cortical-surfaces-freesurfer/sub-12/mri/transforms/T2raw.dat.log

Logfile for bbregister
Thu Aug  8 23:21:56 CEST 2013

setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/scripts
/opt/freesurfer/5.3.0/bin/bbregister --s sub012 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/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/sub012/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/template.nii
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/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/sub012/mri/orig/T2raw.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.99935, -0.0323756, -0.0158427)
j_ras = (-0.0335643, 0.996097, 0.081636)
k_ras = (-0.0131379, -0.0821147, 0.996536)
writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/template.nii...
fslregister --s sub012 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/fslregister --dof 6 --fsvol brainmask.mgz

Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/reg.init.dat.fslregister.log

Thu Aug  8 23:22:01 CEST 2013
--s sub012 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/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/sub012/scripts
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/fslregister/refvol.fslregister.nii
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/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/sub012/mri/brainmask.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 6.98492e-10, -9.31323e-10)
j_ras = (1.86265e-09, -2.23517e-08, -1)
k_ras = (-5.82077e-10, 1, 7.45058e-09)
writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/fslregister/refvol.fslregister.nii...
--------------------------------------
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/scripts
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/fslregister/movvol.fslregister.nii --frame 0
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/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/sub012/mri/transforms/tmp.bbregister.19618/template.nii...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.99935, -0.0323756, -0.0158427)
j_ras = (-0.0335643, 0.996097, 0.081636)
k_ras = (-0.0131379, -0.0821147, 0.996536)
keeping frame 0
writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/fslregister/movvol.fslregister.nii...
Mov determinant is -0.311066
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/scripts
tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/fslregister/movvol.fslregister.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/fslregister/reg0.19671.dat --regheader --fslregout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/reg.init.dat.fsl.mat0 --s sub012 --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/sub012/mri/transforms/tmp.bbregister.19618/fslregister/movvol.fslregister.nii
reg file       /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/fslregister/reg0.19671.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/sub012/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/sub012/mri/transforms/tmp.bbregister.19618/fslregister/movvol.fslregister.nii
Tmov: --------------------
-0.700   0.000   0.000   95.886;
 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   0.032   0.016   0.000;
-0.013  -0.082   0.997   0.000;
 0.034  -0.996  -0.082  -0.000;
 0.000   0.000   0.000   1.000;
---------------------------------------
---- Input registration matrix --------
 0.999   0.032   0.016   0.000;
-0.013  -0.082   0.997   0.000;
 0.034  -0.996  -0.082  -0.000;
 0.000   0.000   0.000   1.000;
Determinant 1
subject = sub012
RegMat ---------------------------
 0.999   0.032   0.016   0.000;
-0.013  -0.082   0.997   0.000;
 0.034  -0.996  -0.082  -0.000;
 0.000   0.000   0.000   1.000;
FSLOUTPUTTYPE NIFTI 
tkreg2FSL: mov det = -0.311066, ref det = -1
Thu Aug  8 23:22:10 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/scripts
flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/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/sub012/mri/transforms/tmp.bbregister.19618/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/reg.init.dat.fsl.mat0
Thu Aug  8 23:26:32 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/scripts
flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/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/sub012/mri/transforms/tmp.bbregister.19618/reg.init.dat.fsl.mat -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/fslregister/fslmat0.trans.mat -schedule /opt/freesurfer/5.3.0/bin/flirt.newdefault.20080811.sch
tkregister2_cmdl --s sub012 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/reg.init.dat --fslreg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/reg.init.dat.fsl.mat --noedit
tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl
---- FSL registration matrix --------
 0.999   0.034   0.018   25.382;
 0.021  -0.073  -0.997   264.823;
-0.033   0.997  -0.073   11.942;
 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/sub012/mri/transforms/tmp.bbregister.19618/template.nii
reg file       /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/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/sub012/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/sub012/mri/transforms/tmp.bbregister.19618/template.nii
Tmov: --------------------
-0.700   0.000   0.000   95.886;
 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 = -0.311066, ref det = -1
---- Input registration matrix (computed) --------
 0.999   0.033   0.021  -0.039;
-0.018  -0.073   0.997   1.782;
 0.034  -0.997  -0.073  -1.134;
 0.000   0.000   0.000   1.000;
---------------------------------------
---- Input registration matrix --------
 0.999   0.033   0.021  -0.039;
-0.018  -0.073   0.997   1.782;
 0.034  -0.997  -0.073  -1.134;
 0.000   0.000   0.000   1.000;
Determinant 1
subject = sub012
RegMat ---------------------------
 0.999   0.033   0.021  -0.039;
-0.018  -0.073   0.997   1.782;
 0.034  -0.997  -0.073  -1.134;
 0.000   0.000   0.000   1.000;
 
