Hi FSL users,

I am a PET researcher and use a dopamine D2/3 receptor ligand whose binding sites are mainly in the subcortical areas.

I wonder anyone knows if one can better spatially normalize MRIs (in terms of the subcortical areas) if one uses FSL FIRST (specifically, first_flirt), which normalize a MRI twice.

In relation to this, I would like to know how one can quantitatively evaluate if the normalized images (specifically, the subcorital areas) are closely aligned to each other (I am only able to do this visually by diplaying the images like a movie).

Thank you,

Buyean Lee