I’m running several subjects from the ADNI dataset through fmriprep, and I’ve found a number of subjects where just a little too much brain is stripped off in the skull stripping (usually in the temporal an frontal regions, where the atrophy is particularly bad). This is a common problem in subjects with severe atrophy - I originally switched from using BET to fmriprep because it’s much better at it. However, it’s not perfect, and I was wondering if anybody had any better success using alternative templates.
I notice that fmriprep uses antsBrainExtraction.sh to do the skull stripping, and that it defaults to the OASIS brain template. Looking here it seems like this template is based on 15 subjects ranging in age from 19 to 34. I’m thinking that an older/wider range of subject ages might work better on AD brains. The webpage above lists 4 templates that come with antsBrainExtractor - IXI, Oasis, NKI-1 and Kirby/MMRR. fmriprep allows you to use Oasis and NKI. Is there a way to use the others? IXI in particular seems to go up to age 90, so it might be better for my purpose. Would this just involve getting IXI into templateflow, or is templateflow only for registration targets? I’d be happy to try stuffing the IXI images into templateflow, if I could then use it as a brain template.
Any other tips and tricks for stripping brains with lots of atrophy would also be welcome…