Hi,
When I used preproc-sess processing my data, the registration output is off a
great of deal. The functional data was collected using 7T, and the surface was
reconstructed successfully from 3T data and was checked visually multiple
times. I am using fs5.3 installed on a linux system. Attached is the
registration log file.
Any suggestions will be appreciated.
Xiaomin Yue
Logfile for bbregister
Thu Oct 16 10:54:36 EDT 2014
setenv SUBJECTS_DIR /misc/data41/yuex/human_anat
cd /misc/data41/yuex/humanfMRI/human_curvature/subjdata/field090514
/opt/freesurfer-530/bin/bbregister --s field --init-fsl --6 --bold --mov
bold/template.nii --reg bold/register.dof6.dat --init-reg-out
bold/init.register.dof6.dat
$Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $
Linux konis 2.6.32-431.20.5.el6.x86_64 #1 SMP Fri Jul 25 08:34:44 UTC 2014
x86_64 x86_64 x86_64 GNU/Linux
FREESURFER_HOME /opt/freesurfer-530
mri_convert bold/template.nii bold/tmp.bbregister.16782/template.nii
mri_convert bold/template.nii bold/tmp.bbregister.16782/template.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from bold/template.nii...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999653, -0.00336006, -0.0261388)
j_ras = (-2.83047e-08, -0.991839, 0.127499)
k_ras = (-0.0263539, 0.127455, 0.991494)
writing to bold/tmp.bbregister.16782/template.nii...
fslregister --s field --mov bold/tmp.bbregister.16782/template.nii --reg
bold/tmp.bbregister.16782/reg.init.dat --niters 1 --maxangle 90 --nobetmov
--tmp bold/tmp.bbregister.16782/fslregister --dof 6 --fsvol brainmask.mgz
Log file is bold/tmp.bbregister.16782/reg.init.dat.fslregister.log
Thu Oct 16 10:54:37 EDT 2014
--s field --mov bold/tmp.bbregister.16782/template.nii --reg
bold/tmp.bbregister.16782/reg.init.dat --niters 1 --maxangle 90 --nobetmov
--tmp bold/tmp.bbregister.16782/fslregister --dof 6 --fsvol brainmask.mgz
$Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $
konis
Linux konis 2.6.32-431.20.5.el6.x86_64 #1 SMP Fri Jul 25 08:34:44 UTC 2014
x86_64 x86_64 x86_64 GNU/Linux
nIters 1
--------------------------------------
/misc/data41/yuex/humanfMRI/human_curvature/subjdata/field090514
mri_convert /misc/data41/yuex/human_anat/field/mri/brainmask.mgz
bold/tmp.bbregister.16782/fslregister/refvol.fslregister.nii
mri_convert /misc/data41/yuex/human_anat/field/mri/brainmask.mgz
bold/tmp.bbregister.16782/fslregister/refvol.fslregister.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /misc/data41/yuex/human_anat/field/mri/brainmask.mgz...
TR=6.88, TE=2.72, TI=725.00, flip angle=10.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to bold/tmp.bbregister.16782/fslregister/refvol.fslregister.nii...
--------------------------------------
/misc/data41/yuex/humanfMRI/human_curvature/subjdata/field090514
mri_convert bold/tmp.bbregister.16782/template.nii
bold/tmp.bbregister.16782/fslregister/movvol.fslregister.nii --frame 0
mri_convert bold/tmp.bbregister.16782/template.nii
bold/tmp.bbregister.16782/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 bold/tmp.bbregister.16782/template.nii...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999653, -0.00336006, -0.0261388)
j_ras = (-2.83047e-08, -0.991839, 0.127499)
k_ras = (-0.0263539, 0.127455, 0.991494)
keeping frame 0
writing to bold/tmp.bbregister.16782/fslregister/movvol.fslregister.nii...
Mov determinant is 2.94386
Swapping dims for pos det
WARNING:: Flipping Left/Right orientation (as det < 0)
tkregister_tcl /opt/freesurfer-530/tktools/tkregister2.tcl
target volume bold/tmp.bbregister.16782/fslregister/movvol.fslregister.nii
movable volume bold/tmp.bbregister.16782/template.nii
reg file bold/tmp.bbregister.16782/fslregister/swapreg.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
bold/tmp.bbregister.16782/fslregister/movvol.fslregister.nii
INFO: target does not conform to COR format, so I'm going to
reslice to COR. This will not affect the final registration.
