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
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:
the preprocessing pipeline runs the ICA algorithm for an automatic removal of eyes and heart related artefacts
the power pipeline computes the power spectral density (PSD) on sensor space
the inverse solution pipeline computes the inverse solution starting from raw/epoched data
the connectivity pipeline perform connectivity analysis in sensor or source space
Installation¶
To install the ephypype package, we recommend you first install MNE python by following the MNE python installation instructions.
The dependencies (mne, nipype, h5py) are automatically installed during ephypype installation.
Install ephypype¶
Then, to install ephypype package, you can use the Pypi version
$ pip install ephypype
$ pip install jupyter
or alternatively, you can download from github the last version and install it:
$ git clone https://github.com/neuropycon/ephypype.git
$ cd ephypype
$ python setup.py develop
Note
ephypype works with python3
Freesurfer¶
Download Freesurfer software:
https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
Follow the Installation instructions