Along-tract statistics

1. Overview
2. Install
3. Support
4. License

Overview

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:

1. Tools - A modular set of MATLAB functions to perform individual tasks on the tract groups (load, plot, save, interpolate, etc.).
2. Experiment wrappers - Several examples of how you can link these tools together to perform a full analysis. These will be a good starting point to adapt to your own needs.
3. Example data - So you can get a feel for running these tools and verify that they are behaving the same way as in the example documentation.

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

Install

Requirements

• MATLAB
• MATLAB Curve Fitting Toolbox (or Spline Toolbox prior to r2010b)
• FSL (mainly for read_avw)

Recommended

• MATLAB Statistics Toolbox: Nicely handle Excel-type data tables
• MATLAB Parallel Computing Toolbox: Speed up streamline processing
• TrackVis: 3D visualization
• R: Statistical inference and graphics

Install

1. Click the Downloads link towards the top-right on Github. Download and extract either the .zip or .tar.gz versions.
2. Add the along-tract-stats directory to your matlab path. (Adjust these paths according to your setup)
   • addpath('/path/to/along-tract-stats')
3. Add the FSL matlab directory to your matlab path.
   • addpath('/usr/local/fsl/etc/matlab')
4. Save these changes with savepath.
5. Set the $FSLDIR environment variable in MATLAB.
   • setenv('FSLDIR', '/usr/local/fsl')
6. To save this setting for future sessions, consider putting it in your startup.m file.

Support and Usage

• Github Wiki - The main source of online documentation. Information on basic usage and tutorials.
• ColbyImaging Wiki - Video tutorials (can't be embedded on Github).
• Github Issues - Questions, comments, feedback, bugs, etc.. (Sign up for a GitHub account first)
• Offline documentation - There are several sources of offline documentation included with this package:
  • MATLAB help - Type 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.
  • MATLAB demo - Open the index.html file in the html directory to see the demo output that is published by trk_demo.m
  • Inline code comments - The code is written in plain text with comments throughout.

License

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/.