Brown University MRS Data Collection and Preprocessing Protocol

This documentation is adapted from a tutorial by Meghan A. Gonsalves, PhD on 2/21/2024. It is continuously updated by the BNC as changes to the software are released.

A note on terminology:

In MR Spectroscopy, there are two types of sequences that are acquired for every voxel at the scanner. Those two scans are both used in preprocessing to construct a single metabolite spectrum. Since the signal from various metabolites are significantly smaller (~10,000x) than that of water, one run is collected with suppressed water signal. Additionally, a non water suppressed run is collected to provide a signal intensity baseline. This scan is also used for various corrections such as eddy-current distortion correction. There are multiple ways to refer to these two scan types, and many of the terms are interchangeable . Here are lists of the various terms used to refer to the same type of sequences:

Water-suppressed data: "standard", "metabolite", "wsat on" (water saturation on), "glx", "svs" (single voxel spectroscopy)

Water un-suppressed data: "reference", "lineshape", "wsat off" (water saturation off), "wat", "mrsref" (mrs reference)

When organizing your MRS data according to BIDS, the suffix of the file name will indicate the sequence type. It will either be named "filename_svs.nii" or "filename_mrsref.nii".

For the sake of clarity in this tutorial, we will refer to the data as "water reference" and "metabolite".