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Binning

Description

This example described how to perform data binning with different number of profiles which is generaly used for self-gating acquisition in order to reconstruct images along the cardiac/respiratory cycle :

  1. Trotier AJ, Castets CR, Lefrançois W, et al. USPIO-enhanced 3D-cine self-gated cardiac MRI based on a stack-of-stars golden angle short echo time sequence: Application on mice with acute myocardial infarction. Journal of Magnetic Resonance Imaging 2016;44:355–365 doi: 10.1002/jmri.25150.
  2. Ribot EJ, Duriez TJ, Trotier AJ, Thiaudiere E, Franconi J-M, Miraux S. Self-gated bSSFP sequences to detect iron-labeled cancer cells and/or metastases in vivo in mouse liver at 7 Tesla. Journal of Magnetic Resonance Imaging 2015;41:1413–1421 doi: 10.1002/jmri.24688.

Here, we will create a simulated 2D radial acquisition and split the projections in 2 parts along the contrast dimension. The number of projection into each bin will be different to show how MRIReco handle that case.

Setup

using CairoMakie
using ImageUtils: shepp_logan
using MRIReco, MRISimulation

function plot_im2D(im2D;title::String="")
    f = Figure()
    ax = Axis(f[1, 1],aspect = DataAspect(), yreversed = true, title = title)
    image!(ax, im2D')
    hidedecorations!(ax, grid = false)
    f
end
plot_im2D (generic function with 1 method)

Simulate a radial acquisition

N = 256
x = shepp_logan(N)

params = Dict{Symbol, Any}()
params[:simulation] = "fast"
params[:trajName] = "Radial"
params[:numProfiles] = round(Int64,400)
params[:numSamplingPerProfile] = round(Int64,N)

