Macapype is an open-source multi-modal brain data analysis kit which provides Python-based pipelines for advanced multi-thread processing of MRI anatomical data of NPH brain images. Macapype is based on Nipype, a tool developed in fMRI field, which facilitates data analyses by wrapping many commonly-used neuro-imaging software into a common python framework.
API, describing the different pipelines and nodes, can be found here
Choose your install¶
git clone https://github.com/Macatools/macapype.git
(see Git install)
pip install macapype
(see Pypi install)
docker pull macatools/macapype:latest
(see Docker install)
The macapype_users forum can be be found here (requires a framateam/framagit account, but should be accessible with a github or bitbucket account).
See the section Forum for more information on how to connect.
See Installation for installation on your local system if you have adequate softwares (i.e. FSL, AFNI, Ants, SPM) running on your machine/clusters.
A Dockerfile, and a docker image are also available, explanations can be found here
Running workflows can be found here
Explanations on how to modify the processing can be found here
Explanations of the various pipelines are found here
Several examples can be found here
Some useful tips to reorient and crop images here
Some advices on how to contribute to the source code can be found here
Table of contents¶
- Docker install
- How to run workflows
- Individual Parameters
- Pipeline examples
- External Pipelines
- How to contribute to the sources of the project
- Useful tips (before processing)