Title: Macapype: external pipelines
Project lead and collaborators:
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 :
Putative schedule :
Required skills :
Good first issues : Wrapping in nipype a script to reorient anatomical image to normalized orientation