acqRad = simulation(x, params)
rawRad = RawAcquisitionData(acqRad)
RawAcquisitionData(Dict{String, Any}("H1resonanceFrequency_Hz" => 1, "encodedFOV" => [0.0, 0.0, 0.0], "receiverChannels" => 1, "encodedSize" => [256, 256], "trajectory" => "Radial"), Profile[Profile(AcquisitionHeader(0x0000, 0x0000000000000000, 0x00000000, 0x00000001, 0x00000000, (0x00000000, 0x00000000, 0x00000000), 0x0100, 0x0001, 0x0001, (0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000), 0x0000, 0x0000, 0x0000, 0x0000, 0x0002, 3.90625f0, (0.0f0, 0.0f0, 0.0f0), (1.0f0, 0.0f0, 0.0f0), (0.0f0, 1.0f0, 0.0f0), (0.0f0, 0.0f0, 1.0f0), (0.0f0, 0.0f0, 0.0f0), EncodingCounters(0x0000, 0x0000, 0x0000, 0x0000, 0x0000, 0x0000, 0x0000, 0x0000, 0x0000, (0x0000, 0x0000, 0x0000, 0x0000, 0x0000, 0x0000, 0x0000, 0x0000)), (0, 0, 0, 0, 0, 0, 0, 0), (0.0f0, 0.0f0, 0.0f0, 0.0f0, 0.0f0, 0.0f0, 0.0f0, 0.0f0)), Float32[0.5 0.49609375 … -0.4921875 -0.49609375; 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0.023553226 0.023369215 … -0.023185207 -0.023369215], ComplexF32[6.647192f0 - 4.513237f0im; -5.344577f0 - 6.1087575f0im; … ; 8.043451f0 - 3.0312684f0im; -5.344577f0 + 6.1087575f0im;;]), Profile(AcquisitionHeader(0x0000, 0x0000000000000000, 0x00000000, 0x0000018c, 0x00000000, (0x00000000, 0x00000000, 0x00000000), 0x0100, 0x0001, 0x0001, (0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000), 0x0000, 0x0000, 0x0000, 0x0000, 0x0002, 3.90625f0, (0.0f0, 0.0f0, 0.0f0), (1.0f0, 0.0f0, 0.0f0), (0.0f0, 1.0f0, 0.0f0), (0.0f0, 0.0f0, 1.0f0), (0.0f0, 0.0f0, 0.0f0), EncodingCounters(0x018b, 0x0000, 0x0000, 0x0000, 0x0000, 0x0000, 0x0000, 0x0000, 0x0000, (0x0000, 0x0000, 0x0000, 0x0000, 0x0000, 0x0000, 0x0000, 0x0000)), (0, 0, 0, 0, 0, 0, 0, 0), (0.0f0, 0.0f0, 0.0f0, 0.0f0, 0.0f0, 0.0f0, 0.0f0, 0.0f0)), Float32[0.4996145 0.49571127 … -0.49180803 -0.49571127; -0.019629909 -0.01947655 … 0.01932319 0.01947655], ComplexF32[-2.8462155f0 + 2.9520223f0im; -6.325454f0 + 10.3677635f0im; … ; 9.9572f0 + 3.585513f0im; -6.325454f0 - 10.3677635f0im;;]), Profile(AcquisitionHeader(0x0000, 0x0000000000000000, 0x00000000, 0x0000018d, 0x00000000, (0x00000000, 0x00000000, 0x00000000), 0x0100, 0x0001, 0x0001, (0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000), 0x0000, 0x0000, 0x0000, 0x0000, 0x0002, 3.90625f0, (0.0f0, 0.0f0, 0.0f0), (1.0f0, 0.0f0, 0.0f0), (0.0f0, 1.0f0, 0.0f0), (0.0f0, 0.0f0, 1.0f0), (0.0f0, 0.0f0, 0.0f0), EncodingCounters(0x018c, 0x0000, 0x0000, 0x0000, 0x0000, 0x0000, 0x0000, 0x0000, 0x0000, (0x0000, 0x0000, 0x0000, 0x0000, 0x0000, 0x0000, 0x0000, 0x0000)), (0, 0, 0, 0, 0, 0, 0, 0), (0.0f0, 0.0f0, 0.0f0, 0.0f0, 0.0f0, 0.0f0, 0.0f0, 0.0f0)), Float32[-0.49975327 -0.49584895 … 0.49194464 0.49584895; 0.015705379 0.015582682 … -0.015459983 -0.015582682], ComplexF32[10.063043f0 + 2.208339f0im; -4.4534216f0 + 16.219978f0im; … ; 2.3117576f0 + 1.4369543f0im; -4.4534216f0 - 16.219978f0im;;]), Profile(AcquisitionHeader(0x0000, 0x0000000000000000, 0x00000000, 0x0000018e, 0x00000000, (0x00000000, 0x00000000, 0x00000000), 0x0100, 0x0001, 0x0001, (0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000), 0x0000, 0x0000, 0x0000, 0x0000, 0x0002, 3.90625f0, (0.0f0, 0.0f0, 0.0f0), (1.0f0, 0.0f0, 0.0f0), (0.0f0, 1.0f0, 0.0f0), (0.0f0, 0.0f0, 1.0f0), (0.0f0, 0.0f0, 0.0f0), EncodingCounters(0x018d, 0x0000, 0x0000, 0x0000, 0x0000, 0x0000, 0x0000, 0x0000, 0x0000, (0x0000, 0x0000, 0x0000, 0x0000, 0x0000, 0x0000, 0x0000, 0x0000)), (0, 0, 0, 0, 0, 0, 0, 0), (0.0f0, 0.0f0, 0.0f0, 0.0f0, 0.0f0, 0.0f0, 0.0f0, 0.0f0)), Float32[0.4998612 0.49595606 … -0.4920509 -0.49595606; -0.011779882 -0.011687852 … 0.011595822 0.011687852], ComplexF32[16.642672f0 - 1.3222855f0im; -2.337967f0 - 8.295842f0im; … ; 2.082176f0 + 0.3756948f0im; -2.337967f0 + 8.295842f0im;;]), Profile(AcquisitionHeader(0x0000, 0x0000000000000000, 0x00000000, 0x0000018f, 0x00000000, (0x00000000, 0x00000000, 0x00000000), 0x0100, 0x0001, 0x0001, (0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000), 0x0000, 0x0000, 0x0000, 0x0000, 0x0002, 3.90625f0, (0.0f0, 0.0f0, 0.0f0), (1.0f0, 0.0f0, 0.0f0), (0.0f0, 1.0f0, 0.0f0), (0.0f0, 0.0f0, 1.0f0), (0.0f0, 0.0f0, 0.0f0), EncodingCounters(0x018e, 0x0000, 0x0000, 0x0000, 0x0000, 0x0000, 0x0000, 0x0000, 0x0000, (0x0000, 0x0000, 0x0000, 0x0000, 0x0000, 0x0000, 0x0000, 0x0000)), (0, 0, 0, 0, 0, 0, 0, 0), (0.0f0, 0.0f0, 0.0f0, 0.0f0, 0.0f0, 0.0f0, 0.0f0, 0.0f0)), Float32[-0.4999383 -0.49603254 … 0.4921268 0.49603254; 0.007853659 0.007792302 … -0.007730945 -0.007792302], ComplexF32[3.0176444f0 - 0.27731967f0im; -7.6356697f0 - 18.21156f0im; … ; 8.107416f0 - 7.63516f0im; -7.6356697f0 + 18.21156f0im;;]), Profile(AcquisitionHeader(0x0000, 0x0000000000000000, 0x00000000, 0x00000190, 0x00000000, (0x00000000, 0x00000000, 0x00000000), 0x0100, 0x0001, 0x0001, (0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000, 0x0000000000000000), 0x0000, 0x0000, 0x0000, 0x0000, 0x0002, 3.90625f0, (0.0f0, 0.0f0, 0.0f0), (1.0f0, 0.0f0, 0.0f0), (0.0f0, 1.0f0, 0.0f0), (0.0f0, 0.0f0, 1.0f0), (0.0f0, 0.0f0, 0.0f0), EncodingCounters(0x018f, 0x0000, 0x0000, 0x0000, 0x0000, 0x0000, 0x0000, 0x0000, 0x0000, (0x0000, 0x0000, 0x0000, 0x0000, 0x0000, 0x0000, 0x0000, 0x0000)), (0, 0, 0, 0, 0, 0, 0, 0), (0.0f0, 0.0f0, 0.0f0, 0.0f0, 0.0f0, 0.0f0, 0.0f0, 0.0f0)), Float32[0.4999846 0.49607846 … -0.49217233 -0.49607846; -0.0039269505 -0.003896271 … 0.003865592 0.003896271], ComplexF32[5.0861206f0 - 0.14333908f0im; -7.22011f0 + 3.4893963f0im; … ; 3.9865615f0 + 6.037969f0im; -7.22011f0 - 3.4893963f0im;;])])