Started at Thu Aug 8 23:22:01 CEST 2013 
Ended   at Thu Aug  8 23:32:49 CEST 2013
 
fslregister Done
 
To check results, run:
tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/reg.init.dat --surf orig
 
mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/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/sub012/scripts
mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/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/sub012/mri/transforms/tmp.bbregister.19618/template.nii
regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/reg.init.dat
subject sub012
dof 6
outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/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 1376013066
TransRandMax 0.000000
RotRandMax 0.000000
Translations 0.000000 0.000000 0.000000
Rotations   0.000000 0.000000 0.000000
Input reg
 0.999   0.033   0.021  -0.039;
-0.018  -0.073   0.997   1.782;
 0.034  -0.997  -0.073  -1.134;
 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   1.019944
 1  -25.0 -25.0  25.0   0.990081
 2  -25.0  25.0 -25.0   0.977208
 3  -25.0  25.0  25.0   0.990547
 4   25.0 -25.0 -25.0   1.016361
 5   25.0 -25.0  25.0   0.985752
 6   25.0  25.0 -25.0   1.035616
 7   25.0  25.0  25.0   1.029429
REL:  8  0.265850    8.044937  1.005617 rel = 0.264365 
Initial costs ----------------
Number of surface hits 2825
WM  Intensity    56.9313 +/-  10.0728
Ctx Intensity    71.6130 +/-  12.1422
Pct Contrast     22.6311 +/-  20.8464
Cost   0.2658
RelCost   0.2644