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 bold/tmp.bbregister.16782/template.nii
Tmov: --------------------
-1.408 0.000 0.000 100.000;
0.000 0.000 1.484 -30.422;
0.000 -1.408 0.000 100.000;
0.000 0.000 0.000 1.000;
mkheaderreg = 1, float2int = 0
Computing reg from header (and possibly input matrix)
---- Input registration matrix (computed) --------
1.000 0.003 0.026 1.408;
-0.026 0.127 0.991 0.000;
0.000 0.992 -0.127 -0.000;
0.000 0.000 0.000 1.000;
---------------------------------------
---- Input registration matrix --------
1.000 0.003 0.026 1.408;
-0.026 0.127 0.991 0.000;
0.000 0.992 -0.127 -0.000;
0.000 0.000 0.000 1.000;
Determinant -1
subject = subject-unknown
RegMat ---------------------------
-1.000 0.000 -0.000 1.408;
0.000 1.000 0.000 -0.000;
0.000 -0.000 1.000 -0.000;
0.000 0.000 0.000 1.000;
/misc/data41/yuex/humanfMRI/human_curvature/subjdata/field090514
tkregister2_cmdl --mov
bold/tmp.bbregister.16782/fslregister/movvol.fslregister.nii --reg
bold/tmp.bbregister.16782/fslregister/reg0.16852.dat --regheader --fslregout
bold/tmp.bbregister.16782/reg.init.dat.fsl.mat0 --s field --noedit
tkregister_tcl /opt/freesurfer-530/tktools/tkregister2.tcl
INFO: no target volume specified, assuming FreeSurfer orig volume.
target volume orig
movable volume bold/tmp.bbregister.16782/fslregister/movvol.fslregister.nii
reg file bold/tmp.bbregister.16782/fslregister/reg0.16852.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 /misc/data41/yuex/human_anat/field/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
bold/tmp.bbregister.16782/fslregister/movvol.fslregister.nii
Tmov: --------------------
-1.408 0.000 0.000 100.000;
0.000 0.000 1.484 -30.422;
0.000 -1.408 0.000 100.000;
0.000 0.000 0.000 1.000;
mkheaderreg = 1, float2int = 0
Computing reg from header (and possibly input matrix)
---- Input registration matrix (computed) --------
-1.000 -0.003 -0.026 -3.599;
-0.026 0.127 0.991 37.395;
0.000 0.992 -0.127 5.728;
0.000 0.000 0.000 1.000;
---------------------------------------
---- Input registration matrix --------
-1.000 -0.003 -0.026 -3.599;
-0.026 0.127 0.991 37.395;
0.000 0.992 -0.127 5.728;
0.000 0.000 0.000 1.000;
Determinant 1
subject = field
RegMat ---------------------------
-1.000 -0.003 -0.026 -3.599;
-0.026 0.127 0.991 37.395;
0.000 0.992 -0.127 5.728;
0.000 0.000 0.000 1.000;
FSLOUTPUTTYPE NIFTI
tkreg2FSL: mov det = -2.94386, ref det = -1
Thu Oct 16 10:54:40 EDT 2014
/misc/data41/yuex/humanfMRI/human_curvature/subjdata/field090514
flirt.fsl -ref bold/tmp.bbregister.16782/fslregister/refvol.fslregister.nii -in
bold/tmp.bbregister.16782/fslregister/movvol.fslregister.nii -bins 256 -cost
corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0
-omat bold/tmp.bbregister.16782/fslregister/fslmat0.trans.mat -schedule
/opt/fsl/etc/flirtsch/xyztrans.sch -init
bold/tmp.bbregister.16782/reg.init.dat.fsl.mat0
Thu Oct 16 10:54:46 EDT 2014
/misc/data41/yuex/humanfMRI/human_curvature/subjdata/field090514
flirt.fsl -ref bold/tmp.bbregister.16782/fslregister/refvol.fslregister.nii -in
bold/tmp.bbregister.16782/fslregister/movvol.fslregister.nii -bins 256 -cost
corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0
-omat bold/tmp.bbregister.16782/reg.init.dat.fsl.mat -init
bold/tmp.bbregister.16782/fslregister/fslmat0.trans.mat -schedule
/opt/freesurfer-530/bin/flirt.newdefault.20080811.sch
tkregister2_cmdl --s field --mov
bold/tmp.bbregister.16782/fslregister/movvol.fslregister.nii --reg
bold/tmp.bbregister.16782/reg.init.dat --fslreg
bold/tmp.bbregister.16782/reg.init.dat.fsl.mat --noedit
tkregister_tcl /opt/freesurfer-530/tktools/tkregister2.tcl
---- FSL registration matrix --------
-0.977 -0.168 0.132 237.045;
-0.044 -0.446 -0.894 247.166;
0.209 -0.879 0.429 165.812;
0.000 0.000 0.000 1.000;
---------------------------------------
INFO: no target volume specified, assuming FreeSurfer orig volume.
