Macapype: external pipeline

Project info

Title: Macapype: external pipelines

Project lead and collaborators:

• David Meunier
• Kepkee Loh
• Julien Sein
• Bastien Cagna
• Olivier Coulon

Description: Macapype is a python package based on nipype, wrapping the tools required for NHP MRI anatomical segmentation. Macapype provide several processing pipelines, allowing optimisation and adaptation, depending on the quality of the images (SNR), acquisition sequences and antenna types, as well as species. Today, macapype is provided as a github repo, a pip install, and a docker/singularity image. The accepted inputs have to be in BIDS format, and macapype pipelines are callable thanks to a command line interface (CLI).

Links : Macapype Github: https://github.com/Macatools/macapype Macapype Documentation: https://macatools.github.io/macapype/index.html

Goals for Brainhack Marseille Macapype is mostly oriented to PNH anatomical segmentation. However, many applications can be included starting from a good segmentation quality :

• ACT (anatomically contrained tractography) from diffusion data,
• mesh and surfaces generation that are not pure PNH but that are useful to be linked to macapype segementation. We would like to discuss the possibility of integration of this tools as external pipelines, i.e. not directly part of macapype, but that can be added in global workflows based on nipype.

Putative schedule :

• Monday 6th of December , 2pm (Central Europe Time): presentation of macapype, past and future functionalities
• Tuesday 7th of December, 2pm (CET) : diffusion and tractography of PNH data : discussion, and strategies

Communication channels:

• mattermost: https://mattermost.brainhack.org/brainhack/channels/primedre-brainhack-2021-macapype
• zoom channel: https://univ-amu-fr.zoom.us/j/94628657623?pwd=bG5ZdnArcEtLanVNcktFSjdaMG5OUT09

Required skills :

• PNH anatomical MRI processing 30-100 %
• Python 50-100 %
• Nipype 30-100 %

Good first issues : Wrapping in nipype a script to reorient anatomical image to normalized orientation

Striking Image