sf-mouse 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 sf-mouse 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.

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

• BIDS compliant
• Meta metric QC across mouses