target volume orig
movable volume bold/tmp.bbregister.16782/fslregister/movvol.fslregister.nii
reg file bold/tmp.bbregister.16782/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 /misc/data41/yuex/human_anat/field/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
bold/tmp.bbregister.16782/fslregister/movvol.fslregister.nii
Tmov: --------------------
-1.408 0.000 0.000 100.000;
0.000 0.000 1.484 -30.422;
0.000 -1.408 0.000 100.000;
0.000 0.000 0.000 1.000;
mkheaderreg = 0, float2int = 0
FSLOUTPUTTYPE NIFTI
fsl2TkReg: mov det = -2.94386, ref det = -1
---- Input registration matrix (computed) --------
-0.977 -0.209 -0.044 -3.920;
-0.132 0.429 0.894 45.467;
-0.168 0.879 -0.446 -4.702;
0.000 0.000 0.000 1.000;
---------------------------------------
---- Input registration matrix --------
-0.977 -0.209 -0.044 -3.920;
-0.132 0.429 0.894 45.467;
-0.168 0.879 -0.446 -4.702;
0.000 0.000 0.000 1.000;
Determinant 1
subject = field
RegMat ---------------------------
-0.977 -0.209 -0.044 -3.920;
-0.132 0.429 0.894 45.467;
-0.168 0.879 -0.446 -4.702;
0.000 0.000 0.000 1.000;
mri_matrix_multiply -im bold/tmp.bbregister.16782/fslregister/swapreg.dat -im
bold/tmp.bbregister.16782/reg.init.dat -om
bold/tmp.bbregister.16782/reg.init.dat
Started at Thu Oct 16 10:54:37 EDT 2014
Ended at Thu Oct 16 10:54:55 EDT 2014
fslregister Done
To check results, run:
tkregister2 --mov bold/tmp.bbregister.16782/template.nii --reg
bold/tmp.bbregister.16782/reg.init.dat --surf orig
mri_segreg --mov bold/tmp.bbregister.16782/template.nii --init-reg
bold/tmp.bbregister.16782/reg.init.dat --out-reg
bold/tmp.bbregister.16782/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 /misc/data41/yuex/human_anat
cd /misc/data41/yuex/humanfMRI/human_curvature/subjdata/field090514
mri_segreg --mov bold/tmp.bbregister.16782/template.nii --init-reg
bold/tmp.bbregister.16782/reg.init.dat --out-reg
bold/tmp.bbregister.16782/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 konis
machine x86_64
user yuex
movvol bold/tmp.bbregister.16782/template.nii
regfile bold/tmp.bbregister.16782/reg.init.dat
subject field
dof 6
outregfile bold/tmp.bbregister.16782/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 1413976737
TransRandMax 0.000000
RotRandMax 0.000000
Translations 0.000000 0.000000 0.000000
Rotations 0.000000 0.000000 0.000000
Input reg
0.977 0.209 0.044 5.329;
-0.132 0.429 0.894 45.467;
-0.168 0.879 -0.446 -4.702;
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 1.060951
1 -25.0 -25.0 25.0 1.079854
2 -25.0 25.0 -25.0 1.010896
3 -25.0 25.0 25.0 0.976003
4 25.0 -25.0 -25.0 0.991040
5 25.0 -25.0 25.0 1.056359
6 25.0 25.0 -25.0 1.034184
7 25.0 25.0 25.0 1.030553
REL: 8 1.081220 8.239841 1.029980 rel = 1.04975
Initial costs ----------------
Number of surface hits 950
WM Intensity 1926.3137 +/- 632.0443
Ctx Intensity 1824.4384 +/- 642.8431
Pct Contrast -6.5655 +/- 34.3464
Cost 1.0812
RelCost 1.0497
WARNING: initial G-W contrast is negative, but expecting positive.
If the mov data has a T1 contrast, re-run with --T1
------------------------------------
Brute force preopt -4 4 4, n = 729
0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 1.1055
1.1055 0.0
1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 1.0629
1.0629 0.0
2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 1.0403
1.0403 0.0
14 -4.0000 -4.0000 -4.0000 0.0000 0.0000 4.0000 1.0339
1.0339 0.0
15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 1.0287
1.0287 0.0
18 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 -4.0000 1.0278
1.0278 0.0
