# ica2gat

Clojure program to generate data for graph analysis tools from ICA input.

This program reads sets of node names, representing the "components"
found by Independent Component Analysis and produces data files
suitable for ingestion by graph analysis tools. The types of output
data files produced may be specified on the command line and currently
includes a sequence of node adjacency tuples (for Gephi) and/or partial
or complete adjacency matrices (for Olaf Sporns' Brain Connectivity Toolbox
(in MATLAB)).

Each line of the input data file contains a comma-separated list of
the node names for the nodes of a single ICA component. The node names
must not contain spaces or quotes. Example input data file with 3 components:
   LGN, STG_R, STG_L
   BA1, BA2
   STG_L, LGN, BA1, BA45

The output files will be named according to the specified contents and
the required basename. For example, the output file for the entire
adjacency matrix will be named 'XXX_mat.csv', if XXX was specified
as the basename argument.


## Usage

java -jar ica2gat.jar (-glt | -gut | -mat | -mlt | -mut)... -o outfile-basename infile-name

where:
   -glt = output a list of lower triangle data tuples (for Gephi)
   -gut = output a list of upper triangle data tuples (for Gephi)
   -mat = output an adjacency matrix (for BCT in MATLAB)
   -mlt = output lower triangle of adjacency matrix (for BCT in MATLAB)
   -mut = output upper triangle of adjacency matrix (for BCT in MATLAB)
   -o = the basename (without extension) for the output file(s)


## License

Copyright (C) 2011 Tohono Consulting.

Distributed under the Eclipse Public License, the same as Clojure.