Hi,
I have successfully run 126 subjects through bbregister and mri_vol2vol in
order to translate the wmparc volume into TBSS space. However, there are 2
subjects that exited prematurely from bbregister. I think it may have to
do with my naming system? 126 of the subjects have the subjid
CVRAM_###_recon. But these 2 subjects that exited in error have 4 numbers:
CVRAM_####_recon. I don't know how that would make a difference, but I've
attached the bbregister logs. Although it doesn't say this in the log
itself, in the terminal window right before it stops it gives me this
message:
"Loading mov
Loading lh.white surf
Loading lh.thickness for GM
GM Proj: 1 0.500000 2.000000
WM Proj: 0 0.500000 2.000000
Projecting LH Surfs
Projecting RH Surfs
Loading rh.white surf
Loading rh.thickness
Segmentation fault"
I'm running the following commands in the dev environment:
naming example:
subject = CVRAM_####_recon (FS subjdir)
basename = CVRAM_####
Commands:
bbregister --s $subject --mov
$DTI_DIR/${basename}_dti/preTBSS_0.4thresh-LAS/lowb-swap.nii.gz --dti
--init-fsl --reg $DTI_DIR/${basename}_dti/${basename}_lowb-to-anat.reg
mri_vol2vol --targ $SUBJECTS_DIR/$subject/mri/wmparc.mgz --mov
$DTI_DIR/${basename}_dti/preTBSS_0.4thresh-LAS/lowb-swap.nii.gz --o
$DTI_DIR/${basename}_dti/${basename}_wmparc-in-lowb.nii.gz --reg
$DTI_DIR/${basename}_dti/${basename}_lowb-to-anat.reg --inv --interp
nearest
Thank you very much!
Tori
Logfile for bbregister
Mon Aug 24 17:09:39 EDT 2009
setenv SUBJECTS_DIR /autofs/space/lang_012/users/CVRAM
cd /autofs/space/orion_002/users/DTI/SCRIPTS
/usr/local/freesurfer/dev/bin/bbregister --s CVRAM_1045_recon --mov
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/preTBSS_0.4thresh-LAS/lowb-swap.nii.gz
--dti --init-fsl --reg
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/CVRAM_1045_lowb-to-anat.reg
$Id: bbregister,v 1.30 2009/08/07 22:20:40 greve Exp $
Linux compute-0-54.local 2.6.18-53.1.19.el5 #1 SMP Tue Apr 22 03:01:10 EDT 2008
x86_64 x86_64 x86_64 GNU/Linux
FREESURFER_HOME /usr/local/freesurfer/dev
mri_convert
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/preTBSS_0.4thresh-LAS/lowb-swap.nii.gz
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/template.nii
mri_convert
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/preTBSS_0.4thresh-LAS/lowb-swap.nii.gz
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/template.nii
$Id: mri_convert.c,v 1.159 2009/07/15 18:52:28 greve Exp $
reading from
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/preTBSS_0.4thresh-LAS/lowb-swap.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -4.65661e-09, -9.31323e-10)
j_ras = (6.0536e-09, 1, 2.98023e-08)
k_ras = (-1.86265e-09, 0, 1)
writing to
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/template.nii...
fslregister --s CVRAM_1045_recon --mov
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/template.nii
--reg
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/reg.init.dat
--niters 1 --maxangle 90 --nobetmov --tmp
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/fslregister
--dof 6
Log file is
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/reg.init.dat.fslregister.log
Mon Aug 24 17:09:40 EDT 2009
--s CVRAM_1045_recon --mov
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/template.nii
--reg
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/reg.init.dat
--niters 1 --maxangle 90 --nobetmov --tmp
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/fslregister
--dof 6
$Id: fslregister,v 1.29 2009/07/31 22:22:46 greve Exp $
compute-0-54.local
Linux compute-0-54.local 2.6.18-53.1.19.el5 #1 SMP Tue Apr 22 03:01:10 EDT 2008
x86_64 x86_64 x86_64 GNU/Linux
nIters 1
--------------------------------------
/autofs/space/orion_002/users/DTI/SCRIPTS
mri_convert
/autofs/space/lang_012/users/CVRAM/CVRAM_1045_recon/mri/brainmask.mgz
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/fslregister/refvol.fslregister.nii
mri_convert
/autofs/space/lang_012/users/CVRAM/CVRAM_1045_recon/mri/brainmask.mgz
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/fslregister/refvol.fslregister.nii
$Id: mri_convert.c,v 1.159 2009/07/15 18:52:28 greve Exp $
reading from
/autofs/space/lang_012/users/CVRAM/CVRAM_1045_recon/mri/brainmask.mgz...