22 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.0000 1.0007
1.0007 0.0
24 -4.0000 -4.0000 -4.0000 4.0000 4.0000 -4.0000 0.9934
0.9934 0.0
32 -4.0000 -4.0000 0.0000 -4.0000 0.0000 4.0000 0.9521
0.9521 0.0
45 -4.0000 -4.0000 0.0000 4.0000 -4.0000 -4.0000 0.9411
0.9411 0.0
63 -4.0000 -4.0000 4.0000 0.0000 -4.0000 -4.0000 0.9392
0.9392 0.0
235 -4.0000 4.0000 4.0000 4.0000 -4.0000 0.0000 0.9170
0.9170 0.0
Brute Force --------------------------
Min cost was 0.916969
Number of iterations 729
Search time 0.742000 sec
Parameters at best (transmm, rotdeg)
-4.000 4.000 4.000 4.000 -4.000 0.000
--------------------------------------------
Starting Powell Minimization
Init Powel Params dof = 6
0 -4
1 4
2 4
3 4
4 -4
5 0
8 -3.917 4.000 4.000 4.000 -4.000 0.000 0.9165411210
9 -3.953 4.000 4.000 4.000 -4.000 0.000 0.9157219616
11 -3.947 4.000 4.000 4.000 -4.000 0.000 0.9156704455
14 -3.946 4.000 4.000 4.000 -4.000 0.000 0.9156692861
23 -3.946 4.066 4.000 4.000 -4.000 0.000 0.9134709439
26 -3.946 4.064 4.000 4.000 -4.000 0.000 0.9134644332
27 -3.946 4.062 4.000 4.000 -4.000 0.000 0.9134638440
38 -3.946 4.062 3.984 4.000 -4.000 0.000 0.9130255627
39 -3.946 4.062 3.975 4.000 -4.000 0.000 0.9129089055
40 -3.946 4.062 3.969 4.000 -4.000 0.000 0.9128597309
42 -3.946 4.062 3.966 4.000 -4.000 0.000 0.9128409988
43 -3.946 4.062 3.961 4.000 -4.000 0.000 0.9128296138
52 -3.946 4.062 3.961 3.794 -4.000 0.000 0.9100269104
53 -3.946 4.062 3.961 3.808 -4.000 0.000 0.9100260980
58 -3.946 4.062 3.961 3.812 -4.000 0.000 0.9100095252
59 -3.946 4.062 3.961 3.815 -4.000 0.000 0.9099962192
68 -3.946 4.062 3.961 3.815 -4.267 0.000 0.9094265643
69 -3.946 4.062 3.961 3.815 -4.170 0.000 0.9072434154
70 -3.946 4.062 3.961 3.815 -4.141 0.000 0.9064106850
73 -3.946 4.062 3.961 3.815 -4.143 0.000 0.9064054824
84 -3.946 4.062 3.961 3.815 -4.143 0.001 0.9064040237
86 -3.946 4.062 3.961 3.815 -4.143 0.002 0.9064039348
87 -3.892 4.125 3.921 3.630 -4.285 0.004 0.9027192437
94 -3.896 4.120 3.924 3.645 -4.274 0.004 0.9024736980
95 -3.896 4.119 3.925 3.646 -4.273 0.004 0.9024724576
96 -3.896 4.119 3.925 3.646 -4.273 0.004 0.9024718486
106 -3.945 4.119 3.925 3.646 -4.273 0.004 0.9018553972
107 -3.951 4.119 3.925 3.646 -4.273 0.004 0.9017821473
108 -3.977 4.119 3.925 3.646 -4.273 0.004 0.9016635904
109 -3.973 4.119 3.925 3.646 -4.273 0.004 0.9016340851
110 -3.968 4.119 3.925 3.646 -4.273 0.004 0.9016257392
111 -3.969 4.119 3.925 3.646 -4.273 0.004 0.9016249172
120 -3.969 4.121 3.925 3.646 -4.273 0.004 0.9016172028
124 -3.969 4.129 3.925 3.646 -4.273 0.004 0.9015394601
125 -3.969 4.134 3.925 3.646 -4.273 0.004 0.9014979661
128 -3.969 4.136 3.925 3.646 -4.273 0.004 0.9014892022
135 -3.969 4.136 3.924 3.646 -4.273 0.004 0.9014392066
138 -3.969 4.136 3.877 3.646 -4.273 0.004 0.9001414586
140 -3.969 4.136 3.880 3.646 -4.273 0.004 0.9001378792
158 -3.969 4.136 3.880 3.647 -4.273 0.004 0.9001331973
179 -3.970 4.135 3.880 3.648 -4.273 0.004 0.9001042789
184 -3.970 4.135 3.880 3.648 -4.273 0.004 0.9000943733
194 -3.999 4.135 3.880 3.648 -4.273 0.004 0.8997865834
196 -3.989 4.135 3.880 3.648 -4.273 0.004 0.8996434070
197 -3.988 4.135 3.880 3.648 -4.273 0.004 0.8996417812
221 -3.988 4.135 3.865 3.648 -4.273 0.004 0.8995321209
222 -3.988 4.135 3.868 3.648 -4.273 0.004 0.8995247373
223 -3.988 4.135 3.869 3.648 -4.273 0.004 0.8995244465
275 -3.995 4.135 3.864 3.648 -4.273 0.004 0.8995098988
276 -3.992 4.135 3.866 3.648 -4.273 0.004 0.8995021752
277 -3.992 4.135 3.866 3.648 -4.273 0.004 0.8995019692
309 -3.992 4.133 3.866 3.648 -4.273 0.004 0.8994973234
321 -3.992 4.133 3.865 3.648 -4.273 0.004 0.8994970625
