External Packages

Some VISTASOFT functions require external software. Some of these functions are required for basic VISTASOFT functions, such as alignment (e.g., Matlab and SPM). Others are optional packages that lab members often rely upon for various things (e.g., Freesurfer, mrTrix). We describe the usages here.

VISTASOFT Required Packages

The following software packages are required to use VISTASOFT.

Matlab

VISTASOFT is written in Matlab.

SPM

Download SPM5

Some of the code included in mrVista depends upon certain routines from SPM. Thus, anyone who plans on doing analysis with mrVista should have a copy of SPM in their Matlab path to ensure that those functions can be found. The version of SPM used by the mrVista code is SPM5. Visit the http://www.fil.ion.ucl.ac.uk/spm/ SPM for information regarding downloading SPM5 and adding the directory to your matlab path.

SPM is an academic software toolkit for the analysis of functional imaging data, for users familiar with the underlying statistical, mathematical and image processing concepts. For a more detailed introduction to SPM (by Friston) you can check out SPM's introduction page.

1. 1. 1. FSL

• Jump to FSL Page

For general info regarding FSL and FSL tools, including download and install instructions, you can visit the FSL website. Here we will just mention, for those who don't know, that FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. FSL is written mainly by members of the Analysis Group, FMRIB, Oxford, UK. FSL runs on Apple, PCs (Linux and Windows) and Sun, and is very easy to install. Most of the tools can be run both from the command line and as GUIs ("point-and-click" graphical user interfaces).

Our lab uses a variety of FSL tools to view files and process data. You can jump to the FSL page for information on getting FSL to run via the command line on the white network.

1. 1. 1. FreeSurfer

 * Jump to [[FreeSurfer|FreeSurfer Page]] 
 * [http://surfer.nmr.mgh.harvard.edu/ FreeSurfer home page] (Non-VISTA Lab members)

Some of the code included in mrVista can use certain processing algorithms from FreeSurfer. For example, we use FreeSurfer for aligning multiple subjects to the MNI template using the spherical methods advocated by Harvard, Wash. U. and BrainVoyager. We used this method for identifying common ROIs across the children in the DTI data set.

See the FreeSurfer page for installation instructions and examples of how we use their code.

1. 1. 1. Numerical Fiber Generator (NFG)

Soon someone will describe external routine NFG and the Matlab hooks into it.

1. 1. 1. MRtrix

MRtrix provides a set of tools to perform diffusion-weighted MR white-matter tractography in a manner robust to crossing fibres, using constrained spherical deconvolution (CSD) and probabilistic streamlines. The MRtrix page describes how to install and use this package on lab machines using data in the VISTA laboratory.