Installation

Installation Procedure

To install all the libraries for the python script to run

1. Install all the source files from the requirements folder in the same order

   sudo pip install numpy==1.11.0 sudo pip install networkx==1.11 sudo pip install nibabel==2.0.2 sudo pip install pydot3==1.0.8 sudo pip install python-louvain==0.5 Install Graphviz through the graphviz website--(http://www.graphviz.org) sudo pip install pygraphviz==1.3.1 sudo pip install vtk (if the version bundled with pip does not include the vtkNiftiImageReader function, you must install a version that does) sudo pip install qt-sdk; sudo pip install PySide sudo pip install decorator>=3.4.0

These are some of the recommended links for download:

[Numpy](https://sourceforge.net/projects/numpy/files/NumPy/1.11.0/numpy-1.11.0.tar.gz/download)`
[Decorator](https://pypi.python.org/packages/68/04/621a0f896544814ce6c6a0e6bc01d19fc41d245d4515a2e4cf9e07a45a12/decorator-4.0.9.tar.gz#md5=f12c5651ccd707e12a0abaa4f76cd69a)
[Networkx](https://pypi.python.org/packages/c2/93/dbb41b03cf7c878a7409c8e92226531f840a423c9309ea534873a83c9192/networkx-1.11.tar.gz#md5=6ef584a879e9163013e9a762e1cf7cd1)
[Nibabel](http://nipy.org/nibabel/installation.html#installation) 
[Louvain](https://pypi.python.org/packages/5d/81/497a95ba9d79d5bf04f9318256d1c0102329dd6a77b9d1e4dd84871e1089/python-louvain-0.5.tar.gz)
[PyDot](https://pypi.python.org/pypi/pydot3/1.0.8)
[PyGraphViz](https://pypi.python.org/packages/98/bb/a32e33f7665b921c926209305dde66fe41003a4ad934b10efb7c1211a419/pygraphviz-1.3.1.tar.gz#md5=7f690295dfe77edaa9e552d09d98d279)
Note: If after installing, "import pygraphviz" returns an error, then uninstall and reinstall using: 	pip install pygraphviz --install-option="--include-path=/usr/local/include/graphviz" --install-option="--library-path=/usr/local/lib/graphviz/" (https://github.com/pygraphviz/pygraphviz/issues/72)
[VTK and PyVTK](http://kazenotaiyo.blogspot.com/2010/06/installing-vtk-in-ubuntu-and-making.html)

and then, type python and paste these commands
	import numpy
	import networkx
	import nibabel
	import pydot
	import community 
	import pygraphviz
	import vtk
	import PySide
	import decorator
If none of them returns an error then you are set

2. Configure the data paths in BrainViewerDataPaths.py and configure paths to run BrainViewer.py