Hello all,
I am attempting to run bbregister on 4D HARDI data that has already been
motion, eddy, and epi-distortion corrected in fsl. I run the command:
bbregister --s lindsay --mov hardi/ffiltered_func_data_01.nii.gz --dti
--init-fsl --reg register.dat and get a number of errors that seem to begin
in the mri_convert section as seen below.
Any insight?
Cheers,
Corinna
FREESURFER_HOME /usr/local/freesurfer
mri_convert hardi/ffiltered_func_data_01.nii.gz
./tmp.bbregister.15356/template.nii
mri_convert hardi/ffiltered_func_data_01.nii.gz
./tmp.bbregister.15356/template.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from hardi/ffiltered_func_data_01.nii.gz...
TR=17843.91, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.991204, -0.025762, 0.129811)
j_ras = (-0.0259819, 0.999662, 0)
k_ras = (0.129768, 0.00337275, 0.991539)
writing to ./tmp.bbregister.15356/template.nii...
fslregister --s lindsay --mov ./tmp.bbregister.15356/template.nii --reg
./tmp.bbregister.15356/reg.init.dat --niters 1 --maxangle 90 --nobetmov
--tmp ./tmp.bbregister.15356/fslregister --dof 6 --fsvol brainmask
Log file is ./tmp.bbregister.15356/reg.init.dat.fslregister.log
Mon Mar 25 12:22:23 EDT 2013
--s lindsay --mov ./tmp.bbregister.15356/template.nii --reg
./tmp.bbregister.15356/reg.init.dat --niters 1 --maxangle 90 --nobetmov
--tmp ./tmp.bbregister.15356/fslregister --dof 6 --fsvol brainmask
$Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $
lotfi
Linux lotfi 3.2.0-38-generic #61-Ubuntu SMP Tue Feb 19 12:18:21 UTC 2013
x86_64 x86_64 x86_64 GNU/Linux
nIters 1
--------------------------------------
/usr/local/freesurfer/subjects/symmetry/lindsay
mri_convert ERROR: could not determine file for
/usr/local/freesurfer/subjects/symmetry/lindsay/mri/ERROR:
./tmp.bbregister.15356/fslregister/refvol.fslregister.nii
mri_convert ERROR: could not determine file for
/usr/local/freesurfer/subjects/symmetry/lindsay/mri/ERROR:
./tmp.bbregister.15356/fslregister/refvol.fslregister.nii
mri_convert: extra arguments ("not" and following)
type mri_convert -u for usage
--------------------------------------
/usr/local/freesurfer/subjects/symmetry/lindsay
mri_convert ./tmp.bbregister.15356/template.nii
./tmp.bbregister.15356/fslregister/movvol.fslregister.nii --frame 0
mri_convert ./tmp.bbregister.15356/template.nii
./tmp.bbregister.15356/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 ./tmp.bbregister.15356/template.nii...
TR=17843.91, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.991204, -0.025762, 0.129811)
j_ras = (-0.0259819, 0.999662, 0)
k_ras = (0.129768, 0.00337275, 0.991539)
keeping frame 0
writing to ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii...
Mov determinant is -6.125
/usr/local/freesurfer/subjects/symmetry/lindsay
tkregister2_cmdl --mov
./tmp.bbregister.15356/fslregister/movvol.fslregister.nii --reg
./tmp.bbregister.15356/fslregister/reg0.15393.dat --regheader --fslregout
./tmp.bbregister.15356/reg.init.dat.fsl.mat0 --s lindsay --noedit
tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl
INFO: no target volume specified, assuming FreeSurfer orig volume.
