EtienneCmb / ephypype

Neuropycon package of functions for electrophysiology analysis, can be used from graphpype and nipype

README

Description

Neuropycon package of functions for electrophysiology analysis, can be used from graphpype and nipype

Installation

Requirements

ephypype works both with python2 and python3

• numpy
• scikit-learn
• ipywidgets
• matplotlib
• pandas
• mne
• nipype
• graphpype

Some of these dependencies you should install manually (see conda_install), others are installed automatically during ephypype installation (see ephy_install). To install graphpype see graph_install.

We also recommend to install the development master version of (see mne_install).

Note

If you have Anaconda it is possible to create an environment using python2 by the command conda create -n py27 python=2.7 ipykernel

Warning

We also recommend to use the nipype version 0.13 pip install nipype==0.13

Install package

Install ephypype

git clone https://github.com/neuropycon/ephypype.git
cd ephypype
pip install .
cd ..

Install graphpype

git clone https://github.com/neuropycon/graphpype.git
cd graphpype
pip install .
cd ..

see for more information.

Install MNE python

git clone git://github.com/mne-tools/mne-python.git
cd mne-python
sudo python setup.py develop
cd ..

see for more information.

Install dependencies with conda

conda install pandas
conda install ipywidgets
conda install matplotlib

Software

Freesurfer

1. Download Freesurfer software:

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

2. Follow the Installation instructions

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

MNE

1. Download MNE software:

http://martinos.org/mne/dev/install_mne_c.html