[Freesurfer] advice in registering a binary mask to Freesurfer space.

Hi All,

I wanted to get peoples advice on the best method of registration/interpolation to use on a manually traced segmentation (and its structural) that is not in the same space and orientation as the structurals I started Freesurfer with (although they both originally came from the same image. I want to maintain the integrity of the manual traced binary mask through this registration and reslice. For a number of reasons, I do not want to take Freesurfers output to the space of the manual segmentation.

What do people think is a good technique? Flirt nearest neighbor interpolation? Something different from Freesurfer? ANTs? - Josh