bbregister error with hardi data - Freesurfer

25 Mar 2013

Hi Corinna, can you run

fslregister --debug --s lindsay --mov
hardi/ffiltered_func_data_01.nii.gz --reg fsl.reg.dat --niters 1
--maxangle 90 --nobetmov --tmp ./tmp.fslregister --dof 6 --fsvol
brainmask |& tee dng.log

and send me the dng.log?

doug

On 03/25/2013 12:39 PM, Corinna Bauer wrote:
> 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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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 <tel:617-724-2358>
Fax: 617-726-7422 <tel:617-726-7422>

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