=========================
Installation Instructions
=========================

.. warning:: This software is for research purposes only and shall not be used for
             any clinical use. This software has not been reviewed or approved by
             the Food and Drug Administration or equivalent authority, and is for
             non-clinical, IRB-approved Research Use Only. In no event shall data
             or images generated through the use of the Software be used in the
             provision of patient care.

.. note:: Please `REGISTER <http://www.cmtk.org/users/register>`_ when before you start to use The Connectome Analyzer or the Connectome Mapping Toolkit.

Installation on Ubuntu/Debian
-----------------------------

Upgrade `R <http://www.r-project.org/>`_ to version 2.6.0::

	firefox http://www.r-project.org/

.. note:: 

	Make sure R is compiled as a shared library (ie: you should find a file named Rlib.so in the folder $R_HOME/lib/).

Install the `iGraph library <http://igraph.sourceforge.net/>`_ v0.6.5 for R::

	firefox http://igraph.sourceforge.net/

`Download <download.html>`_ the Connectome Analyzer zip file and move it to the folder you want to install it (eg: /usr/local/The_Connectome_Analyzer).


Move to the installation folder::

	cd <path to The_Connectome_Analyzer.tar.gz>

Extract the source code::

	tar xzf The_Connectome_Analyzer.tar.gz

Everything is set if you want to use the R scripts. They are stored in "<path to The_Connectome_Analyzer>/Rscripts" folder. Just edit and run the desired analysis in your favorite R environment.

If you want to use the GUI, upgrade python to v2.7::

	firefox http://www.python.org/

You will also need Traits, Traits GUI, and rpy2::

	sudo apt-get install python-traits python-traitsgui rpy2


Set the required environmental variables

	If you are using the tcsh shell::

		setenv LD_LIBRARY_PATH $LD_LIBRARY_PATH:<path to folder containing the Rlib.so shared library file>
		setenv R_HOME <path to main R folder>
		setenv ConnectomeAnalyzerPath <path to The_Connectome_Analyzer>/Rfiles

	For the bash shell::

		export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:<path to folder containing the Rlib.so shared library file>
		export R_HOME=<path to main R folder>
		export ConnectomeAnalyzerPath=<path to The_Connectome_Analyzer>/Rfiles

	.. note:: Note that the ConnectomeAnalyzerPath variable ends with "/Rfiles"

To avoid setting the environmental variables each time you run The Connectome Analyzer, you can edit your bash configuration file...::

	gedit /home/<username>/.bashrc

...And add the following (adapted to your installation folders) before saving the changes::

	# Configuration for The Connectome Analyzer
	export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:<path to folder containing the Rlib.so shared library file>
	export R_HOME=<path to main R folder>
	export ConnectomeAnalyzerPath=<path to The_Connectome_Analyzer>/Rfiles

Make sure that you have the environment variables pointing at the appropriate locations. You should have the environment variables: LD_LIBRARY_PATH, R_HOME and ConnectomeAnalyzerPath. You can check this by entering the following commands in the bash shell (they should give you the correct paths)::

	echo $LD_LIBRARY_PATH
	echo $R_HOME
	echo $ConnectomeAnalyzerPath

After `organizing your data <data_organisation.html>`_, you will be ready to `run The Connectome Analyzer <run_CMA.html>`_