TR=2730.00, TE=3.31, TI=1000.00, flip angle=7.00
i_ras = (-1, -1.5775e-09, 5.01362e-10)
j_ras = (-7.17543e-11, -2.72532e-09, -1)
k_ras = (2.14413e-09, 1, -2.47023e-08)
writing to
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/fslregister/refvol.fslregister.nii...
--------------------------------------
/autofs/space/orion_002/users/DTI/SCRIPTS
mri_convert
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/template.nii
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/fslregister/movvol.fslregister.nii
--frame 0
mri_convert
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/template.nii
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/fslregister/movvol.fslregister.nii
--frame 0
$Id: mri_convert.c,v 1.159 2009/07/15 18:52:28 greve Exp $
reading from
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/template.nii...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -4.65661e-09, -9.31323e-10)
j_ras = (6.0536e-09, 1, 2.98023e-08)
k_ras = (-1.86265e-09, 0, 1)
keeping frame 0
writing to
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/fslregister/movvol.fslregister.nii...
/autofs/space/orion_002/users/DTI/SCRIPTS
tkregister2_cmdl --mov
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/fslregister/movvol.fslregister.nii
--reg
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/fslregister/reg0.27445.dat
--regheader --fslregout
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/reg.init.dat.fsl.mat0
--s CVRAM_1045_recon --noedit
tkregister_tcl /usr/local/freesurfer/dev/lib/tcl/tkregister2.tcl
INFO: no target volume specified, assuming FreeSurfer orig volume.
target volume orig
movable volume
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/fslregister/movvol.fslregister.nii
reg file
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/fslregister/reg0.27445.dat
LoadVol 0
ZeroCRAS 0
$Id: tkregister2.c,v 1.108 2009/04/02 17:14:46 mreuter Exp $
Diagnostic Level -1
INFO: loading target
/autofs/space/lang_012/users/CVRAM/CVRAM_1045_recon/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
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/fslregister/movvol.fslregister.nii
Tmov: --------------------
-2.000 0.000 0.000 128.000;
0.000 0.000 2.000 -60.000;
0.000 -2.000 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) --------
1.000 -0.000 0.000 -0.011;
-0.000 -0.000 1.000 -22.143;
0.000 -1.000 -0.000 -13.995;
0.000 0.000 0.000 1.000;
---------------------------------------
---- Input registration matrix --------
1.000 -0.000 0.000 -0.011;
-0.000 -0.000 1.000 -22.143;
0.000 -1.000 -0.000 -13.995;
0.000 0.000 0.000 1.000;
Determinant 1
subject = CVRAM_1045_recon
RegMat ---------------------------
1.000 -0.000 0.000 -0.011;
-0.000 -0.000 1.000 -22.143;
0.000 -1.000 -0.000 -13.995;
0.000 0.000 0.000 1.000;
register: file
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/fslregister/reg0.27445.dat
written
FSLOUTPUTTYPE NIFTI
tkreg2FSL: mov det = -8, ref det = -1
Mon Aug 24 17:09:44 EDT 2009
/autofs/space/orion_002/users/DTI/SCRIPTS
flirt -ref
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/fslregister/refvol.fslregister.nii
-in
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/fslregister/movvol.fslregister.nii
-bins 256 -omat
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/reg.init.dat.fsl.mat
-cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90
-verbose 0 -schedule
/usr/local/freesurfer/dev/bin/flirt.newdefault.20080811.sch -init
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/reg.init.dat.fsl.mat0
tkregister2_cmdl --s CVRAM_1045_recon --mov
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/template.nii
--reg
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/reg.init.dat
--fslreg
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/reg.init.dat.fsl.mat
--noedit
tkregister_tcl /usr/local/freesurfer/dev/lib/tcl/tkregister2.tcl
---- FSL registration matrix --------
1.000 -0.004 -0.003 -0.108;
-0.003 -0.001 -1.000 169.355;
0.004 1.000 -0.001 -13.748;
0.000 0.000 0.000 1.000;
---------------------------------------
INFO: no target volume specified, assuming FreeSurfer orig volume.
