Installation

The SAMS pipeline consists of shell scripts requiring several executable programs as dependencies.

Operating System Requirements

The SAMS pipeline is set up to run in a Linux environment (Mac is possible). It has been tested on the Ubuntu 14.04 platform. Window users with access to Linux server can execute the pipeline using a terminal emulator, or set up a Linux environment using VirtualBox.

Executable Software Dependencies

The following software are needed to operate the SAMS pipeline:

AFNI - Analysis of Functional NeuroImages

Analyze- Analyze 12.0

ANTs - Advanced Normalization Tools

C3D - Convert3D

FSL - FMRIB Software Library

MATLAB - MATLAB is preferred by the VTLab to render resulting SAMS-processed mandible for visual inspection.

Alternatives

The following is a list of open-source software that can be used as alternatives to Analyze 12.0 and/or MATLAB:

ImageJ

ITKSNAP

Slicer

Cluster Computing Environment

This pipeline is designed to work with cluster computing for optimal performance. The Vocal Tract Development Lab employs High Throughput Computing (HTC) resources from the Center for High Throughput Computing at the University of Wisconsin-Madison. It can be adapted to use on other cluster computing environment for users who may have access to similar resources.