Hi Chris,

Is it possible to use a custom atlas with mri_reface? I know the -faceMask argument will accept a custom set of masks. I would like to replace the group mean T1w image, from which the replacement voxels are taken. If there isn't a CLI argument for this, is there another way to swap out the images at runtime?

What I'm trying to do is match the intensity profile, as the replacement voxels from the MCALT atlas tend to be brighter than those in my dataset. So I can achieve this even if the atlases match spatially. I see the MCALT atlas repo includes the steps to create the atlas. It looks similar to what I've done before with DARTEL, with an intensity adjustment step. So assuming I can create the atlas, can I use it with mri_reface?

Many thanks

Paul