cortical-surfaces-freesurfer/sub-11/mri/transforms/T2raw.dat.log

Logfile for bbregister
Thu Aug  8 22:59:45 CEST 2013

setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts
/opt/freesurfer/5.3.0/bin/bbregister --s sub011 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/T2raw.lta --init-fsl --T2

$Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $
Linux snake6 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/sub011/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/template.nii
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/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/sub011/mri/orig/T2raw.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998102, -0.0611237, 0.00753358)
j_ras = (-0.0606425, 0.996759, 0.0528636)
k_ras = (0.0107404, -0.0523064, 0.998573)
writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/template.nii...
fslregister --s sub011 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/fslregister --dof 6 --fsvol brainmask.mgz

Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/reg.init.dat.fslregister.log

Thu Aug  8 22:59:51 CEST 2013
--s sub011 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/fslregister --dof 6 --fsvol brainmask.mgz
$Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $
snake6
Linux snake6 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/sub011/scripts
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/fslregister/refvol.fslregister.nii
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/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/sub011/mri/brainmask.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 1.31549e-08, 0)
j_ras = (0, -1.11759e-08, -1)
k_ras = (5.47152e-09, 1, -3.72529e-09)
writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/fslregister/refvol.fslregister.nii...
--------------------------------------
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/fslregister/movvol.fslregister.nii --frame 0
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/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/sub011/mri/transforms/tmp.bbregister.22917/template.nii...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998102, -0.0611237, 0.00753358)
j_ras = (-0.0606425, 0.996759, 0.0528636)
k_ras = (0.0107404, -0.0523064, 0.998573)
keeping frame 0
writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/fslregister/movvol.fslregister.nii...
Mov determinant is -0.311072
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts
tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/fslregister/movvol.fslregister.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/fslregister/reg0.22957.dat --regheader --fslregout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/reg.init.dat.fsl.mat0 --s sub011 --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/sub011/mri/transforms/tmp.bbregister.22917/fslregister/movvol.fslregister.nii
reg file       /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/fslregister/reg0.22957.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/sub011/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/sub011/mri/transforms/tmp.bbregister.22917/fslregister/movvol.fslregister.nii
Tmov: --------------------
-0.700   0.000   0.000   95.888;
 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) --------
 0.998   0.061  -0.008   0.000;
 0.011  -0.052   0.999  -0.000;
 0.061  -0.997  -0.053  -0.000;
 0.000   0.000   0.000   1.000;
---------------------------------------
---- Input registration matrix --------
 0.998   0.061  -0.008   0.000;
 0.011  -0.052   0.999  -0.000;
 0.061  -0.997  -0.053  -0.000;
 0.000   0.000   0.000   1.000;
Determinant 1
subject = sub011
RegMat ---------------------------
 0.998   0.061  -0.008   0.000;
 0.011  -0.052   0.999  -0.000;
 0.061  -0.997  -0.053  -0.000;
 0.000   0.000   0.000   1.000;
FSLOUTPUTTYPE NIFTI 
tkreg2FSL: mov det = -0.311072, ref det = -1
Thu Aug  8 22:59:59 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts
flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/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/sub011/mri/transforms/tmp.bbregister.22917/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/reg.init.dat.fsl.mat0
Thu Aug  8 23:04:29 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/scripts
flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/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/sub011/mri/transforms/tmp.bbregister.22917/reg.init.dat.fsl.mat -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/fslregister/fslmat0.trans.mat -schedule /opt/freesurfer/5.3.0/bin/flirt.newdefault.20080811.sch
tkregister2_cmdl --s sub011 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/reg.init.dat --fslreg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/reg.init.dat.fsl.mat --noedit
tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl
---- FSL registration matrix --------
 0.998   0.056  -0.006   25.361;
-0.003  -0.054  -0.999   262.100;
-0.057   0.997  -0.053   11.865;
 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/sub011/mri/transforms/tmp.bbregister.22917/template.nii
reg file       /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/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/sub011/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/sub011/mri/transforms/tmp.bbregister.22917/template.nii
Tmov: --------------------
-0.700   0.000   0.000   95.888;
 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 = -0.311072, ref det = -1
---- Input registration matrix (computed) --------
 0.998   0.057  -0.003  -0.394;
 0.006  -0.053   0.999  -0.884;
 0.056  -0.997  -0.054  -0.749;
 0.000   0.000   0.000   1.000;
---------------------------------------
---- Input registration matrix --------
 0.998   0.057  -0.003  -0.394;
 0.006  -0.053   0.999  -0.884;
 0.056  -0.997  -0.054  -0.749;
 0.000   0.000   0.000   1.000;
Determinant 0.999999
subject = sub011
RegMat ---------------------------
 0.998   0.057  -0.003  -0.394;
 0.006  -0.053   0.999  -0.884;
 0.056  -0.997  -0.054  -0.749;
 0.000   0.000   0.000   1.000;
 
