rodent_anat is an open source image pre-processing pipeline for rodent structural MRI (i.e., T2-weighted scans). It is modelled on the fsl_anat interface.
What you can do with rodent_anat
The primary purpose of rodent_anat is to provide rodent structural MRI research with a standard, flexible, and robust image processing platform, which can generalise across scanners and acquisition protocols.
rodent_anat is used in conjunction with https://github.com/SPMIC-UoN/brkraw and https://github.com/jennahanmer/DiffPreproc_rodent. https://github.com/SPMIC-UoN/brkraw is a verion of brkraw that has been modified such that it is better equipped for diffusion weighted imaging. https://github.com/jennahanmer/DiffPreproc_rodent preprocesses rodent dw-scans. It requires, as input, the T2-weighted scan and brain mask, created by rodent_anat.
Preprocessing
Development
This pipeline was developed by Jenna Hanmer, with support from Martin Craig, under the supervision of Matteo Bastiani, Stamatios Sotiropoulos, Paul Morgan & Tracy Farr. It is still a work-in-process.