← Back to Course Home

Week 11: Magnetic Resonance Spectroscopy

Magnetic Resonance Spectroscopy (MRS) exploits the chemical shift phenomenon to detect and quantify endogenous brain metabolites in vivo. This week covers shielding constants, parts-per-million (ppm) scales, time-domain FID signal processing, water and lipid suppression, spectral editing, and quantification of NAA, Creatine, Choline, Glutamate, and GABA.

Interactive Demos & Activities

• MRS Metabolite Basis Set & LCModel Spectral Fitter

  Primary Week Simulator · Basis Deconvolution, Chemical Shift Dispersion & CRLB

  Deconstruct in-vivo $^1\text{H}$ MR spectra into basis spectra for NAA, Creatine, Choline, Myo-inositol, Glutamate, and Lactate. Explore B0 field dispersion (1.5T vs 3T vs 7T), shim linewidths, macromolecular baselines, and Cramer-Rao Lower Bounds (CRLB %SD) across clinical tumor, stroke, and dementia presets.

• MRI Simulator: Scanner, Sequences, k-space & Spectroscopy

  Integrated 3 T Simulator · Pulse-Sequence Language, Phantoms, Artifacts, Reconstruction & MRS

  Write pulse sequences in a small language, image a brain or a test phantom on a schematic 3 T scanner, and watch k-space fill line by line as the hardware plays the sequence. Reconstruct the data several ways (filters, zero-filling, partial Fourier, SENSE, gridding), switch on artifacts that arise from their physical cause, and acquire a non-localised proton FID with water suppression and hands-on shimming. Thirteen guided lessons.

• Free Induction Decay (FID) & Spin Relaxation

  Raw Spectroscopic Signal · Time-Domain FID

  Review the physical origin of the time-domain FID signal recorded following an RF excitation pulse, which forms the raw data that gets Fourier-transformed into frequency/ppm spectra in MRS.

• Interactive MRS Analysis Pipeline & Spectrum Simulator

  Comprehensive Processing Workstation Simulator

  A complete in-browser spectroscopy workstation. Adjust coil thermal noise, toggle the broad macromolecule baseline, apply a 10,000:1 water suppression filter, tune exponential apodization/line broadening (SNR vs. resolution), test zero-filling, and apply zero- and first-order phase corrections.

• Hyperpolarized & Multinuclear MRS Primer Hub

  Advanced Spectroscopy Resources · Multinuclear Physics

  Explore advanced spectroscopy protocols including dissolved-phase hyperpolarized Xenon-129 (129xe_dissolved.html), Carbon-13 metabolic flux (13c_liver.html), and jMRUI software workflows (jmrui.html).

Topics Covered

• Chemical Shift & Shielding: How electron clouds around distinct molecular groups shield the nucleus from $B_0$, shifting resonance frequencies by parts-per-million (ppm).
• From Time-Domain FID to Frequency Spectrum: How free induction decay signals from multiple chemical resonances superimpose in time and are separated via the Fourier Transform.
• Core Brain Metabolites: N-acetylaspartate (NAA at 2.0 ppm; neuronal integrity), Creatine (3.0 ppm; bioenergetics), Choline (3.2 ppm; membrane turnover), and Myo-inositol (3.5 ppm; glial marker).