target volume orig
movable volume
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/template.nii
reg file
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/reg.init.dat
LoadVol 0
ZeroCRAS 0
$Id: tkregister2.c,v 1.108 2009/04/02 17:14:46 mreuter Exp $
Diagnostic Level -1
INFO: loading target
/autofs/space/lang_012/users/CVRAM/CVRAM_1045_recon/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
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/template.nii
Tmov: --------------------
-2.000 0.000 0.000 128.000;
0.000 0.000 2.000 -60.000;
0.000 -2.000 0.000 128.000;
0.000 0.000 0.000 1.000;
mkheaderreg = 0, float2int = 0
FSLOUTPUTTYPE NIFTI
fsl2TkReg: mov det = -8, ref det = -1
---- Input registration matrix (computed) --------
1.000 -0.004 -0.003 -0.775;
0.003 -0.001 1.000 -19.179;
-0.004 -1.000 -0.001 -13.297;
0.000 0.000 0.000 1.000;
---------------------------------------
---- Input registration matrix --------
1.000 -0.004 -0.003 -0.775;
0.003 -0.001 1.000 -19.179;
-0.004 -1.000 -0.001 -13.297;
0.000 0.000 0.000 1.000;
Determinant 1
subject = CVRAM_1045_recon
RegMat ---------------------------
1.000 -0.004 -0.003 -0.775;
0.003 -0.001 1.000 -19.179;
-0.004 -1.000 -0.001 -13.297;
0.000 0.000 0.000 1.000;
register: file
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/reg.init.dat
written
(standard_in) 1: illegal character: V
(standard_in) 1: illegal character: R
(standard_in) 1: parse error
(standard_in) 1: illegal character: M
(standard_in) 1: illegal character: _
(standard_in) 1: illegal character: _
Started at Mon Aug 24 17:09:40 EDT 2009
Ended at Mon Aug 24 17:10:11 EDT 2009
fslregister Done
To check results, run:
tkregister2 --mov
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/template.nii
--reg
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/reg.init.dat
--surf orig
mri_segreg --mov
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/template.nii
--init-reg
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/reg.init.dat
--out-reg
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/bbr.pass1.dat
--subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4
--gm-proj-frac 0.5 --gm-gt-wm 0.5
$Id: mri_segreg.c,v 1.84 2009/07/21 14:15:11 fischl Exp $
setenv SUBJECTS_DIR /autofs/space/lang_012/users/CVRAM
cd /autofs/space/orion_002/users/DTI/SCRIPTS
mri_segreg --mov
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/template.nii
--init-reg
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/reg.init.dat
--out-reg
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/bbr.pass1.dat
--subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4
--gm-proj-frac 0.5 --gm-gt-wm 0.5
sysname Linux
hostname compute-0-54.local
machine x86_64
user tori
movvol
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/template.nii
regfile
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/reg.init.dat
subject CVRAM_1045_recon
dof 6
outregfile
/autofs/space/orion_002/users/DTI/CVRAM_1045_dti/tmp.bbregister.27403/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
DoPowell 1
TolPowell 0.000100
nMaxItersPowell 36
n1dmin 3
Profile 0
Gdiag_no -1
AddNoise 0 (0)
SynthSeed 1252146426
TransRandMax 0.000000
RotRandMax 0.000000
Translations 0.000000 0.000000 0.000000
Rotations 0.000000 0.000000 0.000000
Input reg
1.000 -0.004 -0.003 -0.775;
0.003 -0.001 1.000 -19.179;
-0.004 -1.000 -0.001 -13.297;
0.000 0.000 0.000 1.000;
Loading mov
Loading lh.white surf
Loading lh.thickness for GM
GM Proj: 1 0.500000 2.000000
WM Proj: 0 0.500000 2.000000
Projecting LH Surfs
Projecting RH Surfs
Loading rh.white surf
Loading rh.thickness
Logfile for bbregister
Mon Aug 24 17:10:21 EDT 2009
setenv SUBJECTS_DIR /autofs/space/lang_012/users/CVRAM
cd /autofs/space/orion_002/users/DTI/SCRIPTS
/usr/local/freesurfer/dev/bin/bbregister --s CVRAM_1046_recon --mov
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/preTBSS_0.4thresh-LAS/lowb-swap.nii.gz
--dti --init-fsl --reg
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/CVRAM_1046_lowb-to-anat.reg
$Id: bbregister,v 1.30 2009/08/07 22:20:40 greve Exp $
Linux compute-0-54.local 2.6.18-53.1.19.el5 #1 SMP Tue Apr 22 03:01:10 EDT 2008
x86_64 x86_64 x86_64 GNU/Linux
FREESURFER_HOME /usr/local/freesurfer/dev
mri_convert
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/preTBSS_0.4thresh-LAS/lowb-swap.nii.gz
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/template.nii
mri_convert
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/preTBSS_0.4thresh-LAS/lowb-swap.nii.gz
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/template.nii
$Id: mri_convert.c,v 1.159 2009/07/15 18:52:28 greve Exp $
reading from
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/preTBSS_0.4thresh-LAS/lowb-swap.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 1.86265e-09, 0)
j_ras = (0, 1, 7.45058e-09)
k_ras = (-7.45058e-09, -7.45058e-09, 1)
writing to
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/template.nii...
