This is a set of tools for conducting an along-tract analysis of white matter fiber tracts derived from diffusion MRI data. It allows you to analyze a scalar metric (e.g. fractional anisotropy; FA) parameterized along a tract, rather than the more typical method of collapsing the variability in these measures into single tract-averaged mean estimates.
This package contains 3 things:
An accompanying manuscript has been published in the journal NeuroImage. If you find these tools useful, please cite this work as:
Colby J. B., Soderberg L., Lebel C., Dinov I. D., Thompson P. M., and Sowell E. R.. Along-tract statistics allow for enhanced tractography analysis. Neuroimage. In press.
DOI: 10.1016/j.neuroimage.2011.11.004
read_avw
)along-tract-stats
directory to your matlab path. (Adjust these paths according to your setup)
addpath('/path/to/along-tract-stats')
matlab
directory to your matlab path.
addpath('/usr/local/fsl/etc/matlab')
savepath
.$FSLDIR
environment variable in MATLAB.
setenv('FSLDIR', '/usr/local/fsl')
startup.m
file.help <command_name>
at the MATLAB command prompt (e.g. help trk_plot
) to get specific info on usage, inputs, and outputs for each function.html
directory to see the demo output that is published by trk_demo.m
Unless otherwise specified in the source code: Copyright 2010, John Colby
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License version 3 as published by the Free Software Foundation.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.