Neuropycon is an open-source multi-modal brain data analysis kit which provides Python-based pipelines for advanced multi-thread processing of fMRI, MEG and EEG data, with a focus on connectivity and graph analyses. Neuropycon 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.

Neuropycon project includes two different packages:

  • ephypype based on MNE python includes pipelines for electrophysiology analysis
  • graphpype based on radatools includes pipelines for graph theoretical analysis of neuroimaging data

Neuropycon provides a very common and fast framework to develop workflows for advanced analyses, in particular defines a set of different pipelines that can be used stand-alone or as lego of a bigger workflow: the input of a pipeline will be the output of another pipeline.

For each possible workflow the input data can be specified in three different ways:

  • raw MEG data in .fif and .ds format
  • time series of connectivity matrices in .mat (Matlab) or .npy (Numpy) format
  • connectivity matrices in .mat (Matlab) or .npy (Numpy) format

Main inputs and subsequent pipeline steps

Each pipeline based on nipype engine is defined by nodes connected together, where each node maybe wrapping of existing software (as MNE-python modules or radatools functions) as well as providing easy ways to implement function defined by the user.

We also provide neuropycon with a Command Line Interface (CLI) that up to now wraps only some of the functionality of the ephypype package but will be expanded in the future. A detailed explanation of the command line interface operation principles and examples can be found here.


The ephypype package includes pipelines for electrophysiology analysis. It’s based mainly on MNE-Python package, as well as more standard python libraries such as Numpy and Scipy. Current implementations allow for

  • MEG/EEG data import
  • MEG/EEG data pre-processing and cleaning by an automatic removal of eyes and heart related artifacts
  • sensor or source-level connectivity analyses

The ephypype package provides the following pipelines:


ephypype works with python3

  • mne>0.14
  • nipype
  • h5py

These dependencies are automatically installed during ephypype installation.

We also recommend to install MNE python by following the MNE python installation instructions.

Install ephypype

$ pip install ephypype


  1. Download Freesurfer software:

  1. Follow the Installation instructions