fslregister --s CVRAM_1046_recon --mov
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/template.nii
--reg
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/reg.init.dat
--niters 1 --maxangle 90 --nobetmov --tmp
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/fslregister
--dof 6
Log file is
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/reg.init.dat.fslregister.log
Mon Aug 24 17:10:22 EDT 2009
--s CVRAM_1046_recon --mov
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/template.nii
--reg
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/reg.init.dat
--niters 1 --maxangle 90 --nobetmov --tmp
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/fslregister
--dof 6
$Id: fslregister,v 1.29 2009/07/31 22:22:46 greve Exp $
compute-0-54.local
Linux compute-0-54.local 2.6.18-53.1.19.el5 #1 SMP Tue Apr 22 03:01:10 EDT 2008
x86_64 x86_64 x86_64 GNU/Linux
nIters 1
--------------------------------------
/autofs/space/orion_002/users/DTI/SCRIPTS
mri_convert
/autofs/space/lang_012/users/CVRAM/CVRAM_1046_recon/mri/brainmask.mgz
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/fslregister/refvol.fslregister.nii
mri_convert
/autofs/space/lang_012/users/CVRAM/CVRAM_1046_recon/mri/brainmask.mgz
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/fslregister/refvol.fslregister.nii
$Id: mri_convert.c,v 1.159 2009/07/15 18:52:28 greve Exp $
reading from
/autofs/space/lang_012/users/CVRAM/CVRAM_1046_recon/mri/brainmask.mgz...
TR=2730.00, TE=3.31, TI=1000.00, flip angle=7.00
i_ras = (-1, 6.48571e-10, -2.03171e-09)
j_ras = (-6.45517e-09, 1.95524e-10, -1)
k_ras = (-2.3879e-10, 1, -6.07039e-10)
writing to
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/fslregister/refvol.fslregister.nii...
--------------------------------------
/autofs/space/orion_002/users/DTI/SCRIPTS
mri_convert
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/template.nii
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/fslregister/movvol.fslregister.nii
--frame 0
mri_convert
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/template.nii
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/fslregister/movvol.fslregister.nii
--frame 0
$Id: mri_convert.c,v 1.159 2009/07/15 18:52:28 greve Exp $
reading from
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/template.nii...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 1.86265e-09, 0)
j_ras = (0, 1, 7.45058e-09)
k_ras = (-7.45058e-09, -7.45058e-09, 1)
keeping frame 0
writing to
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/fslregister/movvol.fslregister.nii...
/autofs/space/orion_002/users/DTI/SCRIPTS
tkregister2_cmdl --mov
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/fslregister/movvol.fslregister.nii
--reg
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/fslregister/reg0.27601.dat
--regheader --fslregout
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/reg.init.dat.fsl.mat0
--s CVRAM_1046_recon --noedit
tkregister_tcl /usr/local/freesurfer/dev/lib/tcl/tkregister2.tcl
INFO: no target volume specified, assuming FreeSurfer orig volume.
