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Week 04: Functional MRI (fMRI)

Functional MRI does not measure action potentials directly; instead, it detects the localized hemodynamic response to neural metabolic demand. This week examines neurovascular coupling, the Blood Oxygenation Level Dependent (BOLD) effect, and the physical mechanisms underlying the canonical Hemodynamic Response Function (HRF).

Interactive Demos & Activities

• EPI Geometric Distortion & Susceptibility Dropout

  Primary EPI Acquisition Simulator · Phase-Encode Bandwidth & TOPUP

  Explore why single-shot EPI scans have severe geometric stretching/compression along the phase-encoding axis and irreversible signal dropout near paranasal sinuses, and test blip-up / blip-down unwarping.

• fMRI GLM & Convolution Studio

  Analysis Engine · HRF Convolution & BOLD Time Series

  Connect neural events to the BOLD time series by convolving stimulus boxcars with the canonical double-gamma HRF, observing how metabolic delays shape voxel signals.

• Interactive BOLD Signal (HRF) Simulator

  Interactive Hemodynamic Simulator · Neurovascular Coupling

  Trigger a 1-second sensory stimulus to contrast instantaneous electrical neural spiking with the sluggish BOLD Hemodynamic Response Function (HRF) peaking 5–6 seconds later, accompanied by a dynamic cortical activation display.

• Local Field Potentials (LFP) vs. Spikes

  Population Electrophysiology Simulator · BOLD Signal Origin

  Simulate 150 neurons to see how synchronized postsynaptic potentials (LFPs) create macro-signals that drive astrocytic signaling and metabolic blood flow changes far more strongly than sparse action potentials.

• Stochastic Leaky Integrate-and-Fire (LIF) Neuron

  Single-Neuron Biophysics · Metabolic Demand

  Examine the cellular electrophysiological threshold, ion pumping energy requirements, and spike generation that necessitate local hemodynamic overcompensation.

• Ferroquant: Deoxyhemoglobin as an Endogenous Contrast Agent

  Biophysical Foundations of BOLD

  Review how the paramagnetic electron spin of deoxygenated hemoglobin distorts the local $B_0$ field, accelerating $T_2^*$ decay, and how functional hyperemia replaces deoxyhemoglobin with diamagnetic oxyhemoglobin.

Topics Covered

• The Tripartite Synapse & Neurovascular Coupling: Astrocytic end-feet, glutamate uptake, nitric oxide, and local vasodilation.
• The BOLD Effect: The balance between cerebral metabolic rate of oxygen ($CMRO_2$), cerebral blood flow ($CBF$), and cerebral blood volume ($CBV$).
• Spatiotemporal Characteristics of the HRF: Initial dip, 5-second peak, post-stimulus undershoot, and spatial localization limits.