MouseFlow pipeline is developed by the Sherbrooke Connectivity Imaging Lab (SCIL) and Neurofunctional Imaging Group (GIN-IMN) in order to process diffusion MRI dataset from the raw data to the tractography.

Using on diffusion data MouseFlow is a nextflow pipeline based on nf-neuro.

It incorporates essential steps: denoising, corrections of some artefacts, registration to a template (Allen Mouse Brain Atlas), the DTI and QBall reconstructions, extraction of some metrics, until constructing a whole brain tractogram of the mouse brain and extracting some bundles. It is capable of adapting the resolution of the atlas according to the native data, for better anatomical alignment.

⚠️ WARNING ⚠️

This pipeline is currently in development. We highly encourage everyone to give it a try and give us feedback and raise issues if any.

In development features (non exhaustive list)

• BIDS compliant
• Meta metric QC across mouses