target volume orig
movable volume
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/fslregister/movvol.fslregister.nii
reg file
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/fslregister/reg0.27601.dat
LoadVol 0
ZeroCRAS 0
$Id: tkregister2.c,v 1.108 2009/04/02 17:14:46 mreuter Exp $
Diagnostic Level -1
INFO: loading target
/autofs/space/lang_012/users/CVRAM/CVRAM_1046_recon/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
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/fslregister/movvol.fslregister.nii
Tmov: --------------------
-2.000 0.000 0.000 128.000;
0.000 0.000 2.000 -60.000;
0.000 -2.000 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) --------
1.000 -0.000 0.000 -3.668;
0.000 -0.000 1.000 -25.734;
-0.000 -1.000 -0.000 -3.235;
0.000 0.000 0.000 1.000;
---------------------------------------
---- Input registration matrix --------
1.000 -0.000 0.000 -3.668;
0.000 -0.000 1.000 -25.734;
-0.000 -1.000 -0.000 -3.235;
0.000 0.000 0.000 1.000;
Determinant 1
subject = CVRAM_1046_recon
RegMat ---------------------------
1.000 -0.000 0.000 -3.668;
0.000 -0.000 1.000 -25.734;
-0.000 -1.000 -0.000 -3.235;
0.000 0.000 0.000 1.000;
register: file
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/fslregister/reg0.27601.dat
written
FSLOUTPUTTYPE NIFTI
tkreg2FSL: mov det = -8, ref det = -1
Mon Aug 24 17:10:26 EDT 2009
/autofs/space/orion_002/users/DTI/SCRIPTS
flirt -ref
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/fslregister/refvol.fslregister.nii
-in
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/fslregister/movvol.fslregister.nii
-bins 256 -omat
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/reg.init.dat.fsl.mat
-cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90
-verbose 0 -schedule
/usr/local/freesurfer/dev/bin/flirt.newdefault.20080811.sch -init
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/reg.init.dat.fsl.mat0
tkregister2_cmdl --s CVRAM_1046_recon --mov
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/template.nii
--reg
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/reg.init.dat
--fslreg
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/reg.init.dat.fsl.mat
--noedit
tkregister_tcl /usr/local/freesurfer/dev/lib/tcl/tkregister2.tcl
---- FSL registration matrix --------
1.000 -0.009 -0.004 -3.309;
-0.004 0.003 -1.000 162.838;
0.009 1.000 0.003 -4.390;
0.000 0.000 0.000 1.000;
---------------------------------------
INFO: no target volume specified, assuming FreeSurfer orig volume.
target volume orig
movable volume
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/template.nii
reg file
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/reg.init.dat
LoadVol 0
ZeroCRAS 0
$Id: tkregister2.c,v 1.108 2009/04/02 17:14:46 mreuter Exp $
Diagnostic Level -1
INFO: loading target
/autofs/space/lang_012/users/CVRAM/CVRAM_1046_recon/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
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/template.nii
Tmov: --------------------
-2.000 0.000 0.000 128.000;
0.000 0.000 2.000 -60.000;
0.000 -2.000 0.000 128.000;
0.000 0.000 0.000 1.000;
mkheaderreg = 0, float2int = 0
FSLOUTPUTTYPE NIFTI
fsl2TkReg: mov det = -8, ref det = -1
---- Input registration matrix (computed) --------
1.000 -0.009 -0.004 -4.609;
0.004 0.003 1.000 -25.289;
-0.009 -1.000 0.003 -3.122;
0.000 0.000 0.000 1.000;
---------------------------------------
---- Input registration matrix --------
