Template registration in murine models of disease

Dear AFNI community,

I am writing to seek advice when it comes to an experiment we are performing using a mouse model of vascular lesions in the cerebellum. Our mice, an established model of the disease Cerebral Cavernous Malformation, develop hallmark large popcorn-shaped lesions primarily in the cerebellum. In a pilot experiment, the lesions appear hypointense on a multi-echo GRE scan.

Our lab would like to track the development of these lesions over time, and I anticipate that the workflow for processing the images would require skull-stripping and template registration first to a reference template (I have thought to use the allen brain waxholm 2014 atlas) and then for each subject over time as the lesions grow.

I guess I would expect to use @animal_warper here, but then I was wondering if the large lesions, which turn the cerebellum into swiss-cheese, will interfere with the registration process.

I would be grateful for any advice. I would like to avoid potential pitfalls, and to figure out the best approach before collecting a bunch of data.

Thanks for your time and your expertise.



Regarding the swiss cheese part, that will be problematic possibly for the nonlinear alignment. You might start with just an affine alignment to a template to start, where I would expect the “holiness” of the cerebellum not to have a big enough influence on the optimum, single affine matrix transformation for the whole volume. Another approach is to limit the nonlinear alignment to just the initial stages with -maxlev. Alternatively mask the cerebellum off before the alignment or make it an exclusion mask in the nonlinear warping step.