2D dynamic

This example illustrates 2D dynamic MRI image reconstruction from golden angle (GA) radial sampled k-space data collected with multiple coils (parallel MRI), with temporal "TV" regularizer (corner-rounded) using the Julia language.

This entire page was generated using a single Julia file: 3-2d-t.jl. In any such Julia documentation, you can access the source code using the "Edit on GitHub" link in the top right.

The corresponding notebook can be viewed in nbviewer here: 3-2d-t.ipynb, and opened in binder here: 3-2d-t.ipynb.

using ImageGeoms: ImageGeom
using ImagePhantoms: shepp_logan, SouthPark, phantom, Ellipse
using MIRTjim: jim, prompt
using MIRT: Anufft, diffl_map, ncg
using MIRT: ir_mri_sensemap_sim, ir_mri_kspace_ga_radial
using Plots: gui, plot, scatter, default; default(markerstrokecolor=:auto, label="")
using Plots: gif, @animate, Plots
using LinearAlgebra: norm, dot, Diagonal
using LinearMapsAA: LinearMapAA, block_diag
using Random: seed!
jim(:abswarn, false); # suppress warnings about display of |complex| images

The following line is helpful when running this jl-file as a script; this way it will prompt user to hit a key after each image is displayed.

isinteractive() && jim(:prompt, true);

Create (synthetic) data

Generate dynamic image sequence:

N = (60,64)
fov = 220
nt = 8 # frames
ig = ImageGeom(; dims = N, deltas=(fov,fov) ./ N)

object0 = shepp_logan(SouthPark(); fovs = (fov,fov))
objects = Array{typeof(object0)}(undef, nt)
xtrue = Array{ComplexF32}(undef, N..., nt)
for it=1:nt
    tmp = copy(object0)
    width2 = 15 + 5 * sin(2*pi*it/nt) # mouth open/close
    mouth = tmp[2]
    tmp[2] = Ellipse(mouth.center, (mouth.width[1], width2), mouth.angle[1], mouth.value)
    objects[it] = tmp
    xtrue[:,:,it] = phantom(axes(ig)..., tmp, 4)
end
jimxy = (args...; kwargs...) -> jim(axes(ig)..., args...; kwargs...)
jimxy(xtrue, "True images")

Animate true image:

anim1 = @animate for it in 1:nt
    jimxy(xtrue[:,:,it], title="Frame $it")
end
gif(anim1; fps = 6)

Plot one time course to see temporal change:

ix,iy = 30,14
plot(1:nt, abs.(xtrue[ix,iy,:]), label="ix=$ix, iy=$iy",
    marker=:o, xlabel="frame")
isinteractive() && jim(:prompt, true);

Generate k-space sampling and data:

accelerate = 3
nspf = round(Int, maximum(N)/accelerate) # spokes per frame

Nro = maximum(N)
Nspoke = nspf * nt
kspace = ir_mri_kspace_ga_radial(Nro = Nro, Nspoke = Nspoke)
fovs = (fov, fov)
kspace[:,:,1] ./= fovs[1]
kspace[:,:,2] ./= fovs[2]
kspace = reshape(kspace, Nro, nspf, nt, 2)
(size(kspace), extrema(kspace))
((64, 21, 8, 2), (-0.0022727272f0, 0.002272619f0))

Plot sampling (in units of cycles/pixel):

ps = Array{Any}(undef, nt)
for it=1:nt
    ps[it] = scatter(kspace[:,:,it,1] * fovs[1], kspace[:,:,it,2] * fovs[2],
        xtick=(-1:1)*0.5, ytick=(-1:1)*0.5, xlim=(-1,1).*0.52, ylim=(-1,1).*0.52,
        aspect_ratio=1, markersize=1, title="Frame $it")
end
plot(ps..., layout=(2,4))