Chemical Shift Artifact; Setting Up A Basic Fmri Experiment; Study Design - Siemens fMRI User Manual

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5.4 Chemical shift artifact

Figure 10. Chemical shift artifact in EPI.

Note that the fat pixels are shifted spatially in the image in the phase-encoding direction due to their chemical shift frequency offset

(440 Hz at 3T).

In an EPI sequence, the readout bandwidth is quite large, on the order of 1300-2000 Hz/pixel. At 3T, this results in

a fat-water pixel shift of only approximately half a pixel. The bandwidth in the phase-encoding direction however

is much lower, in the range of 20-30 Hz/pixel for a typical protocol. For these bandwidths, the fat pixels will

be shifted by 10-20 pixels, or about 3-4 cm at typical spatial resolutions. To avoid chemical shift artifacts, a fat

suppression pulse is implemented prior to each imaging volume.

Let's run a basic experiment to get started on fMRI. We will run a block design experiment, i.e. ON and OFF

design, with a simple motor task such as finger tapping. In this task, the subject touches his/her thumb

consecutively with the index, middle, ring, and little fingers of one hand at a time. After a specified time, the

subject switches finger tapping to the other hand.

Baseline

Rt. hand

10 meas.

Figure 11. Block design finger tapping motor task.

We will set up the EPI sequence for a TR of 3s and 60 measurements. On the BOLD card on the protocol menu,

define the GLM paradigm size as 20, with the first 10 measurements as "Baseline" and the next 10 measurements

as "Active." What this defines then is our ON time and OFF time in the block design, i.e. we will now have (10

measurements x 3s) time of right-hand finger tapping (or "Baseline" state) and (10 measurements x 3s) time or

left-hand finger tapping (or "Active" state). In data analysis, the BOLD signal variation is compared to the motor

task timing to estimate correlation. For slice positioning, we have to cover the motor cortex. To minimize slice

planning, we will scan a large number of slices, covering the whole brain.

The EPI sequence and the motor task can be synchronized manually by giving the subject instructions to "switch"

hands through the microphone. Since our paradigm size is 20 measurements, with 10 measurements "Baseline"

and 10 measurements "Active," the subject will have to switch hands every 10 measurements or 30s.

Active

Lt. hand