Dear Stefano,
You just need to do a 6 DOF registration between your diffusion
image (typically the b0 image) and a structural image of the same
subject. This can be done with a single call to FLIRT (with the -dof 6
option) and we would recommend brain extracted images in both
cases (that is, run BET if there is visible non-brain tissue in the
images in order to get rid of this).
All the best,
Mark
On 20 May 2011, at 21:56, Stefano Delli Pizzi wrote:
> Hi list,
>
> how can I change
>
> bet my_structural my_betted_structural
> flirt -ref ${FSLDIR}/data/standard/MNI152_T1_2mm_brain -in my_betted_structural -omat my_affine_transf.mat
> fnirt --in=my_structural --aff=my_affine_transf.mat --cout=my_nonlinear_transf --config=T1_2_MNI152_2mm
> applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_2mm --in=my_structural --warp=my_nonlinear_transf --out=my_warped_structural
>
> to transform for each subject dti image on a structural image?
>
> Thank in advance,
>
>
> Stefano
>
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