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
Paul,
The current release does not have a command-line argument to
replace the template. It's a reasonable feature to add for expert
users who can create a template that has sufficiently aligned
anatomy but want to match their specific scanners/sequences, but
it's not something I'd ever thought of, and I thank you for the
suggestion. The only way I can think of is that Matlab's compiled
binary `mri_reface` is a .zip and can be opened with .zip file
readers, so maybe you could swap in a different
MCALT_FaceTemplate_T1.nii with the same name and spatially aligned
anatomy, but I'm not sure whether or not Matlab's runtime libraries
would refuse to run it. There's probably a checksum or something
like that.
We are currently validating a new major version/feature where the replacement voxels much better match the intensity profiles of the original, and the early results are very promising. I think this will meet your needs soon-ish. For 0.3.x, it's true that sometimes the replacement face voxel intensity could be better matched in some sequences/tracers, but we've also found this to have pretty minimal effects on brain measurements and the deviations are still smaller than with other programs that don't really attempt to match the intensities in the first place.
Chris