333 -3.992 4.133 3.865 3.651 -4.273 0.004 0.8994703867
356 -3.993 4.133 3.865 3.651 -4.273 0.004 0.8994697639
360 -3.993 4.133 3.865 3.651 -4.273 0.004 0.8994697483
Powell done niters = 3
Computing relative cost
0 -25.0 -25.0 -25.0 1.074594
1 -25.0 -25.0 25.0 1.091803
2 -25.0 25.0 -25.0 1.064029
3 -25.0 25.0 25.0 1.015808
4 25.0 -25.0 -25.0 1.042443
5 25.0 -25.0 25.0 0.996388
6 25.0 25.0 -25.0 0.964784
7 25.0 25.0 25.0 1.046877
REL: 8 0.899470 8.296725 1.037091 rel = 0.867301
Number of iterations 3
Min cost was 0.899470
Number of FunctionCalls 363
TolPowell 0.000100
nMaxItersPowell 36
OptimizationTime 0.364000 sec
Parameters at optimum (transmm) -3.99275 4.13266 3.86469
Parameters at optimum (rotdeg) 3.65113 -4.27252 0.00400
Final costs ----------------
Number of surface hits 814
WM Intensity 1787.3310 +/- 612.2335
Ctx Intensity 1807.2624 +/- 643.9524
Pct Contrast 0.6529 +/- 31.6639
Cost 0.8995
RelCost 1.0497
Reg at min cost was
0.987 0.141 0.073 1.452;
-0.121 0.372 0.920 49.807;
-0.102 0.918 -0.384 2.470;
0.000 0.000 0.000 1.000;
Writing optimal reg to bold/tmp.bbregister.16782/bbr.pass1.dat, type = 14
Original Reg
0.977 0.209 0.044 5.329;
-0.132 0.429 0.894 45.467;
-0.168 0.879 -0.446 -4.702;
0.000 0.000 0.000 1.000;
Original Reg - Optimal Reg
-0.010 0.068 -0.029 3.877;
-0.011 0.057 -0.027 -4.340;
-0.065 -0.039 -0.062 -7.172;
0.000 0.000 0.000 0.000;
Computing change in lh position
LH rmsDiffMean 8.547457
Computing change in rh position
Surface RMS Diff (mm) 9.872335 14.654105
WARNING: initial G-W contrast was negative, but expected positive.
If the mov data has a T1 contrast, re-run with --T1
mri_segreg done
mri_segreg --mov bold/tmp.bbregister.16782/template.nii --init-reg
bold/tmp.bbregister.16782/bbr.pass1.dat --out-reg bold/register.dof6.dat
--brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3
--c0 0 --mincost bold/register.dof6.dat.mincost --dof 6 --nmax 36 --param
bold/register.dof6.dat.param --surf white --cur-reg
bold/tmp.bbregister.16782/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 /misc/data41/yuex/human_anat
cd /misc/data41/yuex/humanfMRI/human_curvature/subjdata/field090514
mri_segreg --mov bold/tmp.bbregister.16782/template.nii --init-reg
bold/tmp.bbregister.16782/bbr.pass1.dat --out-reg bold/register.dof6.dat
--brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3
--c0 0 --mincost bold/register.dof6.dat.mincost --dof 6 --nmax 36 --param
bold/register.dof6.dat.param --surf white --cur-reg
bold/tmp.bbregister.16782/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm
0.5
sysname Linux
hostname konis
machine x86_64
user yuex
movvol bold/tmp.bbregister.16782/template.nii
regfile bold/tmp.bbregister.16782/bbr.pass1.dat
subject field
dof 6
outregfile bold/register.dof6.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 1414220614
TransRandMax 0.000000
RotRandMax 0.000000
Translations 0.000000 0.000000 0.000000
Rotations 0.000000 0.000000 0.000000
Input reg
0.987 0.141 0.073 1.452;
-0.121 0.372 0.920 49.807;
-0.102 0.918 -0.384 2.470;
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 1.041423
1 -25.0 -25.0 25.0 1.058492
2 -25.0 25.0 -25.0 1.076482
3 -25.0 25.0 25.0 1.040607
4 25.0 -25.0 -25.0 1.041040
5 25.0 -25.0 25.0 1.008015
6 25.0 25.0 -25.0 1.003799
7 25.0 25.0 25.0 1.053811
REL: 8 0.988398 8.323668 1.040459 rel = 0.949964
Initial costs ----------------
Number of surface hits 81800
WM Intensity 1792.5866 +/- 600.1171
Ctx Intensity 1789.8013 +/- 630.6812
Pct Contrast -0.8341 +/- 31.0950
Cost 0.9884
RelCost 0.9500
WARNING: initial G-W contrast is negative, but expecting positive.
