Chemical Shift in an EPI sequence
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B0: Float64 1.5
B1: Float64 1.0e-5
Gmax: Float64 0.06
Smax: Int64 500
ADC_ฮt: Float64 2.0e-6
seq_ฮt: Float64 1.0e-5
GR_ฮt: Float64 1.0e-5
RF_ฮt: Float64 1.0e-6
RF_ring_down_T: Float64 2.0e-5
RF_dead_time_T: Float64 0.0001
ADC_dead_time_T: Float64 1.0e-5
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, :ฮw ; height=400, width=400, view_2d=true)
"../assets/2-phantom2.html"
At the left, you can see the $T_2$ map of the phantom, and at the right, the off-resonance $\Delta\omega$. In this example, the fat is the only source of off-resonance (with $\Delta f = -220\,\mathrm{Hz}$) 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 = read_seq(seq_file)
p3 = plot_seq(seq; range=[0 40], slider=true, height=300)
"../assets/2-seq.html"
Feel free to explore the sequence's plot ๐ below!
If we simulate this sequence we will end up with the following signal.
raw = simulate(obj, seq, sys)
p4 = plot_signal(raw; range=[98.4 103.4] , height=300)
"../assets/2-signal.html"
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 ๐คฏ, 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)
"../assets/2-recon.html"
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