target volume orig
movable volume ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii
reg file ./tmp.bbregister.15356/fslregister/reg0.15393.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
/usr/local/freesurfer/subjects/symmetry/lindsay/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
./tmp.bbregister.15356/fslregister/movvol.fslregister.nii
Tmov: --------------------
-1.750 0.000 0.000 112.000;
0.000 0.000 2.000 -60.000;
0.000 -1.750 0.000 112.000;
0.000 0.000 0.000 1.000;
mkheaderreg = 1, float2int = 0
Computing reg from header (and possibly input matrix)
---- Input registration matrix (computed) --------
0.991 0.026 -0.130 2.508;
0.130 0.003 0.992 -30.941;
0.026 -1.000 -0.000 1.279;
0.000 0.000 0.000 1.000;
---------------------------------------
---- Input registration matrix --------
0.991 0.026 -0.130 2.508;
0.130 0.003 0.992 -30.941;
0.026 -1.000 -0.000 1.279;
0.000 0.000 0.000 1.000;
Determinant 1
subject = lindsay
RegMat ---------------------------
0.991 0.026 -0.130 2.508;
0.130 0.003 0.992 -30.941;
0.026 -1.000 -0.000 1.279;
0.000 0.000 0.000 1.000;
FSLOUTPUTTYPE NIFTI
tkreg2FSL: mov det = -6.125, ref det = -1
Mon Mar 25 12:22:34 EDT 2013
/usr/local/freesurfer/subjects/symmetry/lindsay
flirt.fsl -ref ./tmp.bbregister.15356/fslregister/refvol.fslregister.nii
-in ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii -bins 256
-cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90
-verbose 0 -omat ./tmp.bbregister.15356/fslregister/fslmat0.trans.mat
-schedule /usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init
./tmp.bbregister.15356/reg.init.dat.fsl.mat0
** ERROR (nifti_image_read): failed to find header file for
'./tmp.bbregister.15356/fslregister/refvol.fslregister'
** ERROR:
nifti_image_open(./tmp.bbregister.15356/fslregister/refvol.fslregister):
bad header info
ERROR: failed to open file
./tmp.bbregister.15356/fslregister/refvol.fslregister
ERROR: Could not open image
./tmp.bbregister.15356/fslregister/refvol.fslregister
Image Exception : #22 :: Failed to read volume
./tmp.bbregister.15356/fslregister/refvol.fslregister.nii
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Abort (core dumped)
Mon Mar 25 12:22:34 EDT 2013
/usr/local/freesurfer/subjects/symmetry/lindsay
flirt.fsl -ref ./tmp.bbregister.15356/fslregister/refvol.fslregister.nii
-in ./tmp.bbregister.15356/fslregister/movvol.fslregister.nii -bins 256
-cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90
-verbose 0 -omat ./tmp.bbregister.15356/reg.init.dat.fsl.mat -init
./tmp.bbregister.15356/fslregister/fslmat0.trans.mat -schedule
/usr/local/freesurfer/bin/flirt.newdefault.20080811.sch
** ERROR (nifti_image_read): failed to find header file for
'./tmp.bbregister.15356/fslregister/refvol.fslregister'
** ERROR:
nifti_image_open(./tmp.bbregister.15356/fslregister/refvol.fslregister):
bad header info
ERROR: failed to open file
./tmp.bbregister.15356/fslregister/refvol.fslregister
ERROR: Could not open image
./tmp.bbregister.15356/fslregister/refvol.fslregister
Image Exception : #22 :: Failed to read volume
./tmp.bbregister.15356/fslregister/refvol.fslregister.nii
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Abort (core dumped)
tkregister2_cmdl --s lindsay --mov ./tmp.bbregister.15356/template.nii
--reg ./tmp.bbregister.15356/reg.init.dat --fslreg
./tmp.bbregister.15356/reg.init.dat.fsl.mat --noedit
tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl
ERROR: cannot open ./tmp.bbregister.15356/reg.init.dat.fsl.mat
cat: ./tmp.bbregister.15356/reg.init.dat: No such file or directory
tmp: Subscript out of range.
Started at Mon Mar 25 12:22:23 EDT 2013
Ended at Mon Mar 25 12:22:34 EDT 2013
fslregister Done
To check results, run:
tkregister2 --mov ./tmp.bbregister.15356/template.nii --reg
./tmp.bbregister.15356/reg.init.dat --surf orig
mri_segreg --mov ./tmp.bbregister.15356/template.nii --init-reg
./tmp.bbregister.15356/reg.init.dat --out-reg
./tmp.bbregister.15356/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
regio_read_register(): No such file or directory
Could not open ./tmp.bbregister.15356/reg.init.dat
mri_segreg --mov ./tmp.bbregister.15356/template.nii --init-reg
./tmp.bbregister.15356/bbr.pass1.dat --out-reg register.dat --brute -0.1
0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0
--mincost register.dat.mincost --dof 6 --nmax 36 --param register.dat.param
--surf white --cur-reg ./tmp.bbregister.15356/reg.curopt.dat --gm-proj-frac
0.5 --nsub 1 --gm-gt-wm 0.5
regio_read_register(): No such file or directory
Could not open ./tmp.bbregister.15356/bbr.pass1.dat
Cleaning up
Started at Mon Mar 25 12:22:16 EDT 2013
Ended at Mon Mar 25 12:22:34 EDT 2013
BBR-Run-Time-Sec 18
bbregister Done
To check results, run:
tkregister2 --mov hardi/ffiltered_func_data_01.nii.gz --reg register.dat
--surf
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