Education, tips and tricks to help you conduct better fMRI experiments.
Sure, you can try to fix it during data processing, but you're usually better off fixing the acquisition!

Thursday, February 16, 2012

Physics for understanding fMRI artifacts: CONTENTS

Figured it might be useful to have some summary/contents pages. I'll do similar admin posts as the other series mature, too. And I will label these pages with "Contents" to make them easier to find via the sidebar.

Part One

An introduction to the series, followed by an introductory video courtesy of Sir Paul Callaghan: What is NMR and how does it work?

Part Two

Further videos explaining the principles of nuclear magnetic resonance - how the intrinsic spin of certain atomic nuclei interacts with applied magnetic fields to yield useful information.

Part Three

Videos showing the anatomy of a miniature scanner, a basic NMR experiment, why shimming is important for NMR (and MRI), how and why a spin echo works, and the relaxation of spins back towards their ground state.

Part Four

Mathematics of oscillations: an introduction to imaginary and complex numbers, and frequency and phase.

Part Five

An introduction to the Fourier transform - what it does and how it works. Includes a description of Fourier analysis, and explains conjugate variables and (Fourier) domains.

Part Six

Practical issues arising from the use of the Fourier transform in MRI:
  • Fourier pairs
  • Convolution in pictures
  • Time-decaying signals
  • Finite acquisition periods and signal clipping
  • Digitization
  • The Nyquist frequency
  • Aliasing

Part Seven

Magnetic field gradients and one-dimensional MRI:
  • A magnetic field alters the local resonance frequency
  • Acquiring an MR signal in the presence of a gradient
  • One-dimensional imaging in pictures

Part Eight

Gradient-recalled echoes:
  • An explanation of how GRE works
  • The benefits of acquiring a gradient echo
Slice selection:
  • How slice selection works
  • Using a GRE with slice selection

Part Nine

K-space - conjugate variables redefined:
  • Conjugate variables revisited
  • Representing pictures in reciprocal space
  • One-dimensional imaging as seen in k-space
  • Tracing kx through time
  • Getting off axis (into 2D)

Part Ten

K-space in two dimensions:
  • A useful pictorial representation of imaging pulse sequences
  • The goal revisited
  • Gradients along the x direction (again)
  • Gradients along the y axis
  • The equivalence of frequency and phase encoding
  • Gaining an intuitive understanding of phase encoding

Part Eleven

Resolution and field-of-view as seen in k-space:
  • Spatial frequencies in k-space: what lives where?
  • Why does the signal level change across k-space?
  • Defining parameters in k-space to yield the image you want
  • Image field-of-view
  • Image resolution

Part Twelve

The echo planar imaging (EPI) pulse sequence:
  • Gradient echo EPI pulse sequence
  • Processing 2D k-space for EPI
EPI artifacts:
  • Ghosting
  • Distortion
  • Signal dropout

Part Thirteen

A tour through a real EPI pulse sequence:
  • Interpreting what you see
  • Fat saturation
  • Crusher gradients for fat suppression
  • Crusher gradients to eliminate signal from prior slice excitations
  • Slice selection
  • N/2 ghost correction echoes
  • Phase encode dephasing gradient
  • Readout gradient echoes
  • Relative duration of functional modules in the EPI sequence

Part Fourteen

Partial Fourier EPI.

(Part Fifteen)

To come: Ramp sampling for EPI.

(Part Sixteen)

To come: Eddy currents.

(Part Seventeen)

To come: Crusher/spoiler gradients in EPI.

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