If the mov data has a T1 contrast, re-run with --T1
------------------------------------
Brute force preopt -0.1 0.1 0.1, n = 729
0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.9040
0.9040 0.0
1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.9018
0.9018 0.0
10 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.0000 0.9001
0.9001 0.0
90 -0.1000 0.0000 -0.1000 0.0000 -0.1000 -0.1000 0.8988
0.8988 0.0
91 -0.1000 0.0000 -0.1000 0.0000 -0.1000 0.0000 0.8982
0.8982 0.0
257 0.0000 -0.1000 -0.1000 0.0000 0.0000 0.1000 0.8978
0.8978 0.0
263 0.0000 -0.1000 -0.1000 0.1000 -0.1000 0.1000 0.8976
0.8976 0.0
Brute Force --------------------------
Min cost was 0.897650
Number of iterations 729
Search time 0.725000 sec
Parameters at best (transmm, rotdeg)
0.000 -0.100 -0.100 0.100 -0.100 0.100
--------------------------------------------
Starting Powell Minimization
Init Powel Params dof = 6
0 0
1 -0.1
2 -0.1
3 0.1
4 -0.1
5 0.1
2 1.000 -0.100 -0.100 0.100 -0.100 0.100 0.9798781214
3 2.618 -0.100 -0.100 0.100 -0.100 0.100 0.9562461928
6 3.618 -0.100 -0.100 0.100 -0.100 0.100 0.9546126772
8 3.660 -0.100 -0.100 0.100 -0.100 0.100 0.9542808560
9 3.900 -0.100 -0.100 0.100 -0.100 0.100 0.9536104912
11 3.878 -0.100 -0.100 0.100 -0.100 0.100 0.9535784922
12 3.795 -0.100 -0.100 0.100 -0.100 0.100 0.9533989577
14 3.812 -0.100 -0.100 0.100 -0.100 0.100 0.9533905947
15 3.809 -0.100 -0.100 0.100 -0.100 0.100 0.9533890242
27 3.808 -0.190 -0.100 0.100 -0.100 0.100 0.9533491326
30 3.808 -0.174 -0.100 0.100 -0.100 0.100 0.9532877026
31 3.808 -0.170 -0.100 0.100 -0.100 0.100 0.9532539497
35 3.808 -0.169 -0.100 0.100 -0.100 0.100 0.9532526690
48 3.808 -0.169 -0.094 0.100 -0.100 0.100 0.9532488995
49 3.808 -0.169 -0.093 0.100 -0.100 0.100 0.9532486751
50 3.808 -0.169 -0.091 0.100 -0.100 0.100 0.9532484316
74 3.808 -0.169 -0.091 0.100 -0.101 0.100 0.9532457725
75 3.808 -0.169 -0.091 0.100 -0.113 0.100 0.9532225067
78 3.808 -0.169 -0.091 0.100 -0.112 0.100 0.9532217283
80 3.808 -0.169 -0.091 0.100 -0.111 0.100 0.9532213431
81 3.808 -0.169 -0.091 0.100 -0.110 0.100 0.9532213400
90 3.808 -0.169 -0.091 0.100 -0.110 0.095 0.9532058658
93 3.808 -0.169 -0.091 0.100 -0.110 0.094 0.9532056606
94 3.808 -0.169 -0.091 0.100 -0.110 0.093 0.9532046688
102 3.190 -0.169 -0.091 0.100 -0.110 0.093 0.9520714732
108 3.189 -0.169 -0.091 0.100 -0.110 0.093 0.9520708101
111 3.188 -0.169 -0.091 0.100 -0.110 0.093 0.9520708059
120 3.188 -0.234 -0.091 0.100 -0.110 0.093 0.9517274568
122 3.188 -0.257 -0.091 0.100 -0.110 0.093 0.9514965824
123 3.188 -0.265 -0.091 0.100 -0.110 0.093 0.9514462351
127 3.188 -0.264 -0.091 0.100 -0.110 0.093 0.9514248959
133 3.188 -0.264 0.291 0.100 -0.110 0.093 0.9513007666
134 3.188 -0.264 0.113 0.100 -0.110 0.093 0.9512690686
136 3.188 -0.264 0.035 0.100 -0.110 0.093 0.9512125323
137 3.188 -0.264 -0.013 0.100 -0.110 0.093 0.9511676263
139 3.188 -0.264 -0.027 0.100 -0.110 0.093 0.9511481587
140 3.188 -0.264 -0.028 0.100 -0.110 0.093 0.9511471720
142 3.188 -0.264 -0.030 0.100 -0.110 0.093 0.9511464304
150 3.188 -0.264 -0.030 0.482 -0.110 0.093 0.9510831190
151 3.188 -0.264 -0.030 0.298 -0.110 0.093 0.9506860322
152 3.188 -0.264 -0.030 0.297 -0.110 0.093 0.9506778488
170 3.188 -0.264 -0.030 0.297 -0.111 0.093 0.9506776272