For real acquisition we first create the RawAcquisitionData structure and then convert into the AcquisitionData.

Binning Data

rawRad2 = deepcopy(rawRad)
for i in 1:length(rawRad.profiles)
    if  mod(i,4) == 0
        rawRad2.profiles[i].head.idx.contrast = 0
    else
        rawRad2.profiles[i].head.idx.contrast = 1
    end
end;

We need to tell to MRIReco that our trajectory is a custom one :

rawRad2.params["trajectory"] = "custom";

Reconstruction

To perform the reconstruction we need to convert the RawAcquisitionData into and AcquisitionData structure.

acqRad2 = AcquisitionData(rawRad2)
AcquisitionData{Float32, 2}(Dict{Symbol, Any}(), Trajectory{Float32}[Trajectory{Float32}("Custom", Float32[-0.4998612 -0.49595606 … -0.49217233 -0.49607846; -0.011779882 -0.011687852 … 0.003865592 0.003896271], Float32[0.0, 3.90625f-6, 7.8125f-6, 1.171875f-5, 1.5625f-5, 1.953125f-5, 2.34375f-5, 2.734375f-5, 3.125f-5, 3.515625f-5  …  0.0009609375, 0.0009648437, 0.00096875, 0.00097265624, 0.0009765625, 0.0009804687, 0.000984375, 0.0009882812, 0.0009921875, 0.0009960937], 0.0f0, 0.001f0, 100, 256, 1, false, true), Trajectory{Float32}("Custom", Float32[0.5 0.49609375 … 0.4921268 0.49603254; 0.0 0.0 … -0.007730945 -0.007792302], Float32[0.0, 3.90625f-6, 7.8125f-6, 1.171875f-5, 1.5625f-5, 1.953125f-5, 2.34375f-5, 2.734375f-5, 3.125f-5, 3.515625f-5  …  0.0009609375, 0.0009648437, 0.00096875, 0.00097265624, 0.0009765625, 0.0009804687, 0.000984375, 0.0009882812, 0.0009921875, 0.0009960937], 0.0f0, 0.001f0, 300, 256, 1, false, true)], Matrix{ComplexF32}[[16.566465f0 - 2.3467724f0im; -2.973968f0 + 6.258399f0im; … ; 3.9865615f0 + 6.037969f0im; -7.22011f0 - 3.4893963f0im;;]; [14.993826f0 - 0.0139813805f0im; -2.7452886f0 - 17.48704f0im; … ; 8.107416f0 - 7.63516f0im; -7.6356697f0 + 18.21156f0im;;];;;], [[897, 898, 899, 900, 901, 902, 903, 904, 905, 906  …  102519, 102520, 102521, 102522, 102523, 102524, 102525, 102526, 102527, 102528], [129, 130, 131, 132, 133, 134, 135, 136, 137, 138  …  102263, 102264, 102265, 102266, 102267, 102268, 102269, 102270, 102271, 102272]], (256, 256), (0.0, 0.0, 0.0))

