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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