------------------------------------
Brute force preopt -4 4 4, n = 729
     0  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000      0.9691   0.9691  0.0
     1  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000   0.0000      0.9686   0.9686  0.0
     3  -4.0000  -4.0000  -4.0000  -4.0000   0.0000  -4.0000      0.9561   0.9561  0.0
     4  -4.0000  -4.0000  -4.0000  -4.0000   0.0000   0.0000      0.9516   0.9516  0.0
    15  -4.0000  -4.0000  -4.0000   0.0000   4.0000  -4.0000      0.8749   0.8749  0.0
    21  -4.0000  -4.0000  -4.0000   4.0000   0.0000  -4.0000      0.8475   0.8475  0.0
    39  -4.0000  -4.0000   0.0000   0.0000   0.0000  -4.0000      0.7853   0.7853  0.0
   120  -4.0000   0.0000   0.0000   0.0000   0.0000  -4.0000      0.7445   0.7445  0.0
   301   0.0000  -4.0000   4.0000  -4.0000   0.0000   0.0000      0.7305   0.7305  0.0
   346   0.0000   0.0000  -4.0000   4.0000   0.0000   0.0000      0.6861   0.6861  0.0
   364   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000      0.2658   0.2658  0.0
Brute Force --------------------------
Min cost was 0.265850
Number of iterations   729
Search time 2.586000 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 -0.008  0.000  0.000  0.000  0.000  0.000   0.2656566876
   9 -0.034  0.000  0.000  0.000  0.000  0.000   0.2652321573
  11 -0.033  0.000  0.000  0.000  0.000  0.000   0.2652304875
  15 -0.033 -1.618  0.000  0.000  0.000  0.000   0.2055552161
  16 -0.033 -1.012  0.000  0.000  0.000  0.000   0.1699358816
  20 -0.033 -1.092  0.000  0.000  0.000  0.000   0.1691322582
  21 -0.033 -1.104  0.000  0.000  0.000  0.000   0.1691127096
  23 -0.033 -1.101  0.000  0.000  0.000  0.000   0.1691071269
  28 -0.033 -1.101  1.000  0.000  0.000  0.000   0.1012356854
  33 -0.033 -1.101  0.835  0.000  0.000  0.000   0.0965015641
  34 -0.033 -1.101  0.829  0.000  0.000  0.000   0.0963757882
  35 -0.033 -1.101  0.749  0.000  0.000  0.000   0.0952677401
  38 -0.033 -1.101  0.757  0.000  0.000  0.000   0.0952281590
  39 -0.033 -1.101  0.760  0.000  0.000  0.000   0.0952206571
  41 -0.033 -1.101  0.761  0.000  0.000  0.000   0.0952202157
  50 -0.033 -1.101  0.761 -0.001  0.000  0.000   0.0952167274
  51 -0.033 -1.101  0.761 -0.006  0.000  0.000   0.0952064441
  55 -0.033 -1.101  0.761 -0.007  0.000  0.000   0.0952052723
  66 -0.033 -1.101  0.761 -0.007 -0.022  0.000   0.0951218552
  68 -0.033 -1.101  0.761 -0.007 -0.018  0.000   0.0951085952
  69 -0.033 -1.101  0.761 -0.007 -0.016  0.000   0.0951080683
  76 -0.033 -1.101  0.761 -0.007 -0.016  0.382   0.0873656484
  77 -0.033 -1.101  0.761 -0.007 -0.016  0.291   0.0827595578
  78 -0.033 -1.101  0.761 -0.007 -0.016  0.233   0.0821904552
  79 -0.033 -1.101  0.761 -0.007 -0.016  0.244   0.0821839886
  80 -0.033 -1.101  0.761 -0.007 -0.016  0.240   0.0821769946
  90  0.031 -1.101  0.761 -0.007 -0.016  0.240   0.0803371053
  92  0.039 -1.101  0.761 -0.007 -0.016  0.240   0.0803292905
  93  0.037 -1.101  0.761 -0.007 -0.016  0.240   0.0803268735
  94  0.036 -1.101  0.761 -0.007 -0.016  0.240   0.0803255249
 103  0.036 -1.095  0.761 -0.007 -0.016  0.240   0.0802699387
 104  0.036 -1.090  0.761 -0.007 -0.016  0.240   0.0802651099
 105  0.036 -1.092  0.761 -0.007 -0.016  0.240   0.0802623640
 116  0.036 -1.092  0.758 -0.007 -0.016  0.240   0.0802589877
 127  0.036 -1.092  0.758 -0.021 -0.016  0.240   0.0801308030
 128  0.036 -1.092  0.758 -0.020 -0.016  0.240   0.0801301379
 136  0.036 -1.092  0.758 -0.020 -0.111  0.240   0.0791454765
 137  0.036 -1.092  0.758 -0.020 -0.092  0.240   0.0789673255
 138  0.036 -1.092  0.758 -0.020 -0.083  0.240   0.0788820354
 140  0.036 -1.092  0.758 -0.020 -0.078  0.240   0.0788610758
 142  0.036 -1.092  0.758 -0.020 -0.077  0.240   0.0788601971
 151  0.036 -1.092  0.758 -0.020 -0.077  0.264   0.0787653992