Started at Thu Aug 8 22:59:51 CEST 2013 
Ended   at Thu Aug  8 23:10:51 CEST 2013
 
fslregister Done
 
To check results, run:
tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/reg.init.dat --surf orig
 
mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/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/sub011/scripts
mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/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 snake6
machine  x86_64
user     fkaule
movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/template.nii
regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/reg.init.dat
subject sub011
dof 6
outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/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 1376360729
TransRandMax 0.000000
RotRandMax 0.000000
Translations 0.000000 0.000000 0.000000
Rotations   0.000000 0.000000 0.000000
Input reg
 0.998   0.057  -0.003  -0.394;
 0.006  -0.053   0.999  -0.884;
 0.056  -0.997  -0.054  -0.749;
 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   1.057876
 1  -25.0 -25.0  25.0   0.998681
 2  -25.0  25.0 -25.0   1.013842
 3  -25.0  25.0  25.0   1.042111
 4   25.0 -25.0 -25.0   0.997035
 5   25.0 -25.0  25.0   1.048967
 6   25.0  25.0 -25.0   1.009851
 7   25.0  25.0  25.0   1.018001
REL:  8  0.203528    8.186364  1.023295 rel = 0.198894 
Initial costs ----------------
Number of surface hits 2995
WM  Intensity    56.5723 +/-   9.2411
Ctx Intensity    70.8426 +/-  10.0568
Pct Contrast     22.4807 +/-  17.0063
Cost   0.2035
RelCost   0.1989

