BARSTOOL is a program used to quantify metabolites measured in-vivo. With this program, you can:

• calculate metabolite ratios
• calculate metabolite Cramér-Ráo lower bounds
• calculate metabolite concentrations
• perform brain extraction and gray matter/ white matter / CSF segmentation via a graphical interface to FSL BET and FAST commands
• save results to a Microsoft Excel readable file

BARSTOOL 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 Tab allows you to skull-strip your reference anatomical images. The Brain Segmentation Tab allows you to segment the gray matter (GM), white matter (WM), and cerebrospinal fluid (CSF) areas in your skull-stripped reference anatomical images, producing GM, WM, and CSF masks.
• The Set Parameters Tab allows you to define the various parameters (e.g. T₁ and T₂ relaxation rates for the metabolites, or the relative proton densities of water in GM, WM, CSF as compared to that of pure water) 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.