Overview

This is the rodent version of BARSTOOL. It performs the same general functions as vanilla BARSTOOL, but specifically supports file formats from small animal scanner vendors (Varian and Bruker) and provides tools specifically for rodent brain extraction as well as tissue/cerebrospinal fluid (CSF) segmentation of the rodent brain.

Note that the "Bruker" aspects of this program has yet to be finalized. Use at your own peril!

Layout

BARSTOOL-RV is organized in a tabbed layout format. Each tab corresponds to a step in the process of producing absolute metabolite quantifications.

• The Amplitudes and CRLBs Tab allows you to produce a comma-separated values (*.csv) file containing amplitudes and Cramér-Ráo lower bounds for each component of the fitted model. Read more about Cramér-Ráo lower bounds here.
• The Brain Extraction and Segmentation Tab allows you to skull-strip your reference anatomical images, produce a three-dimensional mask image representing the spectroscopy voxel, and produce a binary segmentation of CSF versus tissue.
• The Set Parameters Tab allows you to define the various parameters required for absolute metabolite quantification.
• Finally, the Quantify Metabolites Tab allows you to produce a *.csv file containing the estimated metabolite concentrations in mM. Read more about how the metabolite concentrations are estimated here.

On the right hand side of the user interface is a "Console Output" panel, which displays important messages and information from all tabs.