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