 152  0.036 -1.092  0.758 -0.020 -0.077  0.261   0.0787602930
 153  0.036 -1.092  0.758 -0.020 -0.077  0.259   0.0787601536
 155  0.104 -1.082  0.755 -0.033 -0.137  0.279   0.0785169783
 161  0.078 -1.086  0.756 -0.028 -0.114  0.271   0.0781085708
 163  0.079 -1.086  0.756 -0.028 -0.115  0.272   0.0781083026
 164  0.079 -1.086  0.756 -0.028 -0.115  0.271   0.0781078102
 175  0.079 -1.086  0.756 -0.028 -0.115  0.273   0.0781027662
 176  0.079 -1.086  0.756 -0.028 -0.115  0.275   0.0781006300
 178  0.079 -1.086  0.756 -0.028 -0.115  0.276   0.0780998434
 188  0.079 -1.109  0.756 -0.028 -0.115  0.276   0.0780112791
 189  0.079 -1.103  0.756 -0.028 -0.115  0.276   0.0780040725
 190  0.079 -1.104  0.756 -0.028 -0.115  0.276   0.0780039492
 200  0.079 -1.104  0.766 -0.028 -0.115  0.276   0.0779733540
 201  0.079 -1.104  0.765 -0.028 -0.115  0.276   0.0779723125
 211  0.079 -1.104  0.765 -0.027 -0.115  0.276   0.0779700967
 212  0.079 -1.104  0.765 -0.026 -0.115  0.276   0.0779691750
 224  0.079 -1.104  0.765 -0.026 -0.099  0.276   0.0778551687
 233  0.089 -1.103  0.764 -0.028 -0.108  0.279   0.0777715409
 235  0.089 -1.103  0.764 -0.028 -0.108  0.279   0.0777715222
 251  0.089 -1.103  0.764 -0.028 -0.108  0.278   0.0777704789
 273  0.089 -1.104  0.768 -0.028 -0.108  0.278   0.0777697640
 274  0.089 -1.104  0.766 -0.028 -0.108  0.278   0.0777692065
 284  0.089 -1.104  0.766 -0.026 -0.108  0.278   0.0777665938
 285  0.089 -1.104  0.766 -0.025 -0.108  0.278   0.0777656298
 297  0.089 -1.104  0.766 -0.025 -0.103  0.278   0.0777347820
 298  0.089 -1.104  0.766 -0.025 -0.101  0.278   0.0777328611
 306  0.091 -1.104  0.766 -0.025 -0.102  0.278   0.0777262728
 307  0.094 -1.103  0.766 -0.026 -0.105  0.279   0.0777238826
 309  0.093 -1.104  0.766 -0.025 -0.104  0.279   0.0777229336
 312  0.093 -1.104  0.766 -0.025 -0.104  0.278   0.0777229228
 314  0.093 -1.104  0.766 -0.025 -0.104  0.279   0.0777228332
 315  0.093 -1.104  0.766 -0.025 -0.104  0.279   0.0777228119
 322  0.094 -1.104  0.767 -0.025 -0.102  0.278   0.0777171662
 341  0.094 -1.104  0.767 -0.025 -0.102  0.283   0.0777169565
 342  0.094 -1.104  0.767 -0.025 -0.102  0.281   0.0777148907
 353  0.094 -1.102  0.767 -0.025 -0.102  0.281   0.0777146898
 374  0.094 -1.102  0.767 -0.024 -0.102  0.281   0.0777142159
 383  0.094 -1.102  0.767 -0.024 -0.102  0.281   0.0777135429
 384  0.096 -1.102  0.767 -0.024 -0.104  0.282   0.0777122866
 386  0.096 -1.102  0.767 -0.024 -0.104  0.281   0.0777117748
 387  0.096 -1.102  0.767 -0.024 -0.104  0.281   0.0777116865
 390  0.095 -1.102  0.767 -0.024 -0.104  0.281   0.0777116567
 397  0.096 -1.102  0.767 -0.024 -0.103  0.281   0.0777116008
 398  0.096 -1.102  0.767 -0.024 -0.103  0.281   0.0777115170
 403  0.096 -1.102  0.767 -0.024 -0.103  0.281   0.0777114238
Powell done niters = 4
Computing relative cost
 0  -25.0 -25.0 -25.0   1.011426
 1  -25.0 -25.0  25.0   1.001825
 2  -25.0  25.0 -25.0   0.985355
 3  -25.0  25.0  25.0   0.993794
 4   25.0 -25.0 -25.0   1.025436
 5   25.0 -25.0  25.0   1.021714
 6   25.0  25.0 -25.0   1.028446
 7   25.0  25.0  25.0   1.024081
REL:  8  0.077711    8.092076  1.011510 rel = 0.0768272 
Number of iterations     4
Min cost was 0.077711
Number of FunctionCalls   405
TolPowell 0.000100
nMaxItersPowell 36
OptimizationTime 1.486000 sec
Parameters at optimum (transmm)  0.09568 -1.10210  0.76704
Parameters at optimum (rotdeg) -0.02375 -0.10328  0.28131 
Final costs ----------------
Number of surface hits 2825
WM  Intensity    55.7725 +/-   9.0266
Ctx Intensity    71.6632 +/-   9.0688
Pct Contrast     25.2038 +/-  14.6607
Cost   0.0777
RelCost   0.2644
Reg at min cost was 
 0.999   0.035   0.016   0.050;
-0.013  -0.074   0.997   0.679;
 0.036  -0.997  -0.073  -0.368;
 0.000   0.000   0.000   1.000;

Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/bbr.pass1.dat, type = 14 
Original Reg 
 0.999   0.033   0.021  -0.039;
-0.018  -0.073   0.997   1.782;
 0.034  -0.997  -0.073  -1.134;
 0.000   0.000   0.000   1.000;

Original Reg - Optimal Reg
-0.000  -0.002   0.005  -0.089;
-0.005   0.000  -0.000   1.103;
-0.002  -0.000   0.000  -0.766;
 0.000   0.000   0.000   0.000;

Computing change in lh position
LH rmsDiffMean 1.434510
Computing change in rh position
Surface RMS Diff (mm) 1.349445 1.557901
mri_segreg done
mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/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/sub012/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/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/sub012/scripts
mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/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/sub012/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/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/sub012/mri/transforms/tmp.bbregister.19618/template.nii
regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/tmp.bbregister.19618/bbr.pass1.dat
subject sub012
dof 6
outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/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 1376868895
TransRandMax 0.000000
RotRandMax 0.000000
Translations 0.000000 0.000000 0.000000
Rotations   0.000000 0.000000 0.000000
Input reg
 0.999   0.035   0.016   0.050;
-0.013  -0.074   0.997   0.679;
 0.036  -0.997  -0.073  -0.368;
 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   1.007627
 1  -25.0 -25.0  25.0   1.008633
 2  -25.0  25.0 -25.0   1.001732
 3  -25.0  25.0  25.0   1.008890
 4   25.0 -25.0 -25.0   1.006382
 5   25.0 -25.0  25.0   0.997078
 6   25.0  25.0 -25.0   1.004804
 7   25.0  25.0  25.0   1.007184
REL:  8  0.093236    8.042331  1.005291 rel = 0.0927455 
Initial costs ----------------
Number of surface hits 282396
WM  Intensity    55.9076 +/-   9.1613
Ctx Intensity    71.6063 +/-   9.1786
Pct Contrast     24.8724 +/-  14.9651
Cost   0.0932
RelCost   0.0927