171 3.188 -0.264 -0.030 0.297 -0.112 0.093 0.9506775922
182 3.188 -0.264 -0.030 0.297 -0.112 -0.005 0.9505029075
187 3.188 -0.264 -0.030 0.297 -0.112 -0.013 0.9504718219
200 3.175 -0.264 -0.030 0.297 -0.112 -0.013 0.9504409404
202 3.171 -0.264 -0.030 0.297 -0.112 -0.013 0.9504379097
211 3.171 -0.242 -0.030 0.297 -0.112 -0.013 0.9502729151
214 3.171 -0.238 -0.030 0.297 -0.112 -0.013 0.9502579966
224 3.171 -0.238 0.127 0.297 -0.112 -0.013 0.9501152728
226 3.171 -0.238 0.120 0.297 -0.112 -0.013 0.9501015204
227 3.171 -0.238 0.117 0.297 -0.112 -0.013 0.9500992221
228 3.171 -0.238 0.115 0.297 -0.112 -0.013 0.9500990034
249 3.171 -0.238 0.115 0.297 -0.040 -0.013 0.9499297028
250 3.171 -0.238 0.115 0.297 0.006 -0.013 0.9496860912
251 3.171 -0.238 0.115 0.297 0.107 -0.013 0.9496078797
252 3.171 -0.238 0.115 0.297 0.070 -0.013 0.9495299658
254 3.171 -0.238 0.115 0.297 0.072 -0.013 0.9495291524
267 3.171 -0.238 0.115 0.297 0.073 -0.033 0.9495083726
268 3.171 -0.238 0.115 0.297 0.073 -0.029 0.9494873469
270 3.171 -0.238 0.115 0.297 0.073 -0.027 0.9494783266
281 3.161 -0.238 0.115 0.297 0.073 -0.027 0.9494373109
283 3.151 -0.238 0.115 0.297 0.073 -0.027 0.9494169007
299 3.151 -0.239 0.115 0.297 0.073 -0.027 0.9494168675
308 3.151 -0.239 0.133 0.297 0.073 -0.027 0.9494106537
309 3.151 -0.239 0.128 0.297 0.073 -0.027 0.9494090531
310 3.151 -0.239 0.127 0.297 0.073 -0.027 0.9494087548
312 3.151 -0.239 0.125 0.297 0.073 -0.027 0.9494081880
325 3.151 -0.239 0.125 0.296 0.073 -0.027 0.9494011607
335 3.151 -0.239 0.125 0.296 0.056 -0.027 0.9493800474
336 3.151 -0.239 0.125 0.296 0.057 -0.027 0.9493794874
337 3.151 -0.239 0.125 0.296 0.059 -0.027 0.9493793202
365 3.147 -0.239 0.125 0.296 0.059 -0.027 0.9493770612
366 3.146 -0.239 0.125 0.296 0.059 -0.027 0.9493768300
390 3.146 -0.239 0.140 0.296 0.059 -0.027 0.9493650667
391 3.146 -0.239 0.139 0.296 0.059 -0.027 0.9493635499
392 3.146 -0.239 0.136 0.296 0.059 -0.027 0.9493615772
394 3.146 -0.239 0.135 0.296 0.059 -0.027 0.9493614546
417 3.146 -0.239 0.135 0.296 0.052 -0.027 0.9493562867
440 3.144 -0.239 0.138 0.296 0.050 -0.027 0.9493547966
441 3.144 -0.239 0.138 0.296 0.050 -0.027 0.9493546971
442 3.144 -0.239 0.138 0.296 0.050 -0.027 0.9493546872
445 3.145 -0.239 0.137 0.296 0.051 -0.027 0.9493546636
465 3.145 -0.239 0.137 0.296 0.050 -0.027 0.9493540703
516 3.145 -0.239 0.137 0.296 0.051 -0.027 0.9493540080
523 3.145 -0.239 0.139 0.296 0.050 -0.027 0.9493537002
526 3.144 -0.239 0.139 0.296 0.050 -0.027 0.9493536936
531 3.144 -0.239 0.139 0.296 0.050 -0.027 0.9493536819
532 3.144 -0.239 0.139 0.296 0.050 -0.027 0.9493536801
547 3.145 -0.239 0.139 0.296 0.050 -0.027 0.9493530914
548 3.146 -0.239 0.139 0.296 0.050 -0.027 0.9493530523
605 3.145 -0.239 0.143 0.296 0.047 -0.027 0.9493522092
606 3.145 -0.239 0.142 0.296 0.048 -0.027 0.9493520486
607 3.145 -0.239 0.142 0.296 0.048 -0.027 0.9493520000
612 3.145 -0.239 0.142 0.296 0.048 -0.027 0.9493519993
614 3.146 -0.239 0.144 0.296 0.046 -0.027 0.9493502781
619 3.146 -0.239 0.146 0.296 0.045 -0.027 0.9493500959
621 3.146 -0.239 0.146 0.296 0.045 -0.027 0.9493500773
640 3.148 -0.239 0.146 0.296 0.045 -0.027 0.9493498793
642 3.147 -0.239 0.146 0.296 0.045 -0.027 0.9493495433
