dmalt / 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

Some of these dependencies you should install manually (see :ref:`conda_install`), others are installed automatically during ephypype installation (see :ref:`ephy_install`).

We also recommend to install the development master version of MNE python (see :ref:`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 MNE python

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

see MNE python 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