Macapype

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.

Installation

See Quick Installation for installation on your local system if you have adequate softwares (i.e. FSL, AFNI, Ants, SPM) running on your machine/clusters

See Container installation for fully compliant installation (no MRI softwares, or Windows / MacOS operating system)

Once installed, see Quick test for testing if your installation is working properly

Command line parameters

macapype is fairly flexible, but requires to specify multiples parameters in command line

See Commands for a description on the avalaible command parameters

Table of contents

• Installation
  • Dependancies
  • Install macapype package
  • Testing the install
• Container install
  • Dockerfile
  • Docker image
  • Note on Singularity
• Quick test
  • Download datasets
  • Testing depending on the installation
  • Testing the macaque and baboon datasets
  • Testing different pipelines and options
• Launching a processing
  • Commands
  • Expected input data
  • Command line parameters
• Parameters
  • Adding -params
  • Advanced parameters settings
• Individual Parameters
  • Adding -indiv
  • Advanced parameters settings