Template registration in murine models of disease

[irosstopher]

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.

/Ross

[dglen]

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.