← Back to Course Home

Week 03: Structural MRI & Contrast

Contrast in magnetic resonance imaging is engineered through pulse sequence timing. This week examines spin-lattice ($T_1$) relaxation, spin-spin ($T_2$) relaxation, magnetic susceptibility ($T_2^*$), and how Repetition Time (TR) and Echo Time (TE) are tuned to distinguish gray matter, white matter, and cerebrospinal fluid.

Interactive Demos & Activities

• 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.

• EPI Geometric Distortion & Susceptibility Dropout

  Artifact Physics · Susceptibility ΔB0 & TOPUP

  Examine macroscopic magnetic susceptibility gradients at air-tissue interfaces (paranasal sinuses) that cause phase-encoding distortion and intra-voxel dephasing signal blackout.

• TR/TE Contrast Explorer

  Interactive Contrast Simulator · T1, T2 & PD Weighting

  Manipulate TR and TE sliders to see real-time spin-echo signal calculations across four tissue types (White Matter, Gray Matter, CSF, and Fat), dynamically identifying T1-weighted, T2-weighted, and PD-weighted regimes.

• Free Induction Decay (FID) & Spin Relaxation

  Relaxation Dynamics · T1 Recovery vs. T2* Decay

  Inspect how fast transverse dephasing ($T_2^*$) extinguishes the induced signal compared to the much slower longitudinal regrowth of $M_z$ ($T_1$) according to the Bloch equations.

• MRI Artifact Simulator

  Interactive Artifact Physics · Chemical Shift, Aliasing & Motion

  Introduce deliberate k-space and spatial distortions to inspect Chemical Shift (fat-water frequency displacement), Aliasing / Wrap-around (reduced FOV), and Motion Ghosting (phase-encode modulation) with variable severity.

• Pulse Sequence Timing Diagram

  Sequence Engineering · Spin Echo Formation

  Interactive spin-echo sequence demonstrating how the 180° refocusing pulse at TE/2 produces an echo at TE to overcome field inhomogeneities.

• The Spin Echo & Echo Trains

  Isochromat Phase Fan · CPMG & Measuring $T_2$

  Watch the isochromat phase fan open at $T_2^*$ and close again under each 180° refocusing pulse. Run a full CPMG train and see every echo peak land on the $T_2$ envelope regardless of shim quality, which is how a multi-echo sequence measures $T_2$.

• Ernst Angle Calculator

  Sequence Optimization Tool · Fast Gradient Echoes

  Calculate the optimal excitation flip angle $\alpha_E = \arccos(e^{-TR/T_1})$ to maximize steady-state signal amplitude for gradient echo sequences at short repetition times.

• Ferroquant: Iron & Hemorrhage Susceptibility Contrast

  Clinical Contrast Primer · Tissue Susceptibility

  Understand how paramagnetic and diamagnetic iron states (oxyhemoglobin, deoxyhemoglobin, methemoglobin, hemosiderin) alter local magnetic fields and shorten $T_2^*$, with a case study on subdural hematoma aging.

• MRI Modality Card Game

  Educational Card Game · Magnets & Physics

  Match magnet types, imaged organs, excitation, relaxation, spatial encoding and reconstruction, and clinical applications.

Topics Covered

• T1, T2, and T2* Relaxation: Differential molecular tumbling rates, hydration layers, and microscopic magnetic field inhomogeneities across brain tissue compartments.
• Spin Echo vs. Gradient Echo: Refocusing static inhomogeneities with 180° pulses versus preserving susceptibility contrast with field gradients.
• Tissue Segmentation & Volumetry: Morphometric post-processing, cortical thickness estimation, and voxel-based morphometry (VBM).