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Imaging Evidence Path

What happens to hydrogen after the RF pulse

Tonight · ~25 min · read + a short video · energy: medium · setup: none

This lesson builds the relaxation mental model — what the protons do, and why two simultaneous relaxations (T1 and T2) exist. Once you can picture longitudinal recovery and transverse decay happening at once, “T1-weighted” and “T2-weighted” stop being jargon.

The anchor: one excitation, two relaxations

An MRI scanner measures a radio-frequency signal from hydrogen nuclei (protons) manipulated by magnetic fields, then reconstructs an image from it (k-space → Fourier, lesson 6). Conceptually:

  • A strong static field B₀ polarises proton magnetisation along the longitudinal (z) axis.
  • An RF excitation pulse tips that magnetisation into the transverse (xy) plane by a flip angle (90° for spin echo).
  • Two simultaneous relaxations then occur:
    • Longitudinal relaxation (T1) — magnetisation recovers along z.
    • Transverse relaxation (T2 / T2*) — magnetisation decays in the xy plane.

The contrast you see is set by when you read out the signal relative to these two relaxations.

Why two relaxations at once

These are not two steps; they are two independent processes happening to the same magnetisation. After the RF pulse tips the net magnetisation into the transverse plane:

  • T1 (spin–lattice) recovery — protons give energy back to the surrounding molecular lattice and the longitudinal magnetisation grows back toward B₀. Different tissues recover at different rates (fat recovers fast; fluid slowly). T1 is the time constant of that recovery.
  • T2 (spin–spin) decay — the transverse magnetisation loses phase coherence as spins precess at slightly different rates (microscopic field inhomogeneities from neighbouring spins). The net transverse signal decays. Different tissues dephase at different rates (fluid stays coherent long; solids/muscle dephase fast). T2 is the time constant of that decay.
flowchart LR
    B0["B0: protons align<br/>(longitudinal)"] -->|RF pulse tips<br/>into transverse| TR["transverse magnetisation<br/>(signal readable)"]
    TR -->|"T1: recover along z<br/>(spin-lattice)"| L1["longitudinal grows back"]
    TR -->|"T2: dephase in xy<br/>(spin-spin)"| L2["transverse decays"]

T2* is the faster dephasing that also includes macroscopic magnetic-field inhomogeneity (relevant to gradient echo and BOLD/fMRI, not routine spin-echo T2).

Watch — to see relaxation

This is the visually difficult idea in the chapter, so watch it rather than only read it.

Watch — the relaxation section

Stanford Medicine BMR — MRI Physics Education Materials (VERIFIED): open the Stanford BMR MRI physics page and watch the “MRI Contrast Mechanisms” section, in particular the “Relaxation, T1 and T2 Contrast” video. (I am pointing you to the named section rather than a specific timestamp, which I have not verified.)

While watching, focus on:

  • how longitudinal magnetisation recovers along z (T1) while transverse magnetisation decays in xy (T2) — simultaneously;
  • why fat and fluid recover/decay at different rates, and how that difference is the raw material of contrast;
  • the read-out timing that decides which relaxation dominates the image (the subject of lesson 3).

You can ignore, for now, the details of gradient and RF hardware.

After watching

Think, then reveal

After a 90° pulse, are T1 and T2 two stages or two simultaneous processes? And which one describes the regrowth of magnetisation along B₀?

They are simultaneous, not sequential — both begin the moment the magnetisation is tipped into the transverse plane. T1 is the one that describes the regrowth of magnetisation along B₀ (longitudinal, spin–lattice recovery); T2 describes the decay of the transverse magnetisation (spin–spin dephasing). Holding “one pulse, two simultaneous relaxations, only one of which regrows along z” is the whole mental model that makes TR/TE weighting click in the next lesson.

What to retain

  1. One excitation produces two simultaneous relaxations: T1 (longitudinal recovery, spin–lattice) and T2 (transverse decay, spin–spin).
  2. Contrast comes from when you read out relative to these relaxations — that is what TR and TE control (lesson 3).
  3. Different tissues recover/decay at different rates; that difference is the raw material of MRI contrast.
  4. T2* adds macroscopic field inhomogeneity to T2 (relevant to gradient echo/BOLD, not routine spin-echo T2).

Next: the two timing parameters that turn relaxation into weighting — how TR and TE make tissue look different.