Neuropycon

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

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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.

ephypype

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:

Installation

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

Freesurfer

  1. Download Freesurfer software:

https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall

  1. Follow the Installation instructions

https://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall