NeuroPycon: A python package for efficient multi-modal brain network analysis

Background. With the exponential increase in data dimension and methodological complexities, brain networks analysis with MEG and EEG has become an increasingly challenging and time-consuming endeavor. To date, performing all the data processing steps that are required for a complete MEG/EEG analysis pipeline often require the use of a multitude of software packages and in-house or custom tools (e.g. MRI segmentation, pre-processing, source reconstruction, graph theoretical analysis, statistics). This is not only cumbersome, but may also increase sources of errors and hinders replication of results. Here we describe NeuroPycon, 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 [1]. Methods. NeuroPycon is based on the NiPype framework [2] which facilitates data analyses by wrapping numerous commonly-used neuroimaging software solutions into a common python framework. NeuroPycon allows accessing and interfacing with the existing open-science neuroimaging software and signal processing toolboxes, within a unified framework relying on several freely available Python packages which are developed for efficient and fast parallel processing. The current implementation of NeuroPycon comprises three different packages: 2 of 3 - ephypype is mainly based on MNE-Python package [3] and includes pipelines for electrophysiology analyses. Current implementation features MEG/EEG data import, data pre-processing and cleaning via an automatic removal of eyes and heart-related artefacts, and sensor or source-level connectivity analyses - graphpype is based on radatools [4], a set of freely distributed applications aimed at analyses of Complex Networks. It comprises pipelines for functional connectivity studies which heavily exploit graph-theoretical metrics including among other things modular partitions - neuropycon_cli is a command line interface for the ephypype package. Notably, NeuroPycon pipelines can be used in a stand-alone mode but they can also be combined within building blocks to form a larger workflow, in which case the input of one pipeline comes from the outputs of the others. Each pipeline, based upon the nipype engine, is defined by connecting different nodes, with each node being either a user-defined function or a python-wrapped external routine (as MNE-python modules or radatools functions). Results and Discussion. NeuroPycon provides a common and fast framework to develop workflows for advanced neuroimaging data analyses. Several workflows have already been developed to analyze different datasets coming from MEG and EEG studies, such as EEG sleep data and MEG resting state measurements. Furthermore, pipelines defined in graphpype have already been used to perform graph theoretical analysis on a different fMRI datasets. Results visualisation for NeuroPycon is provided through the visbrain (http://visbrain.org/), an open-source multi-purpose python software devoted to graphical representation of neuroscientific data and built on top of VisPy [5], a high-performance visualization library leveraging GPU acceleration. NeuroPycon will shortly be available for download via github (installation via Docker) and is currently being documented (https://neuropycon.github.io/neuropycon_doc/). Future developments will include fusion of multi-modal data (ex. MEG and fMRI or iEEG and fMRI) and feature an increased compatibility with the existing Python packages of interest such as machine learning tools. References: 1. Bullmore E, Sporns O (2009), Nat Rev Neuroscience 2. Gorgolewski et al. (2011) Front. Neuroinformatics 3. Gramfort et al. (2013), Front. Neuroscience 4. http://deim.urv.cat/~sergio.gomez/radatools.php 5. Campagnola et al. (2015), Proceedings of the 14th Python in Science Conference