Hi - is your nodif_brain_mask binary? i.e. are the brain voxels 1s?
If not, this would certainly explain the problem ( I guess this is the
problem as you seem to have a nodif_brain_mask_mask, which I suppose is
the binary one). If this isn;t the problem, then feel free to send the
bvecs/bvals files to see if anything obvious pops out for us.
Cheers
T
On Sat, 3 Dec 2005, Gary Strangman wrote:
> Hi,
>
> I'm new to FSL DTI analysis and am having trouble similar to that found in
> the "Problems with eddy_correct and dtifit" post on this list. However,
> the solution there does not appear to work for me. I have 5 b0 images plus
> 30 direction images, all in a data.hdr/.img. Directory listing is thus:
>
> bvals data.hdr DIFFUSION-infodump.dat nodif_brain_mask.img nodif.img
> bvals~ data.img DIFFUSION.mat nodif_brain_mask_mask.hdr
> bvecs DIFFUSION.hdr flf nodif_brain_mask_mask.img
> bvecs~ DIFFUSION.img nodif_brain_mask.hdr nodif.hdr
>
> bedpost_datacheck (attached below) comes up clean, I believe. All file
> creation was done on linux (no ^M isues here), and the bvecs are all
> normalized. But, when I run dtifit, every dti.* output volume is empty
> (all zeros). Any suggestions?
>
> Note, for data.hdr/.img, I've tried 2 things. In one, data.hdr and
> data.img were created via eddy_correct on DIFFUSION.hdr (which gave the
> "Warning both reference and input images have an sform matrix set"). In
> the other approach, I just copied DIFFUSION.hdr/.img to data.hdr/.img. In
> either case, fslview suggests that data.hdr is fine, though timeseries
> view on data.hdr shows the b0 images are substantially stronger signal
> strength (by a factor of 2-5, depending on the voxel).
>
> ---- Results of bedpost_datacheck -----
>
> .../diffusion/023> bedpost_datacheck ./
> .//data
> dim1 128
> dim2 128
> dim3 23
> dim4 35
> datatype 4
> pixdim1 -1.7187500000
> pixdim2 1.7187500000
> pixdim3 6.0000000000
> pixdim4 1.0000000000
> cal_max 0.0000
> cal_min 0.0000
> glmax 0
> glmin 0
> origin1 67
> origin2 83
> origin3 12
> file_type ANALYZE-7.5
>
> .//nodif
> dim1 128
> dim2 128
> dim3 23
> dim4 1
> datatype 4
> pixdim1 1.7187500000
> pixdim2 1.7187500000
> pixdim3 6.0000000000
> pixdim4 5.0000000000
> cal_max 0.0000
> cal_min 0.0000
> glmax 439
> glmin 0
> origin1 67
> origin2 83
> origin3 12
> file_type ANALYZE-7.5
>
> .//nodif_brain_mask
> dim1 128
> dim2 128
> dim3 23
> dim4 1
> datatype 4
> pixdim1 -1.7187500000
> pixdim2 1.7187500000
> pixdim3 6.0000000000
> pixdim4 5.0000000000
> cal_max 127.0000
> cal_min 0.0000
> glmax 0
> glmin 0
> origin1 67
> origin2 83
> origin3 12
> file_type ANALYZE-7.5
>
> num lines in .//bvals
> 1
> num words in .//bvals
> 35
> num lines in .//bvecs
> 3
> num words in .//bvecs
> 105
>
> Any assistance would be greatly appreciated.
>
> -best
> Gary Strangman
>
--
-------------------------------------------------------------------------------
Tim Behrens
Centre for Functional MRI of the Brain
The John Radcliffe Hospital
Headley Way Oxford OX3 9DU
Oxford University
Work 01865 222782
Mobile 07980 884537
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