679 3.147 -0.239 0.146 0.290 0.045 -0.027 0.9493458374
696 3.148 -0.239 0.149 0.290 0.043 -0.027 0.9493453615
700 3.148 -0.239 0.148 0.290 0.044 -0.027 0.9493453591
701 3.148 -0.239 0.148 0.290 0.044 -0.027 0.9493453572
702 3.148 -0.239 0.148 0.290 0.044 -0.027 0.9493452999
707 3.150 -0.239 0.154 0.285 0.040 -0.027 0.9493329264
714 3.150 -0.239 0.154 0.285 0.040 -0.027 0.9493327460
715 3.151 -0.239 0.154 0.285 0.039 -0.027 0.9493325312
717 3.151 -0.239 0.155 0.284 0.039 -0.027 0.9493318303
720 3.151 -0.239 0.155 0.284 0.039 -0.027 0.9493317536
722 3.151 -0.239 0.155 0.284 0.039 -0.027 0.9493317326
737 3.149 -0.239 0.155 0.284 0.039 -0.027 0.9493309425
770 3.147 -0.239 0.151 0.284 0.042 -0.027 0.9493298067
771 3.148 -0.239 0.152 0.284 0.041 -0.027 0.9493293902
775 3.148 -0.239 0.153 0.284 0.041 -0.027 0.9493293854
776 3.148 -0.239 0.152 0.284 0.041 -0.027 0.9493293679
777 3.148 -0.239 0.152 0.284 0.041 -0.027 0.9493293405
778 3.148 -0.239 0.152 0.284 0.041 -0.027 0.9493293348
779 3.148 -0.239 0.152 0.284 0.041 -0.027 0.9493293165
807 3.148 -0.239 0.152 0.284 0.041 -0.027 0.9493292815
808 3.148 -0.239 0.152 0.284 0.041 -0.027 0.9493292113
810 3.148 -0.239 0.152 0.284 0.041 -0.027 0.9493291950
811 3.148 -0.239 0.152 0.284 0.041 -0.027 0.9493291898
812 3.148 -0.239 0.152 0.284 0.041 -0.027 0.9493291796
824 3.149 -0.239 0.152 0.284 0.041 -0.027 0.9493289069
862 3.149 -0.239 0.152 0.284 0.041 -0.027 0.9493288628
870 3.149 -0.239 0.152 0.284 0.041 -0.027 0.9493288576
971 3.149 -0.239 0.152 0.284 0.042 -0.027 0.9493288401
Powell done niters = 10
Computing relative cost
0 -25.0 -25.0 -25.0 1.054557
1 -25.0 -25.0 25.0 1.061450
2 -25.0 25.0 -25.0 1.063480
3 -25.0 25.0 25.0 1.043488
4 25.0 -25.0 -25.0 1.034488
5 25.0 -25.0 25.0 1.027559
6 25.0 25.0 -25.0 0.998397
7 25.0 25.0 25.0 1.053964
REL: 8 0.949329 8.337382 1.042173 rel = 0.910913
Number of iterations 10
Min cost was 0.949329
Number of FunctionCalls 989
TolPowell 0.000000
nMaxItersPowell 36
OptimizationTime 47.672000 sec
Parameters at optimum (transmm) 3.14893 -0.23910 0.15245
Parameters at optimum (rotdeg) 0.28423 0.04171 -0.02742
Final costs ----------------
Number of surface hits 82193
WM Intensity 1808.4431 +/- 585.9213
Ctx Intensity 1814.5868 +/- 621.2398
Pct Contrast -0.5009 +/- 29.2215
Cost 0.9493
RelCost 0.9500
Reg at min cost was
0.987 0.142 0.073 4.627;
-0.121 0.367 0.922 49.554;
-0.104 0.919 -0.380 2.868;
0.000 0.000 0.000 1.000;
Writing optimal reg to bold/register.dof6.dat, type = 14
Original Reg
0.987 0.141 0.073 1.452;
-0.121 0.372 0.920 49.807;
-0.102 0.918 -0.384 2.470;
0.000 0.000 0.000 1.000;
Original Reg - Optimal Reg
0.000 -0.001 -0.000 -3.175;
-0.000 0.005 -0.002 0.253;
0.001 -0.002 -0.005 -0.398;
0.000 0.000 0.000 0.000;
Computing change in lh position
LH rmsDiffMean 3.212828
Computing change in rh position
Surface RMS Diff (mm) 3.209627 3.352517
WARNING: initial G-W contrast was negative, but expected positive.
If the mov data has a T1 contrast, re-run with --T1
mri_segreg done
Cleaning up
Started at Thu Oct 16 10:54:36 EDT 2014
Ended at Thu Oct 16 10:55:56 EDT 2014
BBR-Run-Time-Sec 80
bbregister Done
To check results, run:
tkregister2 --mov bold/template.nii --reg bold/register.dof6.dat --surf
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