I do not have that exact preprocessed version of that subject, but in the first version of preprocessed data I cannot see any problem.
Have you looked at the data to make sure that they look fine at the problematic region? By the way, I don’t think that this is related, but if you use FSL 5.0, this is ~4 years old, you should update to 5.09.
Cheers
Stam
On 12 Mar 2016, at 12:46, Verena Rozanski <[log in to unmask]> wrote:
> Dear Stam,
>
> thank you for your answer!
>
> I used the following datasets:
>
> HCP_mgh_1031_MR_ep2d_Diffusion_Gradwarped,_Eddy_Current_Corrected_Br_20141002144129918_S227836_I445964.nii.gz (renamed to „data.nii.gz“)
> mgh_1031_bvals_ep2d_eddy.txt (renamed to „bvals“)
> mgh_1031_bvecs_fsl_moco_norm_ep2d_eddy.txt (renamed to „bvecs“)
>
> and created a folder named dtifit. There, I ran the dtifit command with FSL 5.0 (/usr/share/fsl/5.0/bin/dtifit --data= mgh_1031/dtifit/data --out=mgh_1031/dtifit/dti --mask= mgh_1031/dtifit/nodif_brain_mask --bvecs=mgh_1031/dtifit/bvecs --bvals=mgh_1031/dtifit/bvals) and studies the outcome.
>
> Thank you,
> best,
>
> Verena
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