TSE - josalggui/MaRGE GitHub Wiki

MRI Sequence Documentation: Turbo Spin Echo (TSE)

Description

The Turbo Spin Echo (TSE) sequence acquires a train of spin echoes following a single excitation pulse. A refocusing RF pulse is applied before each echo, allowing multiple echoes to be collected within a single repetition time (TR). The echo amplitudes decay along the echo train due to transverse relaxation effects.

Different phase cycling strategies (CP, CPMG, APCP, APCPMG) can be selected to control coherence pathways and echo stability.

This implementation acquires a one-dimensional echo train without spatial encoding and is mainly used for relaxation measurements, signal characterization, and system validation.

Sequence Workflow

  1. Initialization

    • System shimming is applied.
    • RF, timing, and acquisition parameters are configured.

  2. Excitation

    • A single RF excitation pulse tips magnetization into the transverse plane.

  3. Echo Train

    • A refocusing RF pulse is applied before each echo.
    • Echoes are separated by a fixed echo spacing (echoSpacing).

  4. Signal Acquisition

    • The received signal is gated and sampled around each echo.
    • Oversampled data are acquired and digitally decimated.

  5. Averaging

    • If multiple scans are performed, signals are averaged to improve SNR.

Input Parameters

The following parameters are configured by the user before running the TSE sequence. They control RF pulses, timing, acquisition, and system behavior.

  • Number of scans (nScans): Number of repetitions used to average the signal and improve SNR.

  • Repetition time (repetitionTime, ms): Time between consecutive excitations.

  • Echo spacing (echoSpacing, ms): Time interval between consecutive echoes in the echo train.

  • Echo train length (etl): Number of echoes acquired after a single excitation pulse.

  • Acquisition time (acqTime, ms): Duration of the readout window for each echo.

  • Phase mode (phase_mode): Phase cycling scheme applied to the refocusing RF pulses. Possible values: "CPMG", "CP", "ACP", "ACPMG"

  • Larmor frequency (larmorFreq, MHz): Resonance frequency of the spins.

  • RF excitation amplitude (rfExAmp, a.u.): Amplitude of the excitation RF pulse.

  • RF refocusing amplitude (rfReAmp, a.u.): Amplitude of the refocusing RF pulses.

  • RF excitation time (rfExTime, µs): Duration of the excitation RF pulse.

  • RF refocusing time (rfReTime, µs): Duration of the refocusing RF pulses.

  • Number of acquired points (nPoints): Number of sampled points per echo before oversampling.

  • Shimming (shimming): Offset applied to the gradient axes to improve field homogeneity.

Output and Results

The sequence produces a complex-valued signal containing the full echo train. Each echo corresponds to a different effective echo time and can be used to estimate transverse relaxation parameters.

During post-processing, the echo amplitudes are extracted and fitted to a monoexponential decay model to estimate T2 and equilibrium magnetization.

All fitted parameters and processed signals are stored in the same .mat file together with the acquisition parameters.

Raw Data

The following variables are saved in the output .mat file.

  • seqName: Sequence name.

  • nScans: Number of scans averaged.

  • repetitionTime: Repetition time (ms).

  • echoSpacing: Time between consecutive echoes (ms).

  • etl: Echo train length (number of echoes).

  • acqTime: Acquisition window per echo (ms).

  • bw: Acquisition bandwidth (Hz).

  • larmorFreq: Larmor frequency (MHz).

  • rfExAmp: RF excitation pulse amplitude (a.u.).

  • rfReAmp: RF refocusing pulse amplitude (a.u.).

  • rfExTime: RF excitation pulse duration (µs).

  • rfReTime: RF refocusing pulse duration (µs).

  • phase_mode: Phase cycling mode for refocusing pulses.

  • shimming: Shimming values applied during the sequence.

  • gradRiseTime: Gradient rise time (µs).

  • gSteps: Number of discrete gradient steps during ramp.

  • dataFull: Complex-valued acquired signal before decimation. Dimensions: [nScans * etl * nPoints * oversamplingFactor]

  • data: Decimated and scan-averaged complex signal containing the full echo train. Dimensions: [etl * nPoints]

  • T21: Estimated transverse relaxation time T2 (ms), obtained from monoexponential fitting of echo amplitudes.

  • M1: Estimated equilibrium magnetization amplitude from the fit.

  • sampledPoint: Complex signal value sampled at the center of the first echo.

  • signal_vs_time: Time-domain representation of the full echo train. Two-column array:

    • column 1: time (ms)
    • column 2: signal amplitude (mV)
    • example shape: [etl * nPoints, 2]

  • echo_amplitude_vs_time: Echo amplitudes sampled at the echo center as a function of echo time. Two-column array:

    • column 1: echo time (ms)
    • column 2: echo amplitude (mV)
    • example shape: [etl, 2]

Notes

  • This sequence does not apply spatial encoding gradients.
  • Echo amplitudes are extracted at the center of each echo.
  • Relaxation fitting assumes a monoexponential decay model.
  • All fitted parameters are stored in the same .mat file as the acquisition parameters to ensure full reproducibility.