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Interactive Neuroimaging Demos

A suite of interactive web-based simulations designed for NBL 425/625 to explore the core physical principles, spatial encoding schemes, contrast mechanisms, statistical modeling, and artifact origins in human neuroimaging.

Course Demos

• EPI Geometric Distortion & Susceptibility Dropout

  EPI Artifacts · Field Offsets ΔB0, Bandwidth & TOPUP Unwarping

  Visualizes how air-tissue interfaces (paranasal sinuses) interact with the low phase-encoding bandwidth of Echo Planar Imaging to cause geometric stretching (P→A) vs. compression (A→P) and intra-voxel signal blackout, and how reversed phase-encode calibration (TOPUP) restores geometry.

• fMRI GLM & Convolution Studio

  fMRI Analysis · HRF Convolution, Design Matrices & OLS Regression

  Design cognitive timelines (block vs. event-related), convolve impulses with the canonical double-gamma Hemodynamic Response Function, inspect collinearity and variance inflation (VIF), and solve the General Linear Model ($Y = X\beta + \epsilon$) in real time with statistical contrasts ($t$-tests).

• Free Induction Decay (FID) & Spin Relaxation

  Induction Physics · Faraday's Law, Mxy Evolution, T1 Recovery & T2* Dephasing

  Directly connects the 3D time evolution of the net magnetic moment to the voltage signal induced in an RF receiver coil. Remembers longitudinal $M_z$ memory across pulses to demonstrate $T_1$ saturation, inversion recovery, and the null point.

• Gradient Encoding Visualizer

  Spatial Encoding · Frequency, Phase & Slice Selection

  Visualizes how linear magnetic field gradients make the Larmor precession frequency position-dependent, demonstrating slice selection (G_z), phase encoding blips (G_y), and frequency encoding readout (G_x).

• Pulse Sequence Timing Diagram

  Sequence Engineering · Spin Echo, TR & TE

  An interactive spin-echo timing diagram. Adjust TE to see the 180° refocusing pulse and echo move synchronously; adjust TR to explore repetition timing, dead time, and phase-encode step evolution.

• TR/TE Contrast Explorer

  Contrast Weighting · T1, T2 & Proton Density

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

• k-space Explorer

  Fourier Reconstruction · Central vs. Peripheral Spatial Frequencies

  Filter k-space with a variable centered window to observe how the center carries coarse image contrast while the periphery contributes edge sharpness. Illustrates Gibbs truncation ringing artifacts.

• MRI Artifact Simulator

  Artifact Physics · Chemical Shift, Aliasing & Motion

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

• DTI Tensor & Tractography Explorer

  Diffusion · Eigenvalues, FA, Streamline Integration & Crossing Fibers

  Build a diffusion tensor from its eigenvalues and orientation, read off FA, MD and the Westin linearity / planarity / sphericity measures, and see the resulting signal attenuation across a 6-, 15- or 30-direction gradient scheme. A synthetic crossing then shows why deterministic tractography stops at fiber intersections, and why loosening the turning-angle limit to get through produces anatomically false tracts.

• fNIRS Modified Beer–Lambert Unmixer

  Optical Imaging · Extinction Spectra, Isosbestic Point & Matrix Conditioning

  Choose two laser wavelengths inside the near-infrared window and see how that single decision determines whether oxy- and deoxy-haemoglobin can be separated at all. Includes the measured extinction spectra, the Modified Beer-Lambert forward model, and a simulated block-design recording solved back to concentrations, with the condition number of the 2x2 system reported live.

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