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!

Wednesday, September 19, 2012

Understanding fMRI artifacts: CONTENTS

An organizational post I'd been meaning to get to for a while. There are some posts to come in this series, in parentheses below. I'll update this page with links as these posts get published.

Understanding fMRI artifacts

An introduction to the post series, defining what we mean by "good" data, and general discussion on viewing and interpreting EPI artifacts in a time series.

Good data

Understanding fMRI artifacts: "Good" axial data

Includes cine loops through time series EPI and statistical images to evaluate the data.

Understanding fMRI artifacts: "Good" coronal and sagittal data

Includes cine loops through time series EPI and statistical images to evaluate the data. (The notes include a description of the slice-dependent gradient switching limits that can prohibit certain slice orientations.)

Common persistent EPI artifacts

Common persistent EPI artifacts: Aliasing, or wraparound

Aliasing effects in the frequency and phase encoding dimensions.

Common persistent EPI artifacts: Gibbs artifact, or ringing

The origin of the ringing problem and demonstrations in phantom and brain data.

Common persistent EPI artifacts: Abnormally high N/2 ghosts (1/2)

Subject-dependent conditions:
  • Asymmetric orientation of the subject's head leading to a poor shim
  • Poor shim as a result of subject motion during/immediately after shimming
  • Presence of FOD or an implant causing a poor shim

Common persistent EPI artifacts: Abnormally high N/2 ghosts (2/2)

Scanner-dependent conditions:
  • Rotated read/phase encode axes
  • No fat suppression
  • Mechanical resonances
  • Excessive ramp sampling

Common persistent EPI artifacts: Distortion and dropout

A brief overview of these two plagues of EPI.

Common persistent EPI artifacts: RF interference

RF screening, adding devices to the scanner environment, modifying the magnet room, and standard operating procedures for fMRI labs.

Common persistent EPI artifacts: Receive coil heterogeneity

Receive fields for phased-array RF coils, and removing receive field heterogeneity with prescan normalization.

Common intermittent EPI artifacts

Common intermittent EPI artifacts: Subject movement
  • Eye movements
  • Head nodding
  • Talking
  • Coughing, swallowing, yawning and sneezing
  • Body movements

(Common intermittent EPI artifacts: Signal drift due to gradient heating)

Use of the scanner in a non-steady state.

Rare intermittent EPI artifacts

Rare intermittent EPI artifacts: Spiking, sparking and arcing

Most common causes:
  • Movement of locking nuts or some other metal component of the gradient electrical cables
  • Movement of locking nuts on shim trays or other components inside the bore tube
  • Conductive debris in the RF coil sockets on the patient bed
  • Other sources of metal-on-metal friction inside the magnet room
  • Items of clothing on subjects

Detecting spikes outside of QA tests.

(Rare intermittent EPI artifacts: Fluctuating ghosts with a 32-ch Rx coil)

Siemens Trio-specific problem.

(Rare intermittent EPI artifacts: Spurious signals due to imperfect crusher gradients)

Pulse sequence-specific problem.

Rare persistent EPI artifacts

(Rare persistent EPI artifacts: Poor shim, even on a phantom)

Movement/loosening of passive shim trays. (May also manifest as an inability to achieve good fat suppression for EPI of head.)

(Rare persistent EPI artifacts: Increased signal dropout with partial Fourier)

Loss of echoes that refocus away from theoretical k-space center.

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