Hi Josh,
I'm guessing that it's not simply a matter of a strange display range
in your image viewer, but it's worth checking that.
Otherwise, my guess is that the order in the bvecs/bvals files do not
match the volume order of the data.
Cheers,
Paul
On 09/10/2018, 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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