------------------------------------
Brute force preopt -4 4 4, n = 729
     0  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000      0.9896   0.9896  0.0
     1  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000   0.0000      0.9788   0.9788  0.0
     3  -4.0000  -4.0000  -4.0000  -4.0000   0.0000  -4.0000      0.9485   0.9485  0.0
    15  -4.0000  -4.0000  -4.0000   0.0000   4.0000  -4.0000      0.8611   0.8611  0.0
    39  -4.0000  -4.0000   0.0000   0.0000   0.0000  -4.0000      0.8176   0.8176  0.0
   120  -4.0000   0.0000   0.0000   0.0000   0.0000  -4.0000      0.6454   0.6454  0.0
   364   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000      0.2035   0.2035  0.0
Brute Force --------------------------
Min cost was 0.203528
Number of iterations   729
Search time 2.491000 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  0.130  0.000  0.000  0.000  0.000  0.000   0.2034642916
   8  0.074  0.000  0.000  0.000  0.000  0.000   0.2031443284
  10  0.085  0.000  0.000  0.000  0.000  0.000   0.2031342843
  14  0.086  0.000  0.000  0.000  0.000  0.000   0.2031340495
  22  0.086 -0.189  0.000  0.000  0.000  0.000   0.1983937281
  24  0.086 -0.149  0.000  0.000  0.000  0.000   0.1980860239
  28  0.086 -0.144  0.000  0.000  0.000  0.000   0.1980705380
  32  0.086 -0.144  1.000  0.000  0.000  0.000   0.1577640908
  36  0.086 -0.144  0.618  0.000  0.000  0.000   0.1438398302
  37  0.086 -0.144  0.644  0.000  0.000  0.000   0.1426996156
  38  0.086 -0.144  0.728  0.000  0.000  0.000   0.1407010084
  42  0.086 -0.144  0.724  0.000  0.000  0.000   0.1406850420
  44  0.086 -0.144  0.722  0.000  0.000  0.000   0.1406820771
  45  0.086 -0.144  0.721  0.000  0.000  0.000   0.1406815801
  53  0.086 -0.144  0.721 -0.152  0.000  0.000   0.1373417461
  58  0.086 -0.144  0.721 -0.155  0.000  0.000   0.1373175690
  59  0.086 -0.144  0.721 -0.158  0.000  0.000   0.1373110666
  70  0.086 -0.144  0.721 -0.158 -0.014  0.000   0.1372380844
  74  0.086 -0.144  0.721 -0.158 -0.018  0.000   0.1372318346
  85  0.086 -0.144  0.721 -0.158 -0.018  0.011   0.1371067201
  86  0.086 -0.144  0.721 -0.158 -0.018  0.014   0.1371022266
  95  0.119 -0.199  0.997 -0.218 -0.025  0.019   0.1347986883
  96  0.109 -0.181  0.908 -0.199 -0.023  0.018   0.1327542424
  97  0.106 -0.177  0.884 -0.194 -0.022  0.017   0.1321923342
  99  0.103 -0.172  0.861 -0.189 -0.022  0.017   0.1319468574
 100  0.103 -0.172  0.859 -0.188 -0.022  0.017   0.1319444511
 109  0.011 -0.172  0.859 -0.188 -0.022  0.017   0.1317341795
 110  0.048 -0.172  0.859 -0.188 -0.022  0.017   0.1313706473
 112  0.038 -0.172  0.859 -0.188 -0.022  0.017   0.1312968957
 114  0.037 -0.172  0.859 -0.188 -0.022  0.017   0.1312965202
 122  0.037 -0.138  0.859 -0.188 -0.022  0.017   0.1305159360
 124  0.037 -0.132  0.859 -0.188 -0.022  0.017   0.1304955314
 134  0.037 -0.132  0.859 -0.188 -0.022  0.000   0.1303771844
 135  0.037 -0.132  0.859 -0.188 -0.022 -0.005   0.1303738252
 136  0.037 -0.132  0.859 -0.188 -0.022 -0.004   0.1303726948
 137  0.037 -0.132  0.859 -0.188 -0.022 -0.003   0.1303725804
 147  0.037 -0.132  0.859 -0.182 -0.022 -0.003   0.1303205523
 148  0.037 -0.132  0.859 -0.180 -0.022 -0.003   0.1303156177
 149  0.037 -0.132  0.859 -0.179 -0.022 -0.003   0.1303153989
 157  0.037 -0.132  0.859 -0.179 -0.095 -0.003   0.1287691551
 160  0.037 -0.132  0.859 -0.179 -0.103 -0.003   0.1287197687
 162  0.037 -0.132  0.859 -0.179 -0.107 -0.003   0.1287177795
 172  0.046 -0.146  0.932 -0.195 -0.108 -0.001   0.1276837702
 174  0.044 -0.142  0.912 -0.190 -0.108 -0.001   0.1275393465
 175  0.044 -0.143  0.913 -0.191 -0.108 -0.001   0.1275355191
 177  0.044 -0.143  0.914 -0.191 -0.108 -0.001   0.1275350705
 187  0.032 -0.143  0.914 -0.191 -0.108 -0.001   0.1274689031
 188  0.034 -0.143  0.914 -0.191 -0.108 -0.001   0.1274682212
 198  0.034 -0.125  0.914 -0.191 -0.108 -0.001   0.1274375066
 199  0.034 -0.133  0.914 -0.191 -0.108 -0.001   0.1273856814
 200  0.034 -0.132  0.914 -0.191 -0.108 -0.001   0.1273855168
 210  0.034 -0.132  0.914 -0.191 -0.108  0.005   0.1273372907
 211  0.034 -0.132  0.914 -0.191 -0.108  0.007   0.1273334255
 212  0.034 -0.132  0.914 -0.191 -0.108  0.006   0.1273333726
 222  0.034 -0.132  0.914 -0.197 -0.108  0.006   0.1273089560
 223  0.034 -0.132  0.914 -0.196 -0.108  0.006   0.1273074994
 224  0.034 -0.132  0.914 -0.195 -0.108  0.006   0.1273073781
 234  0.034 -0.132  0.914 -0.195 -0.087  0.006   0.1272798768
 235  0.034 -0.132  0.914 -0.195 -0.097  0.006   0.1272034896
 246  0.034 -0.132  0.915 -0.195 -0.097  0.006   0.1272033727
 277  0.034 -0.132  0.915 -0.195 -0.097  0.008   0.1272005113
 278  0.034 -0.132  0.915 -0.195 -0.097  0.009   0.1271987565
 289  0.034 -0.132  0.915 -0.198 -0.097  0.009   0.1271953611
 291  0.034 -0.132  0.915 -0.197 -0.097  0.009   0.1271936604
 300  0.034 -0.132  0.915 -0.197 -0.095  0.009   0.1271935051
Powell done niters = 3
Computing relative cost
 0  -25.0 -25.0 -25.0   1.037065
 1  -25.0 -25.0  25.0   0.998962
 2  -25.0  25.0 -25.0   1.011347
 3  -25.0  25.0  25.0   1.042337
 4   25.0 -25.0 -25.0   0.994005
 5   25.0 -25.0  25.0   1.033060
 6   25.0  25.0 -25.0   0.990798
 7   25.0  25.0  25.0   1.017536
REL:  8  0.127194    8.125111  1.015639 rel = 0.125235 
Number of iterations     3
Min cost was 0.127194
Number of FunctionCalls   312
TolPowell 0.000100
nMaxItersPowell 36
OptimizationTime 0.987000 sec
Parameters at optimum (transmm)  0.03368 -0.13187  0.91475
Parameters at optimum (rotdeg) -0.19683 -0.09497  0.00918 
Final costs ----------------
Number of surface hits 2995
WM  Intensity    56.3299 +/-   8.8332
Ctx Intensity    70.5509 +/-   9.3439
Pct Contrast     22.5565 +/-  15.1786
Cost   0.1272
RelCost   0.1989
Reg at min cost was 
 0.998   0.058  -0.003  -0.359;
 0.006  -0.057   0.998  -1.018;
 0.058  -0.997  -0.057   0.168;
 0.000   0.000   0.000   1.000;

Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/bbr.pass1.dat, type = 14 
Original Reg 
 0.998   0.057  -0.003  -0.394;
 0.006  -0.053   0.999  -0.884;
 0.056  -0.997  -0.054  -0.749;
 0.000   0.000   0.000   1.000;

Original Reg - Optimal Reg
 0.000  -0.002   0.000  -0.035;
-0.000   0.003   0.000   0.135;
-0.002  -0.000   0.003  -0.917;
 0.000   0.000   0.000   0.000;

Computing change in lh position
LH rmsDiffMean 0.752483
Computing change in rh position
Surface RMS Diff (mm) 0.794010 1.036774
mri_segreg done
mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/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/sub011/scripts
mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 
sysname  Linux
hostname snake6
machine  x86_64
user     fkaule
movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/template.nii
regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/tmp.bbregister.22917/bbr.pass1.dat
subject sub011
dof 6
outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 1376192635
TransRandMax 0.000000
RotRandMax 0.000000
Translations 0.000000 0.000000 0.000000
Rotations   0.000000 0.000000 0.000000
Input reg
 0.998   0.058  -0.003  -0.359;
 0.006  -0.057   0.998  -1.018;
 0.058  -0.997  -0.057   0.168;
 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   1.018187
 1  -25.0 -25.0  25.0   0.995931
 2  -25.0  25.0 -25.0   1.003818
 3  -25.0  25.0  25.0   1.024126
 4   25.0 -25.0 -25.0   1.007993
 5   25.0 -25.0  25.0   1.014129
 6   25.0  25.0 -25.0   1.009329
 7   25.0  25.0  25.0   1.009792
REL:  8  0.139924    8.083305  1.010413 rel = 0.138482 
Initial costs ----------------
Number of surface hits 299567
WM  Intensity    56.3035 +/-   8.8680
Ctx Intensity    70.8888 +/-   9.3725
Pct Contrast     23.0747 +/-  15.5948
Cost   0.1399
RelCost   0.1385