We can also plot the number of projection for both bin :

nPro1 = Int32(length(acqRad2.kdata[1,1,1])/N)
nPro2 = Int32(length(acqRad2.kdata[2,1,1])/N)
println("Number of projection in : \n
- Bin 1 = $nPro1\n
- Bin 2 = $nPro2")
Number of projection in :

- Bin 1 = 100

- Bin 2 = 300

Now we can perform a standard reconstruction

params = Dict{Symbol, Any}()
params[:reco] = "direct"
params[:reconSize] = (N,N)

Ireco = reconstruction(acqRad2, params)
size(Ireco)
(256, 256, 1, 2, 1, 1)

let's show the results for first bin

plot_im2D(abs.(Ireco[:,:,1,1]),title = "First bin")

and the second bin

plot_im2D(abs.(Ireco[:,:,1,2]),title = "Second bin")

As expected we have more streaking artifacts on the first bin because we reconstruct the image with less projections.

Reproducibility

This page was generated with the following version of Julia:

using InteractiveUtils
io = IOBuffer();
versioninfo(io);
split(String(take!(io)), '\n')
12-element Vector{SubString{String}}:
 "Julia Version 1.10.4"
 "Commit 48d4fd48430 (2024-06-04 10:41 UTC)"
 "Build Info:"
 "  Official https://julialang.org/ release"
 "Platform Info:"
 "  OS: Linux (x86_64-linux-gnu)"
 "  CPU: 4 × AMD EPYC 7763 64-Core Processor"
 "  WORD_SIZE: 64"
 "  LIBM: libopenlibm"
 "  LLVM: libLLVM-15.0.7 (ORCJIT, znver3)"
 "Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)"
 ""

And with the following package versions

import Pkg; Pkg.status()
Status `~/work/MRIReco.jl/MRIReco.jl/docs/Project.toml`
  [13f3f980] CairoMakie v0.12.5
⌃ [e30172f5] Documenter v0.25.2
  [8ad4436d] ImageUtils v0.2.11
  [98b081ad] Literate v2.19.0
  [f7771a9a] MRIBase v0.4.3 `/home/runner/work/MRIReco.jl/MRIReco.jl:MRIBase#master`
  [c57eb701] MRICoilSensitivities v0.1.3 `/home/runner/work/MRIReco.jl/MRIReco.jl:MRICoilSensitivities#master`
  [5a6f062f] MRIFiles v0.3.2 `/home/runner/work/MRIReco.jl/MRIReco.jl:MRIFiles#master`
  [fb1137e3] MRIOperators v0.2.1 `/home/runner/work/MRIReco.jl/MRIReco.jl:MRIOperators#master`
  [bdf86e05] MRIReco v0.9.0 `~/work/MRIReco.jl/MRIReco.jl`
  [9be66c26] MRISampling v0.1.2 `/home/runner/work/MRIReco.jl/MRIReco.jl:MRISampling#master`
  [8988da37] MRISimulation v0.1.2 `/home/runner/work/MRIReco.jl/MRIReco.jl:MRISimulation#master`
  [b77e0a4c] InteractiveUtils
Info Packages marked with ⌃ have new versions available and may be upgradable.

This page was generated using Literate.jl.