------------------------------------
Brute force preopt -0.1 0.1 0.1, n = 729
     0  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000      0.0967   0.0967  0.0
     1  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000   0.0000      0.0953   0.0953  0.0
     4  -0.1000  -0.1000  -0.1000  -0.1000   0.0000   0.0000      0.0936   0.0936  0.0
     9  -0.1000  -0.1000  -0.1000   0.0000  -0.1000  -0.1000      0.0929   0.0929  0.0
    10  -0.1000  -0.1000  -0.1000   0.0000  -0.1000   0.0000      0.0926   0.0926  0.0
    12  -0.1000  -0.1000  -0.1000   0.0000   0.0000  -0.1000      0.0892   0.0892  0.0
    22  -0.1000  -0.1000  -0.1000   0.1000   0.0000   0.0000      0.0885   0.0885  0.0
    30  -0.1000  -0.1000   0.0000  -0.1000   0.0000  -0.1000      0.0873   0.0873  0.0
    31  -0.1000  -0.1000   0.0000  -0.1000   0.0000   0.0000      0.0868   0.0868  0.0
    34  -0.1000  -0.1000   0.0000  -0.1000   0.1000   0.0000      0.0866   0.0866  0.0
    39  -0.1000  -0.1000   0.0000   0.0000   0.0000  -0.1000      0.0849   0.0849  0.0
    40  -0.1000  -0.1000   0.0000   0.0000   0.0000   0.0000      0.0842   0.0842  0.0
    61  -0.1000  -0.1000   0.1000  -0.1000   0.1000   0.0000      0.0838   0.0838  0.0
   120  -0.1000   0.0000   0.0000   0.0000   0.0000  -0.1000      0.0820   0.0820  0.0
   121  -0.1000   0.0000   0.0000   0.0000   0.0000   0.0000      0.0816   0.0816  0.0
   124  -0.1000   0.0000   0.0000   0.0000   0.1000   0.0000      0.0815   0.0815  0.0
   301   0.0000  -0.1000   0.1000  -0.1000   0.0000   0.0000      0.0806   0.0806  0.0
   364   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000      0.0777   0.0777  0.0
Brute Force --------------------------
Min cost was 0.077711
Number of iterations   729
Search time 2.525000 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  0.042  0.000  0.000  0.000  0.000  0.000   0.0932170391
   8  0.023  0.000  0.000  0.000  0.000  0.000   0.0931907482
  10  0.022  0.000  0.000  0.000  0.000  0.000   0.0931906554
  19  0.022  0.087  0.000  0.000  0.000  0.000   0.0925483251
  20  0.022  0.079  0.000  0.000  0.000  0.000   0.0925388897
  21  0.022  0.078  0.000  0.000  0.000  0.000   0.0925386137
  22  0.022  0.077  0.000  0.000  0.000  0.000   0.0925385552
  31  0.022  0.077 -0.007  0.000  0.000  0.000   0.0925250694
  32  0.022  0.077 -0.012  0.000  0.000  0.000   0.0925221943
  41  0.022  0.077 -0.012 -0.059  0.000  0.000   0.0918730027
  50  0.022  0.077 -0.012 -0.059  0.013  0.000   0.0918179386
  51  0.022  0.077 -0.012 -0.059  0.024  0.000   0.0917939081
  52  0.022  0.077 -0.012 -0.059  0.030  0.000   0.0917935268
  53  0.022  0.077 -0.012 -0.059  0.027  0.000   0.0917927976
  62  0.022  0.077 -0.012 -0.059  0.027  0.007   0.0917631597
  63  0.022  0.077 -0.012 -0.059  0.027  0.020   0.0917430121
  73  0.042  0.077 -0.012 -0.059  0.027  0.020   0.0917267601
  74  0.036  0.077 -0.012 -0.059  0.027  0.020   0.0917224111
  75  0.035  0.077 -0.012 -0.059  0.027  0.020   0.0917223344
  83  0.035  0.070 -0.012 -0.059  0.027  0.020   0.0917050356
  84  0.035  0.061 -0.012 -0.059  0.027  0.020   0.0916959737
  93  0.035  0.061  0.041 -0.059  0.027  0.020   0.0913847033
  94  0.035  0.061  0.040 -0.059  0.027  0.020   0.0913842746
  95  0.035  0.061  0.039 -0.059  0.027  0.020   0.0913840267
  97  0.035  0.061  0.037 -0.059  0.027  0.020   0.0913838332
 106  0.035  0.061  0.037 -0.087  0.027  0.020   0.0912028261
 107  0.035  0.061  0.037 -0.091  0.027  0.020   0.0912011888
 108  0.035  0.061  0.037 -0.090  0.027  0.020   0.0912011113
 119  0.035  0.061  0.037 -0.090  0.026  0.020   0.0912010090
 127  0.035  0.061  0.037 -0.090  0.026  0.026   0.0911967725
 130  0.048  0.045  0.086 -0.121  0.025  0.032   0.0909349564
 135  0.056  0.035  0.117 -0.140  0.024  0.035   0.0908987235
 137  0.054  0.037  0.110 -0.136  0.025  0.035   0.0908951436
 141  0.054  0.037  0.111 -0.136  0.025  0.035   0.0908950570
 152  0.052  0.037  0.111 -0.136  0.025  0.035   0.0908945204
 162  0.052  0.031  0.111 -0.136  0.025  0.035   0.0908912011
 163  0.052  0.030  0.111 -0.136  0.025  0.035   0.0908910164
 172  0.052  0.030  0.111 -0.136  0.025  0.033   0.0908902399
 173  0.052  0.030  0.111 -0.136  0.025  0.032   0.0908901644
 182  0.052  0.030  0.111 -0.143  0.025  0.032   0.0908852575
 183  0.052  0.030  0.111 -0.141  0.025  0.032   0.0908849098
 185  0.052  0.030  0.111 -0.142  0.025  0.032   0.0908849036
 193  0.052  0.030  0.111 -0.142  0.017  0.032   0.0908788357
 207  0.052  0.030  0.110 -0.142  0.017  0.032   0.0908788228
 209  0.052  0.030  0.110 -0.142  0.017  0.032   0.0908787598
 220  0.051  0.030  0.110 -0.142  0.017  0.032   0.0908786990
 230  0.051  0.029  0.110 -0.142  0.017  0.032   0.0908785261
 239  0.051  0.029  0.110 -0.142  0.017  0.031   0.0908783626
Powell done niters = 4
Computing relative cost
 0  -25.0 -25.0 -25.0   1.008140
 1  -25.0 -25.0  25.0   1.008236
 2  -25.0  25.0 -25.0   1.002201
 3  -25.0  25.0  25.0   1.009141
 4   25.0 -25.0 -25.0   1.006821
 5   25.0 -25.0  25.0   0.996703
 6   25.0  25.0 -25.0   1.003914
 7   25.0  25.0  25.0   1.006257
REL:  8  0.090878    8.041412  1.005177 rel = 0.0904104 
Number of iterations     4
Min cost was 0.090878
Number of FunctionCalls   329
TolPowell 0.000000
nMaxItersPowell 36
OptimizationTime 56.980000 sec
Parameters at optimum (transmm)  0.05062  0.02943  0.11032
Parameters at optimum (rotdeg) -0.14210  0.01655  0.03097 
Final costs ----------------
Number of surface hits 282396
WM  Intensity    55.9136 +/-   9.1628
Ctx Intensity    71.6165 +/-   9.1401
Pct Contrast     24.8826 +/-  14.8895
Cost   0.0909
RelCost   0.0927
Reg at min cost was 
 0.999   0.034   0.015   0.101;
-0.013  -0.076   0.997   0.708;
 0.036  -0.996  -0.076  -0.259;
 0.000   0.000   0.000   1.000;

Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/T2raw.dat, type = 14 
Original Reg 
 0.999   0.035   0.016   0.050;
-0.013  -0.074   0.997   0.679;
 0.036  -0.997  -0.073  -0.368;
 0.000   0.000   0.000   1.000;

Original Reg - Optimal Reg
-0.000   0.000   0.001  -0.050;
-0.001   0.002   0.000  -0.029;
 0.000  -0.000   0.002  -0.109;
 0.000   0.000   0.000   0.000;

Computing change in lh position
LH rmsDiffMean 0.122343
Computing change in rh position
Surface RMS Diff (mm) 0.127629 0.280210
mri_segreg done
tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/T2raw.dat --noedit --ltaout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/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/sub012/mri/orig/T2raw.mgz
reg file       /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/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   0.034   0.015   0.101;
-0.013  -0.076   0.997   0.708;
 0.036  -0.996  -0.076  -0.259;
 0.000   0.000   0.000   1.000;
float2int = 0
---------------------------------------
INFO: loading target /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/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/sub012/mri/orig/T2raw.mgz
Tmov: --------------------
-0.700   0.000   0.000   95.886;
 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   0.034   0.015   0.101;
-0.013  -0.076   0.997   0.708;
 0.036  -0.996  -0.076  -0.259;
 0.000   0.000   0.000   1.000;
Determinant 1
subject = sub012
RegMat ---------------------------
 0.999   0.034   0.015   0.101;
-0.013  -0.076   0.997   0.708;
 0.036  -0.996  -0.076  -0.259;
 0.000   0.000   0.000   1.000;
transformed matrix:
 1.000  -0.002   0.000  -0.027;
 0.002   1.000   0.006  -0.123;
-0.000  -0.006   1.000  -0.572;
 0.000   0.000   0.000   1.000;
transformed matrix:
 0.699   0.024   0.009   26.083;
 0.011  -0.050  -0.665   264.552;
-0.024   0.664  -0.051   13.295;
 0.000   0.000   0.000   1.000;
Cleaning up
 
Started at Thu Aug 8 23:21:56 CEST 2013 
Ended   at Thu Aug  8 23:34:56 CEST 2013
BBR-Run-Time-Sec 780
 
bbregister Done
To check results, run:
tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub012/mri/transforms/T2raw.dat --surf