------------------------------------
Brute force preopt -0.1 0.1 0.1, n = 729
     0  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000      0.1456   0.1456  0.0
     3  -0.1000  -0.1000  -0.1000  -0.1000   0.0000  -0.1000      0.1405   0.1405  0.0
     6  -0.1000  -0.1000  -0.1000  -0.1000   0.1000  -0.1000      0.1399   0.1399  0.0
     9  -0.1000  -0.1000  -0.1000   0.0000  -0.1000  -0.1000      0.1398   0.1398  0.0
    12  -0.1000  -0.1000  -0.1000   0.0000   0.0000  -0.1000      0.1367   0.1367  0.0
    21  -0.1000  -0.1000  -0.1000   0.1000   0.0000  -0.1000      0.1366   0.1366  0.0
    30  -0.1000  -0.1000   0.0000  -0.1000   0.0000  -0.1000      0.1360   0.1360  0.0
    36  -0.1000  -0.1000   0.0000   0.0000  -0.1000  -0.1000      0.1350   0.1350  0.0
    39  -0.1000  -0.1000   0.0000   0.0000   0.0000  -0.1000      0.1325   0.1325  0.0
   120  -0.1000   0.0000   0.0000   0.0000   0.0000  -0.1000      0.1295   0.1295  0.0
   364   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000      0.1272   0.1272  0.0
Brute Force --------------------------
Min cost was 0.127194
Number of iterations   729
Search time 2.437000 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
   8  0.003  0.000  0.000  0.000  0.000  0.000   0.1399238739
   9  0.002  0.000  0.000  0.000  0.000  0.000   0.1399237850
  18  0.001 -0.011  0.000  0.000  0.000  0.000   0.1399164532
  19  0.001 -0.008  0.000  0.000  0.000  0.000   0.1399159395
  28  0.001 -0.008 -0.025  0.000  0.000  0.000   0.1398514145
  29  0.001 -0.008 -0.024  0.000  0.000  0.000   0.1398509487
  30  0.001 -0.008 -0.023  0.000  0.000  0.000   0.1398503664
  34  0.001 -0.008 -0.022  0.000  0.000  0.000   0.1398503202
  42  0.001 -0.008 -0.022 -0.012  0.000  0.000   0.1398157908
  43  0.001 -0.008 -0.022 -0.013  0.000  0.000   0.1398155572
  51  0.001 -0.008 -0.022 -0.013  0.048  0.000   0.1396358289
  54  0.001 -0.008 -0.022 -0.013  0.049  0.000   0.1396356576
  62  0.001 -0.008 -0.022 -0.013  0.049 -0.043   0.1396089500
  63  0.001 -0.008 -0.022 -0.013  0.049 -0.025   0.1395775731
  64  0.001 -0.008 -0.022 -0.013  0.049 -0.026   0.1395773433
  65  0.001 -0.008 -0.022 -0.013  0.049 -0.027   0.1395772903
  76  0.004 -0.008 -0.022 -0.013  0.049 -0.027   0.1395741771
  77  0.007 -0.008 -0.022 -0.013  0.049 -0.027   0.1395736245
  87  0.007 -0.006 -0.022 -0.013  0.049 -0.027   0.1395723785
  97  0.007 -0.006 -0.021 -0.013  0.049 -0.027   0.1395723097
 106  0.007 -0.006 -0.021 -0.014  0.049 -0.027   0.1395709356
 107  0.007 -0.006 -0.021 -0.016  0.049 -0.027   0.1395702076
 117  0.007 -0.006 -0.021 -0.016  0.052 -0.027   0.1395691506
 118  0.007 -0.006 -0.021 -0.016  0.051 -0.027   0.1395690480
 126  0.007 -0.006 -0.021 -0.016  0.051 -0.019   0.1395681076
 127  0.007 -0.006 -0.021 -0.016  0.051 -0.022   0.1395668976
 130  0.012 -0.003 -0.020 -0.019  0.053 -0.018   0.1395662622
 149  0.009 -0.007 -0.021 -0.016  0.051 -0.022   0.1395658813
 158  0.009 -0.007 -0.018 -0.016  0.051 -0.022   0.1395655102
 168  0.009 -0.007 -0.018 -0.017  0.051 -0.022   0.1395648956
 169  0.009 -0.007 -0.018 -0.018  0.051 -0.022   0.1395645236
 190  0.009 -0.007 -0.018 -0.018  0.051 -0.020   0.1395640269
 192  0.012 -0.008 -0.016 -0.020  0.051 -0.019   0.1395621190
 195  0.016 -0.010 -0.012 -0.023  0.051 -0.016   0.1395602555
 199  0.017 -0.010 -0.011 -0.024  0.051 -0.015   0.1395601198
 218  0.018 -0.010 -0.011 -0.024  0.051 -0.015   0.1395600548
 229  0.018 -0.009 -0.011 -0.024  0.051 -0.015   0.1395600195
 237  0.018 -0.009 -0.008 -0.024  0.051 -0.015   0.1395597334
 248  0.018 -0.009 -0.008 -0.024  0.051 -0.016   0.1395596285
 265  0.019 -0.010 -0.007 -0.025  0.051 -0.015   0.1395595386
 266  0.019 -0.010 -0.007 -0.025  0.051 -0.015   0.1395595061
 267  0.019 -0.009 -0.008 -0.025  0.051 -0.015   0.1395594792
 313  0.018 -0.009 -0.008 -0.025  0.051 -0.016   0.1395594687
 331  0.018 -0.010 -0.007 -0.025  0.051 -0.016   0.1395594184
 334  0.018 -0.010 -0.007 -0.025  0.051 -0.016   0.1395594180
 363  0.018 -0.010 -0.006 -0.025  0.051 -0.016   0.1395593736
 402  0.018 -0.010 -0.006 -0.025  0.051 -0.016   0.1395593565
 465  0.018 -0.010 -0.006 -0.025  0.051 -0.016   0.1395593556
Powell done niters = 6
Computing relative cost
 0  -25.0 -25.0 -25.0   1.018320
 1  -25.0 -25.0  25.0   0.995785
 2  -25.0  25.0 -25.0   1.004295
 3  -25.0  25.0  25.0   1.023517
 4   25.0 -25.0 -25.0   1.007522
 5   25.0 -25.0  25.0   1.014657
 6   25.0  25.0 -25.0   1.009360
 7   25.0  25.0  25.0   1.009739
REL:  8  0.139559    8.083193  1.010399 rel = 0.138123 
Number of iterations     6
Min cost was 0.139559
Number of FunctionCalls   468
TolPowell 0.000000
nMaxItersPowell 36
OptimizationTime 167.267000 sec
Parameters at optimum (transmm)  0.01814 -0.00967 -0.00607
Parameters at optimum (rotdeg) -0.02500  0.05113 -0.01611 
Final costs ----------------
Number of surface hits 299567
WM  Intensity    56.3029 +/-   8.8562
Ctx Intensity    70.8842 +/-   9.3684
Pct Contrast     23.0685 +/-  15.5751
Cost   0.1396
RelCost   0.1385
Reg at min cost was 
 0.998   0.057  -0.003  -0.341;
 0.006  -0.057   0.998  -1.028;
 0.057  -0.997  -0.057   0.163;
 0.000   0.000   0.000   1.000;

Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/T2raw.dat, type = 14 
Original Reg 
 0.998   0.058  -0.003  -0.359;
 0.006  -0.057   0.998  -1.018;
 0.058  -0.997  -0.057   0.168;
 0.000   0.000   0.000   1.000;

Original Reg - Optimal Reg
-0.000   0.001  -0.000  -0.018;
 0.000   0.000   0.000   0.009;
 0.001   0.000   0.000   0.005;
 0.000   0.000   0.000   0.000;

Computing change in lh position
LH rmsDiffMean 0.064368
Computing change in rh position
Surface RMS Diff (mm) 0.071316 0.123242
mri_segreg done
tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/T2raw.dat --noedit --ltaout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/mri/orig/T2raw.mgz
reg file       /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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 --------
 0.998   0.057  -0.003  -0.341;
 0.006  -0.057   0.998  -1.028;
 0.057  -0.997  -0.057   0.163;
 0.000   0.000   0.000   1.000;
float2int = 0
---------------------------------------
INFO: loading target /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/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/sub011/mri/orig/T2raw.mgz
Tmov: --------------------
-0.700   0.000   0.000   95.888;
 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 --------
 0.998   0.057  -0.003  -0.341;
 0.006  -0.057   0.998  -1.028;
 0.057  -0.997  -0.057   0.163;
 0.000   0.000   0.000   1.000;
Determinant 0.999999
subject = sub011
RegMat ---------------------------
 0.998   0.057  -0.003  -0.341;
 0.006  -0.057   0.998  -1.028;
 0.057  -0.997  -0.057   0.163;
 0.000   0.000   0.000   1.000;
transformed matrix:
 1.000   0.004  -0.005   0.079;
-0.004   1.000  -0.005  -0.004;
 0.005   0.005   1.000   0.861;
 0.000   0.000   0.000   1.000;
transformed matrix:
 0.699   0.038  -0.004   25.386;
-0.002  -0.038  -0.666   262.359;
-0.040   0.664  -0.038   13.360;
 0.000   0.000   0.000   1.000;
Cleaning up
 
Started at Thu Aug 8 22:59:45 CEST 2013 
Ended   at Thu Aug  8 23:15:42 CEST 2013
BBR-Run-Time-Sec 956
 
bbregister Done
To check results, run:
tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub011/mri/transforms/T2raw.dat --surf