You interpreted correctly. When I set the DTIFit files manually and using
nodif_brain_mask_mask instead of nodif_brain_mask, all works just fine.
Thanks! Off and running ...
Gary
On Mon, 5 Dec 2005, Tim Behrens wrote:
> 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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