Co-registration of MRI to Allen Mouse Brain Atlas

[dglen]

In AFNI, mentioned in that thread, we have a version of the Allen mouse brain template, an alignment program that works with it (@animal_warper) and it works seamlessly with our standard FMRI pipeline analysis (afni_proc.py).

Results of fmriprep-rodents

As @eilidhmacnicol points out, mouse template alignment has some difficulties like the differences in scale that can happen between mouse subjects and the template. A couple solutions can work though - first allow for the alignment to search over a large range of scale. Another approach is to prescale the data before or as part of the alignment procedure using an approximate scale factor. In AFNI, we include those methods in @animal_warper (options -super_size, -init_scale) along with -feature_s…