Amandine,
Just get the tract indice from the atlas, next create the corresponding mask:
fslmaths atlas -thr indice -uthr indice -bin masktracts
if you want to restrict the mask to your FA skeleton do:
fslmaths atlas -thr indice -uthr indice -bin -mas mean_skeleton_mask masktracts
next use fslmeants to extract diffusion proporties within.
Best,
Arnaud
|