.073202
Number of iterations   729
Search time 2.842000 sec
Parameters at best (transmm, rotdeg)
  0.000   0.000   0.000  0.000  0.000  0.000 
--------------------------------------------

Starting Powell Minimization
Init Powel Params dof = 6
0 0
1 0
2 0
3 0
4 0
5 0
   7 -0.011  0.000  0.000  0.000  0.000  0.000   0.0739579968
   8 -0.023  0.000  0.000  0.000  0.000  0.000   0.0739393766
  10 -0.024  0.000  0.000  0.000  0.000  0.000   0.0739391684
  18 -0.024  0.068  0.000  0.000  0.000  0.000   0.0736410288
  19 -0.024  0.054  0.000  0.000  0.000  0.000   0.0736210929
  28 -0.024  0.054  0.144  0.000  0.000  0.000   0.0712034427
  29 -0.024  0.054  0.145  0.000  0.000  0.000   0.0712014029
  30 -0.024  0.054  0.154  0.000  0.000  0.000   0.0711957153
  32 -0.024  0.054  0.152  0.000  0.000  0.000   0.0711948811
  42 -0.024  0.054  0.152  0.003  0.000  0.000   0.0711937157
  51 -0.024  0.054  0.152  0.003 -0.021  0.000   0.0710840807
  52 -0.024  0.054  0.152  0.003 -0.028  0.000   0.0710745386
  55 -0.024  0.054  0.152  0.003 -0.029  0.000   0.0710742340
  63 -0.024  0.054  0.152  0.003 -0.029  0.003   0.0710718816
  65 -0.024  0.054  0.152  0.003 -0.029  0.005   0.0710714752
  66 -0.024  0.054  0.152  0.003 -0.029  0.006   0.0710712416
  77 -0.013  0.054  0.152  0.003 -0.029  0.006   0.0710605916
  87 -0.013  0.055  0.152  0.003 -0.029  0.006   0.0710605245
  96 -0.013  0.055  0.154  0.003 -0.029  0.006   0.0710602217
 106 -0.013  0.055  0.154  0.004 -0.029  0.006   0.0710595122
 115 -0.013  0.055  0.154  0.004 -0.031  0.006   0.0710593576
 124 -0.013  0.055  0.154  0.004 -0.031  0.010   0.0710563353
 126 -0.013  0.055  0.154  0.004 -0.031  0.011   0.0710561702
 127 -0.013  0.055  0.154  0.004 -0.031  0.012   0.0710560869
 130 -0.003  0.056  0.156  0.006 -0.032  0.018   0.0710552827
 136 -0.007  0.056  0.155  0.005 -0.032  0.016   0.0710535106
 137 -0.008  0.056  0.155  0.005 -0.031  0.015   0.0710534580
 138 -0.008  0.056  0.155  0.005 -0.031  0.016   0.0710533858
 162 -0.008  0.057  0.155  0.005 -0.031  0.016   0.0710532018
 171 -0.008  0.057  0.152  0.005 -0.031  0.016   0.0710519125
 198 -0.006  0.057  0.153  0.005 -0.032  0.016   0.0710517517
 199 -0.006  0.057  0.153  0.005 -0.032  0.016   0.0710517061
 200 -0.007  0.057  0.152  0.005 -0.032  0.016   0.0710517012
 203 -0.007  0.057  0.152  0.005 -0.032  0.016   0.0710516797
 217 -0.007  0.057  0.152  0.005 -0.032  0.017   0.0710516335
 270 -0.007  0.057  0.152  0.005 -0.032  0.017   0.0710516217
Powell done niters = 4
Computing relative cost
 0  -25.0 -25.0 -25.0   1.000527
 1  -25.0 -25.0  25.0   1.012389
 2  -25.0  25.0 -25.0   1.028572
 3  -25.0  25.0  25.0   1.018441
 4   25.0 -25.0 -25.0   1.022629
 5   25.0 -25.0  25.0   1.001609
 6   25.0  25.0 -25.0   1.005235
 7   25.0  25.0  25.0   1.020102
REL:  8  0.071052    8.109503  1.013688 rel = 0.0700922 
Number of iterations     4
Min cost was 0.071052
Number of FunctionCalls   333
TolPowell 0.000000
nMaxItersPowell 36
OptimizationTime 51.287000 sec
Parameters at optimum (transmm) -0.00683  0.05697  0.15243
Parameters at optimum (rotdeg)  0.00519 -0.03151  0.01697 
Final costs ----------------
Number of surface hits 323295
WM  Intensity    60.0684 +/-  10.3946
Ctx Intensity    78.3842 +/-  10.7444
Pct Contrast     26.6871 +/-  15.2674
Cost   0.0711
RelCost   0.0730
Reg at min cost was 
 0.999  -0.036  -0.029   0.243;
 0.025  -0.123   0.992  -0.118;
-0.040  -0.992  -0.122  -0.195;
 0.000   0.000   0.000   1.000;

Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.dat, type = 14 
Original Reg 
 0.999  -0.037  -0.029   0.250;
 0.024  -0.123   0.992  -0.175;
-0.040  -0.992  -0.122  -0.347;
 0.000   0.000   0.000   1.000;

Original Reg - Optimal Reg
-0.000  -0.001   0.000   0.007;
-0.000  -0.000  -0.000  -0.057;
-0.001   0.000  -0.000  -0.153;
 0.000   0.000   0.000   0.000;

Computing change in lh position
LH rmsDiffMean 0.153461
Computing change in rh position
Surface RMS Diff (mm) 0.170445 0.209095
mri_segreg done
tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.dat --noedit --ltaout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.lta
tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl
INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz
reg file       /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.dat
LoadVol        0
ZeroCRAS       0
$Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
Diagnostic Level -1
---- Input registration matrix --------
 0.999  -0.036  -0.029   0.243;
 0.025  -0.123   0.992  -0.118;
-0.040  -0.992  -0.122  -0.195;
 0.000   0.000   0.000   1.000;
float2int = 0
---------------------------------------
INFO: loading target /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig.mgz
Ttarg: --------------------
-1.000   0.000   0.000   128.000;
 0.000   0.000   1.000  -128.000;
 0.000  -1.000   0.000   128.000;
 0.000   0.000   0.000   1.000;
INFO: loading movable /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz
Tmov: --------------------
-0.700   0.000   0.000   95.889;
 0.000   0.000   0.667  -128.000;
 0.000  -0.667   0.000   128.000;
 0.000   0.000   0.000   1.000;
mkheaderreg = 0, float2int = 0
---- Input registration matrix --------
 0.999  -0.036  -0.029   0.243;
 0.025  -0.123   0.992  -0.118;
-0.040  -0.992  -0.122  -0.195;
 0.000   0.000   0.000   1.000;
Determinant 1
subject = sub006
RegMat ---------------------------
 0.999  -0.036  -0.029   0.243;
 0.025  -0.123   0.992  -0.118;
-0.040  -0.992  -0.122  -0.195;
 0.000   0.000   0.000   1.000;
transformed matrix:
 1.000  -0.005   0.001  -0.130;
 0.005   1.000   0.005  -0.080;
-0.001  -0.005   1.000   0.196;
 0.000   0.000   0.000   1.000;
transformed matrix:
 0.699  -0.026  -0.016   40.677;
-0.021  -0.081  -0.661   273.305;
 0.025   0.661  -0.082   13.122;
 0.000   0.000   0.000   1.000;
Cleaning up
 
Started at Thu Aug 8 23:20:09 CEST 2013 
Ended   at Thu Aug  8 23:33:28 CEST 2013
BBR-Run-Time-Sec 799
 
bbregister Done
To check results, run:
tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.dat --surf