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Hi Josh,

Can you share the dtifit command you used, and some screenshots of the
inputs and the resulting FA map?

Cheers,
Paul

On 08/10/2018, Josh Robinson <[log in to unmask]> wrote:
> Hello FSL experts,
>
> I am trying to run dtifit on my data, and it runs through with no errors,
> but when I open the FA map, it looks like it just returned my brain mask. I
> have seen that others have run into this problem before, but none of the
> solutions for them seem to be working here.
>
> Our acquisition is a little old, and includes getting to two identical DTI
> acquisitions with one b0 and 30 directions each. These scans were
> concatenated and run through eddy. The bvals and bvecs files were also
> concatenated (in the same order), in a 3x62 matrix, with the 0s
> corresponding to the b0s in the data (the last volume of each scan). I have
> made sure these files end with the appropriate carriage, I have checked my
> output data from eddy as well as the brain mask and both look normal, and
> running the data through bedpostx_datacheck returns the following:
>
> bedpost/data
> data_type      FLOAT32
> dim1           256
> dim2           256
> dim3           60
> dim4           62
> datatype       16
> pixdim1        0.828000
> pixdim2        0.828000
> pixdim3        2.200000
> pixdim4        1.000000
> cal_max        0.0000
> cal_min        0.0000
> file_type      NIFTI-1+
>
> bedpost/nodif_brain_mask
> data_type      INT16
> dim1           256
> dim2           256
> dim3           60
> dim4           1
> datatype       4
> pixdim1        0.828000
> pixdim2        0.828000
> pixdim3        2.200000
> pixdim4        1.000000
> cal_max        1.0000
> cal_min        0.0000
> file_type      NIFTI-1+
>
>  num lines in bedpost/bvals
> 1
>  num words in bedpost/bvals
> 62
>  num lines in bedpost/bvecs
> 3
>  num words in bedpost/bvecs
> 186
>
> I am wondering if using two scans with the same acquisition is introducing
> this issue? Otherwise my money is on an error being in the bvecs file,
> however after running through eddy successfully I don't know what. Any help
> is much appreciated!
>
> Josh Robinson
>
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