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)

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
• Launching a processing
  • Commands
  • Expected input data
  • Command line parameters
• Parameters
  • Adding -params
  • Advanced parameters settings
• Individual Parameters
  • Adding -indiv
  • Advanced parameters settings