The allen brain atlas provides a reference 3d model for the p56 mouse brain. I looked at the paper by yushkevich et. al. detailing the algorithm which they follow. I would like to follow a similar approach to develop the 3d atlas for mouse brain at p7. I know this is kind of a vague question but if i just follow the approach detailed in the paper will my reconstruction be theoretically as good if everything goes perfectly or is there too much effort required for such an endeavor and im better off extrapolating annotations and structure from the p4 mouse. I dont have a reference 3d mri volume either but the approach followed in the paper doesnt look too complicated especially with the sitk toolkit in python which does most of the heavy lifting. I tried looking for the code for the data processing pipeline which allen brain uses for creating the 3d model but i couldnt find it is it available online somewhere
I noticed that there is a p4 and p14 dataset available to go to a 3d p7 atlas if i just do some kind of diffeomorphic registration to a p7 atlas mri volume(assuming i get it ) will the annotations and structures still make sense (sorry for being such a noob, assuming nothing significant happens between p4 to p7 or p7 to p14). but if i get an mri 3d volume why not just make a 3d atlas following the approach in yushkevich et.al.