14.4 fMRI Image Acquisition

Stimuli in a fMRI Setup

Figure 14.6: Stimuli in a fMRI Setup

The subject in question is given some sort of stimulus or task with a rest condition in between.

The image time series must then be analyzed to see where the signals change in response to stimulation.

fMRI image acquisition is rapid - it takes an image once per few seconds (i.e., 2 - 4 seconds). Anatomical images may take minutes to acquire.

From a k-space to an image

Figure 14.7: From a k-space to an image

The data in a k-space then undergoes a Fourier transform to yield the transformed image.

14.4.1 Shot Trajectories

Trajectories in a fMRI Image Acquisition

Figure 14.8: Trajectories in a fMRI Image Acquisition

The spiral fMRI is the only serious alternative to the EPI shown above. It has a short, apparent TE, is fast, and efficiently utilizes gradient hardware.

It also has different artefacts from a EPI.

14.4.1.1 Trajectory Considerations

Parameters in a fMRI Image Acquisition

Figure 14.9: Parameters in a fMRI Image Acquisition

There are three considerations:

  1. A longer readout means more artefacts. For instance, single-shot (i.e., EPI and spiral) have warping and blurring.
  2. Cartesian vs. radial coordinates.
  3. SNR for N shots with time per shot Tread.

14.4.2 Acquisition Stages

There are two main kinds:

14.4.2.1 Acquisition Stage 1: Anatomical

Stage 1 Anatomical Image Acquisition

Figure 14.10: Stage 1 Anatomical Image Acquisition

These are high-resolution images that have three dimensional data.

14.4.2.2 Anatomical Stage 2: Functional

Stage 2 Anatomical Image Acquisition

Figure 14.11: Stage 2 Anatomical Image Acquisition

The images here are related to neuronal activity and are usually low-resolution images. All slices at a single time lead to a volume.

14.4.3 Limitations in Image Acquisition

Dephasing in air-tissue boundaries

Figure 14.12: Dephasing in air-tissue boundaries

There are several:

  1. BOLD Effect

    BOLD contrasts are based on signal dephasing and requite a long delay for contrasts.

  2. Signal Dropout in BOLD

    Dephasing also occurs near air-tissue boundaries due to abrupt shifts in magnetic susceptibilties.

  3. Image warping

    Imperfections in the magnetic field, signals from readouts, and longer readouts can lead to the final image being altered.

  4. Field offset

    This introduces phase accrual during readouts. An EPI offsets warp images while a spiral offsets blur images.

  5. Physiological noises

    Physiological noises can be “BOLD-like” and increases with TE and B0.