Chemical Shift in an EPI sequence

For a more realistic example, we will use a brain phantom.

obj = brain_phantom2D() # a slice of a brain
p1 = plot_phantom_map(obj, :T2 ; height=400, width=400, view_2d=true)
p2 = plot_phantom_map(obj, :Δw ; height=400, width=400, view_2d=true)

At the left, you can see the map of the phantom, and at the right, the off-resonance . In this example, the fat is the only source of off-resonance (with    ) and you can see it in black in the off-resonance map.

Then, we will load an EPI sequence, that is well known for being affected by off-resonance. With this sequence, we will be able visualize the effect of the chemical shift.

seq_file = joinpath(dirname(pathof(KomaMRI)), "../examples/5.koma_paper/comparison_accuracy/sequences/EPI/epi_100x100_TE100_FOV230.seq")
seq = @suppress read_seq(seq_file)
p3 = plot_seq(seq; range=[0 40], slider=true, height=300)

Feel free to explore the sequence's plot 🔍 below!

If we simulate this sequence we will end up with the following signal.

raw = @suppress simulate(obj, seq, sys)
p4 = plot_signal(raw; range=[98.4 103.4] , height=300)

Now, we need to inspect what effect the off-resonance had in the reconstructed image. As you can see, the fat layer is now shifted to a different position 🤯, this is why the effect is called chemical shift!

# Get the acquisition data
acq = AcquisitionData(raw)
acq.traj[1].circular = false #This is to remove the circular mask

# Setting up the reconstruction parameters
Nx, Ny = raw.params["reconSize"][1:2]
reconParams = Dict{Symbol,Any}(:reco=>"direct", :reconSize=>(Nx, Ny))
image = reconstruction(acq, reconParams)

# Plotting the recon
slice_abs = abs.(image[:, :, 1])
p5 = plot_image(slice_abs; height=400)

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