.. _neuropycon:

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 <http://nipype.readthedocs.io/en/latest/#>`_,
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
* :ref:`graphpype` based on |radatools| includes pipelines for graph theoretical analysis of neuroimaging data


.. |MNE python| raw:: html

   <a href="http://martinos.org/mne/stable/index.html" target="_blank">MNE python</a>

.. |radatools| raw:: html

   <a href="http://deim.urv.cat/~sergio.gomez/radatools.php" target="_blank">radatools</a>

.. |ephypype| raw:: html

   <a href="https://neuropycon.github.io/ephypype/" target="_blank">ephypype</a>


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

.. _lego:

.. figure::  img/tiny_all_input_doors.png
   :width: 50%
   :align:   center

   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.


.. _graphpype:

graphpype
*********

Neuropycon project for graph analysis, can be used from ephypype and nipype. 

The graphpype package provides the following **pipelines**:

* the :ref:`conmat_to_graph pipeline <conmat_to_graph>` runs the graph computation and graph-theoretical tools over connectivity matrices.

* the :ref:`inv_ts_to_graph pipeline <inv_ts_to_graph>` runs the spectral connectivity and the graph computation over time series.

* the :ref:`nii_to_graph <nii_to_graph>` pipeline provide a script to compute connectivity matrices and graphs computations from prepocessed functional MRI.

* the :ref:`inv_ts_to_bct_graph <inv_ts_to_bct_graph>` pipeline provide example scripts to compute graph metrics (so far, KCore) using bctpy (Brain Connectivity Toolbox).

Installation
============

graphpype works with **python3**


.. code-block:: bash

    $ pip install https://api.github.com/repos/neuropycon/graphpype/zipball/master

Or with pip:
    
.. code-block:: bash

    $ pip install graphpype


Radatools
---------
You should add all the directories from radatools to the PATH env variable:

1. Download radatools sotware:

http://deim.urv.cat/~sergio.gomez/radatools.php#download

2. Download and extract the zip file

3. Add following lines in your .bashrc:


For radatools 3.2
^^^^^^^^^^^^^^^^^
RADA_PATH=/home/david/Tools/Software/radatools-3.2-linux32

(replace /home/david/Tools/Software by your path to radatools)

export PATH=$PATH:$RADA_PATH/01-Prepare_Network/

export PATH=$PATH:$RADA_PATH/02-Find_Communities/

export PATH=$PATH:$RADA_PATH/03-Reformat_Results

export PATH=$PATH:$RADA_PATH/04-Other_Tools/


For radatools 4.0
^^^^^^^^^^^^^^^^^
RADA_PATH=/home/david/Tools/Software/radatools-4.0-linux64

(replace /home/david/Tools/Software by your path to radatools)

export PATH=$PATH:$RADA_PATH/Network_Tools

export PATH=$PATH:$RADA_PATH/Network_Properties

export PATH=$PATH:$RADA_PATH/Communities_Detection 

export PATH=$PATH:$RADA_PATH/Communities_Tools


For radatools 5.0
^^^^^^^^^^^^^^^^^
RADA_PATH=/home/david/Tools/Software/radatools-5.0-linux64

(replace /home/david/Tools/Software by your path to radatools)

export PATH=$PATH:$RADA_PATH/Network_Tools