Hi everyone! Through longitudinal assessments, I aim to evaluate differences between healthy and transgenic 5XFAD mice using magnetic resonance imaging (MRI), behavioral testing, frailty index scoring, and biochemical analyses. Last year, when I completed my undergraduate thesis, we decided to use…

This older post might help. [image] Results of fmriprep-rodents Software Support Hi @eeee - First, I should point out that the WHS template is a rat template, not a mouse template, and I’ve found that the size difference is too large for registration algorith…

Thanks. Over the past week I have been doing a lot of reading on what’s available for mouse brain co-regsitration. For anyone else that is interested, I would recommend looking into AIDAmri. here is the githubhttps://github.com/Aswendt-Lab/AIDAmri

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). [image] Results of fmriprep-rodents Software Suppo…

Co-registration of MRI to Allen Mouse Brain Atlas

Software Support

dglen November 13, 2025, 10:38pm 2

This older post might help.