1.000 -0.009 -0.004 -4.609;
0.004 0.003 1.000 -25.289;
-0.009 -1.000 0.003 -3.122;
0.000 0.000 0.000 1.000;
Determinant 1
subject = CVRAM_1046_recon
RegMat ---------------------------
1.000 -0.009 -0.004 -4.609;
0.004 0.003 1.000 -25.289;
-0.009 -1.000 0.003 -3.122;
0.000 0.000 0.000 1.000;
register: file
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/reg.init.dat
written
(standard_in) 1: illegal character: V
(standard_in) 1: illegal character: R
(standard_in) 1: parse error
(standard_in) 1: illegal character: M
(standard_in) 1: illegal character: _
(standard_in) 1: illegal character: _
Started at Mon Aug 24 17:10:23 EDT 2009
Ended at Mon Aug 24 17:10:52 EDT 2009
fslregister Done
To check results, run:
tkregister2 --mov
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/template.nii
--reg
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/reg.init.dat
--surf orig
mri_segreg --mov
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/template.nii
--init-reg
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/reg.init.dat
--out-reg
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/bbr.pass1.dat
--subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4
--gm-proj-frac 0.5 --gm-gt-wm 0.5
$Id: mri_segreg.c,v 1.84 2009/07/21 14:15:11 fischl Exp $
setenv SUBJECTS_DIR /autofs/space/lang_012/users/CVRAM
cd /autofs/space/orion_002/users/DTI/SCRIPTS
mri_segreg --mov
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/template.nii
--init-reg
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/reg.init.dat
--out-reg
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/bbr.pass1.dat
--subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4
--gm-proj-frac 0.5 --gm-gt-wm 0.5
sysname Linux
hostname compute-0-54.local
machine x86_64
user tori
movvol
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/template.nii
regfile
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/reg.init.dat
subject CVRAM_1046_recon
dof 6
outregfile
/autofs/space/orion_002/users/DTI/CVRAM_1046_dti/tmp.bbregister.27559/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
DoPowell 1
TolPowell 0.000100
nMaxItersPowell 36
n1dmin 3
Profile 0
Gdiag_no -1
AddNoise 0 (0)
SynthSeed 1251425381
TransRandMax 0.000000
RotRandMax 0.000000
Translations 0.000000 0.000000 0.000000
Rotations 0.000000 0.000000 0.000000
Input reg
1.000 -0.009 -0.004 -4.609;
0.004 0.003 1.000 -25.289;
-0.009 -1.000 0.003 -3.122;
0.000 0.000 0.000 1.000;
Loading mov
Loading lh.white surf
Loading lh.thickness for GM
GM Proj: 1 0.500000 2.000000
WM Proj: 0 0.500000 2.000000
Projecting LH Surfs
Projecting RH Surfs
Loading rh.white surf
Loading rh.thickness
*** glibc detected *** mri_segreg: free(): invalid next size (normal):
0x000000002daf0d40 ***
======= Backtrace: =========
/lib64/libc.so.6[0x3e42e6f4f4]
/lib64/libc.so.6(cfree+0x8c)[0x3e42e72b1c]
mri_segreg[0x433c1e]
mri_segreg[0x433e3d]
mri_segreg[0x42d1a3]
mri_segreg(vfprintf+0x2b08)[0x40c490]
mri_segreg(vfprintf+0x3253)[0x40cbdb]
mri_segreg[0x40f6a7]
/lib64/libc.so.6(__libc_start_main+0xf4)[0x3e42e1d8a4]
mri_segreg(__gxx_personality_v0+0x172)[0x40abfa]
======= Memory map: ========
00400000-00adc000 r-xp 00000000 00:1f 2868262
/autofs/space/freesurfer/centos4.0_x86_64/dev/bin/mri_segreg
00bdc000-00c61000 rw-p 006dc000 00:1f 2868262
/autofs/space/freesurfer/centos4.0_x86_64/dev/bin/mri_segreg
00c61000-02423000 rw-p 00c61000 00:00 0
1b95a000-2db11000 rw-p 1b95a000 00:00 0
