Hi,
This looks right to me, although your warp output in the second line is called "my_nonlinear_T2toB0" but you've called it "my_nonlinear_transf" in subsequent lines.
All the best,
Mark
> On 21 Aug 2018, at 16:18, C. Roman <[log in to unmask]> wrote:
>
> Hi Matt + FSL Team,
>
> Thanks for your response. If possible, I'd just like to confirm the commands for moving my T2 in b0 space.
>
> flirt -ref my_b0 -in my_t2 -omat my_affine.mat
>
> fnirt --in=my_t2 --aff=my_affine.mat --cout=my_nonlinear_T2toB0 --config=my_b0
>
> applywarp --ref=my_b0 --in=my_t2 --warp=my_nonlinear_transf --out=my_warped_T2
>
>
> Then, if I eventually want to move a binary lesion mask to my b0 space, I would run the following:
>
>
> applywarp --ref=my_b0 --in=binary_lesion_mask --warp=my_nonlinear_transf --out=my_warped_lesion_mask
>
>
> Thanks for your help!
> Cristina
>
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