micalab/micapipe repository overview

⁠Welcome to micapipe's docker!

Micapipe is a processing pipeline providing a robust framework to analyze multimodal MRI data. This pipeline integrates processing streamlines for T1-weighted, microstructure-sensitive, diffusion-weighted, and resting-state functional imaging to facilitate the development of multiscale models of neural organization. For this purpose, we leverage several specialized software packages to bring BIDS-formatted raw MRI data to fully-processed surface-based feature matrices.

⁠Reproducibility

To encourage reproducibility and robustness of investigations using micapipe, we provide a fully containerized version of the pipeline in the form of a Docker container. Step-by-step tutorials⁠ are provided for bare metal and containerized installations. We encourage users to use containerized versions, offered through Docker and Singularity, given the large number of software dependencies⁠ used by the pipeline to handle multiple MRI data modalities.

⁠Datasets

Micapipe has been tested on several locally acquired datasets, as well as openly available repositories such as Cambridge Centre for Ageing and Neuroscience (Cam-CAN)⁠, PREVENT-AD⁠, Healthy Brain Network⁠, and Microstructure-Informed Connectomis (MICs)⁠.

⁠Development and getting involved

Should you have any problems, questions, or suggestions about micapipe, please post an issue⁠ or formulate a pull request⁠ on our repository.

⁠Core development team

Micapipe is developed by MICA-lab⁠ and collaborators at the McConnell Brain Imaging Center of the Montreal Neurological Institute.

• Raúl Rodríguez-Cruces, MICA Lab - Montreal Neurological Institute
• Alex Ngo, MICA Lab - Montreal Neurological Institute
• Jessica Royer, MICA Lab - Montreal Neurological Institute
• Sara Larivière, MICA Lab - Montreal Neurological Institute
• Peer Herholz, NeuroDataScience, ORIGAMI lab - Montreal Neurological Institute
• Jordan DeKraker, MICA Lab - Montreal Neurological Institute
• Youngeun Hwang, MICA Lab - Montreal Neurological Institute
• Nicole Eichert, Jesus College, Oxford
• Yezhou Wang, MICA Lab - Montreal Neurological Institute
• Casey Paquola, MICA Lab - Montreal Neurological Institute
• Oualid Benkarim, MICA Lab - Montreal Neurological Institute
• Boris Bernhardt, MICA Lab - Montreal Neurological Institute

⁠Workflow