3e42a00000-3e42a1a000 r-xp 00000000 08:02 14291920
/lib64/ld-2.5.so
3e42c19000-3e42c1a000 r--p 00019000 08:02 14291920
/lib64/ld-2.5.so
3e42c1a000-3e42c1b000 rw-p 0001a000 08:02 14291920
/lib64/ld-2.5.so
3e42e00000-3e42f46000 r-xp 00000000 08:02 14291921
/lib64/libc-2.5.so
3e42f46000-3e43146000 ---p 00146000 08:02 14291921
/lib64/libc-2.5.so
3e43146000-3e4314a000 r--p 00146000 08:02 14291921
/lib64/libc-2.5.so
3e4314a000-3e4314b000 rw-p 0014a000 08:02 14291921
/lib64/libc-2.5.so
3e4314b000-3e43150000 rw-p 3e4314b000 00:00 0
3e43200000-3e43202000 r-xp 00000000 08:02 14291922
/lib64/libdl-2.5.so
3e43202000-3e43402000 ---p 00002000 08:02 14291922
/lib64/libdl-2.5.so
3e43402000-3e43403000 r--p 00002000 08:02 14291922
/lib64/libdl-2.5.so
3e43403000-3e43404000 rw-p 00003000 08:02 14291922
/lib64/libdl-2.5.so
3e43600000-3e43615000 r-xp 00000000 08:02 14291926
/lib64/libpthread-2.5.so
3e43615000-3e43814000 ---p 00015000 08:02 14291926
/lib64/libpthread-2.5.so
3e43814000-3e43815000 r--p 00014000 08:02 14291926
/lib64/libpthread-2.5.so
3e43815000-3e43816000 rw-p 00015000 08:02 14291926
/lib64/libpthread-2.5.so
3e43816000-3e4381a000 rw-p 3e43816000 00:00 0
3e44200000-3e44282000 r-xp 00000000 08:02 14291700
/lib64/libm-2.5.so
3e44282000-3e44481000 ---p 00082000 08:02 14291700
/lib64/libm-2.5.so
3e44481000-3e44482000 r--p 00081000 08:02 14291700
/lib64/libm-2.5.so
3e44482000-3e44483000 rw-p 00082000 08:02 14291700
/lib64/libm-2.5.so
3e44a00000-3e44a14000 r-xp 00000000 08:02 1312743
/usr/lib64/libz.so.1.2.3
3e44a14000-3e44c13000 ---p 00014000 08:02 1312743
/usr/lib64/libz.so.1.2.3
3e44c13000-3e44c14000 rw-p 00013000 08:02 1312743
/usr/lib64/libz.so.1.2.3
3e44e00000-3e44e0d000 r-xp 00000000 08:02 14291931
/lib64/libgcc_s-4.1.2-20070626.so.1
3e44e0d000-3e4500d000 ---p 0000d000 08:02 14291931
/lib64/libgcc_s-4.1.2-20070626.so.1
3e4500d000-3e4500e000 rw-p 0000d000 08:02 14291931
/lib64/libgcc_s-4.1.2-20070626.so.1
3e45200000-3e45205000 r-xp 00000000 08:02 14291934
/lib64/libcrypt-2.5.so
3e45205000-3e45404000 ---p 00005000 08:02 14291934
/lib64/libcrypt-2.5.so
3e45404000-3e45405000 r--p 00004000 08:02 14291934
/lib64/libcrypt-2.5.so
3e45405000-3e45406000 rw-p 00005000 08:02 14291934
/lib64/libcrypt-2.5.so
3e45406000-3e45434000 rw-p 3e45406000 00:00 0
3e45600000-3e456e6000 r-xp 00000000 08:02 1312308
/usr/lib64/libstdc++.so.6.0.8
3e456e6000-3e458e5000 ---p 000e6000 08:02 1312308
/usr/lib64/libstdc++.so.6.0.8
3e458e5000-3e458eb000 r--p 000e5000 08:02 1312308
/usr/lib64/libstdc++.so.6.0.8
3e458eb000-3e458ee000 rw-p 000eb000 08:02 1312308
/usr/lib64/libstdc++.so.6.0.8
3e458ee000-3e45900000 rw-p 3e458ee000 00:00 0
2aaaaaaab000-2aaaaaaae000 rw-p 2aaaaaaab000 00:00 0
2aaaaaabe000-2aaaaaac3000 rw-p 2aaaaaabe000 00:00 0
2aaaaaac3000-2aaaaaacd000 r-xp 00000000 08:02 14291676
/lib64/libnss_files-2.5.so
2aaaaaacd000-2aaaaaccc000 ---p 0000a000 08:02 14291676
/lib64/libnss_files-2.5.so
2aaaaaccc000-2aaaaaccd000 r--p 00009000 08:02 14291676
/lib64/libnss_files-2.5.so
2aaaaaccd000-2aaaaacce000 rw-p 0000a000 08:02 14291676
/lib64/libnss_files-2.5.so
2aaaaacce000-2aaabdc24000 rw-p 2aaaaacce000 00:00 0
2aaac0000000-2aaac0021000 rw-p 2aaac0000000 00:00 0
2aaac0021000-2aaac4000000 ---p 2aaac0021000 00:00 0
7fffbe9a9000-7fffbe9c0000 rw-p 7fffbe9a9000 00:00 0 [stack]
ffffffffff600000-ffffffffffe00000 ---p 00000000 00:00 0 [vdso]
Projecting RH Surfs
Computing relative cost
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