On 9 Oct 2018, at 13:31, Josh Robinson <[log in to unmask]> wrote:

Yes of course!

dtifit --data=data.nii.gz --out=dtifit --mask=nodif_brain_mask.nii.gz --bvecs=bvecs --bvals=bvals --save_tensor

I have also attached copies of the bvals and bvecs files as well as screenshots as the inputted nodif_brain_mask and the resulting fa map.
***I know the brain mask looks a little funky,  we were unable to run topup thanks to the acquisition so there is still some distortion in the eddy corrected data, but this is not yet for the purposes of data analysis so much as it is an attempt at seeing how we can implement the FSL toolbox to our data.

Thank you in advance,

Josh



On Tue, 9 Oct 2018 09:51:16 +0100, paul mccarthy <[log in to unmask]> wrote:

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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<bvecs><bvals><fa map.jpg><nodif_brain_mask.jpg>