Subspace

Description

This example described how to perform a subspace reconstruction for $T_2$ mapping acceleration.

Setup and define global variable

using CairoMakie
using ImageUtils: shepp_logan
using LinearAlgebra
using  Random
using MRIReco, MRISimulation, MRICoilSensitivities, MRISampling,MRIOperators
using MRIReco.RegularizedLeastSquares
color=Makie.wong_colors() # color for plots

N = 128
T = ComplexF32
nCh = 4
nEchos = 10
TE = 7.0



x = T.(shepp_logan(N))
128×128 Matrix{ComplexF32}:
 0.0+0.0im  0.0+0.0im  0.0+0.0im  …  0.0+0.0im  0.0+0.0im  0.0+0.0im
 0.0+0.0im  0.0+0.0im  0.0+0.0im     0.0+0.0im  0.0+0.0im  0.0+0.0im
 0.0+0.0im  0.0+0.0im  0.0+0.0im     0.0+0.0im  0.0+0.0im  0.0+0.0im
 0.0+0.0im  0.0+0.0im  0.0+0.0im     0.0+0.0im  0.0+0.0im  0.0+0.0im
 0.0+0.0im  0.0+0.0im  0.0+0.0im     0.0+0.0im  0.0+0.0im  0.0+0.0im
 0.0+0.0im  0.0+0.0im  0.0+0.0im  …  0.0+0.0im  0.0+0.0im  0.0+0.0im
 0.0+0.0im  0.0+0.0im  0.0+0.0im     0.0+0.0im  0.0+0.0im  0.0+0.0im
 0.0+0.0im  0.0+0.0im  0.0+0.0im     0.0+0.0im  0.0+0.0im  0.0+0.0im
 0.0+0.0im  0.0+0.0im  0.0+0.0im     0.0+0.0im  0.0+0.0im  0.0+0.0im
 0.0+0.0im  0.0+0.0im  0.0+0.0im     0.0+0.0im  0.0+0.0im  0.0+0.0im
    ⋮                             ⋱     ⋮                  
 0.0+0.0im  0.0+0.0im  0.0+0.0im     0.0+0.0im  0.0+0.0im  0.0+0.0im
 0.0+0.0im  0.0+0.0im  0.0+0.0im  …  0.0+0.0im  0.0+0.0im  0.0+0.0im
 0.0+0.0im  0.0+0.0im  0.0+0.0im     0.0+0.0im  0.0+0.0im  0.0+0.0im
 0.0+0.0im  0.0+0.0im  0.0+0.0im     0.0+0.0im  0.0+0.0im  0.0+0.0im
 0.0+0.0im  0.0+0.0im  0.0+0.0im     0.0+0.0im  0.0+0.0im  0.0+0.0im
 0.0+0.0im  0.0+0.0im  0.0+0.0im     0.0+0.0im  0.0+0.0im  0.0+0.0im
 0.0+0.0im  0.0+0.0im  0.0+0.0im  …  0.0+0.0im  0.0+0.0im  0.0+0.0im
 0.0+0.0im  0.0+0.0im  0.0+0.0im     0.0+0.0im  0.0+0.0im  0.0+0.0im
 0.0+0.0im  0.0+0.0im  0.0+0.0im     0.0+0.0im  0.0+0.0im  0.0+0.0im

simulate MESE acquisition of a shepp logan phantom

First we need to simulate a multi-echo spin-echo phantom. The R₂ maps is based on the value of each voxel the shepp logan phantom. For the T2 we use

rmap = 0.05*abs.(x)
TEnum = Float64.(collect(TE:TE:TE*nEchos))

coilsens = T.(birdcageSensitivity(N, nCh, 4.))
params = Dict{Symbol,Any}()
params[:simulation] = "fast"
params[:trajName] = "Cartesian"
params[:numProfiles] = floor(Int64, N)
params[:numSamplingPerProfile] = N
params[:r2map] = rmap
params[:T_echo] = TEnum
params[:seqName] = "ME"
params[:refocusingAngles] = Float64.(repeat([pi], length(TEnum)))
params[:senseMaps] = coilsens

acqData = simulation(real(x), params)
AcquisitionData{Float32, 2}(Dict{Symbol, Any}(), Trajectory{Float32}[Trajectory{Float32}("Cartesian", Float32[-0.5 -0.4921875 … 0.484375 0.4921875; -0.5 -0.5 … 0.4921875 0.4921875], Float32[0.0, 7.8125f-6, 1.5625f-5, 2.34375f-5, 3.125f-5, 3.9062503f-5, 4.6875f-5, 5.46875f-5, 6.25f-5, 7.0312504f-5  …  0.00092187506, 0.0009296875, 0.00093750004, 0.00094531255, 0.00095312507, 0.0009609375, 0.00096875004, 0.0009765625, 0.000984375, 0.0009921875], 0.0f0, 0.001f0, 128, 128, 1, true, false), Trajectory{Float32}("Cartesian", Float32[-0.5 -0.4921875 … 0.484375 0.4921875; -0.5 -0.5 … 0.4921875 0.4921875], Float32[0.0, 7.8125f-6, 1.5625f-5, 2.34375f-5, 3.125f-5, 3.9062503f-5, 4.6875f-5, 5.46875f-5, 6.25f-5, 7.0312504f-5  …  0.00092187506, 0.0009296875, 0.00093750004, 0.00094531255, 0.00095312507, 0.0009609375, 0.00096875004, 0.0009765625, 0.000984375, 0.0009921875], 0.0f0, 0.001f0, 128, 128, 1, true, false), Trajectory{Float32}("Cartesian", Float32[-0.5 -0.4921875 … 0.484375 0.4921875; -0.5 -0.5 … 0.4921875 0.4921875], Float32[0.0, 7.8125f-6, 1.5625f-5, 2.34375f-5, 3.125f-5, 3.9062503f-5, 4.6875f-5, 5.46875f-5, 6.25f-5, 7.0312504f-5  …  0.00092187506, 0.0009296875, 0.00093750004, 0.00094531255, 0.00095312507, 0.0009609375, 0.00096875004, 0.0009765625, 0.000984375, 0.0009921875], 0.0f0, 0.001f0, 128, 128, 1, true, false), Trajectory{Float32}("Cartesian", Float32[-0.5 -0.4921875 … 0.484375 0.4921875; -0.5 -0.5 … 0.4921875 0.4921875], Float32[0.0, 7.8125f-6, 1.5625f-5, 2.34375f-5, 3.125f-5, 3.9062503f-5, 4.6875f-5, 5.46875f-5, 6.25f-5, 7.0312504f-5  …  0.00092187506, 0.0009296875, 0.00093750004, 0.00094531255, 0.00095312507, 0.0009609375, 0.00096875004, 0.0009765625, 0.000984375, 0.0009921875], 0.0f0, 0.001f0, 128, 128, 1, true, false), Trajectory{Float32}("Cartesian", Float32[-0.5 -0.4921875 … 0.484375 0.4921875; -0.5 -0.5 … 0.4921875 0.4921875], Float32[0.0, 7.8125f-6, 1.5625f-5, 2.34375f-5, 3.125f-5, 3.9062503f-5, 4.6875f-5, 5.46875f-5, 6.25f-5, 7.0312504f-5  …  0.00092187506, 0.0009296875, 0.00093750004, 0.00094531255, 0.00095312507, 0.0009609375, 0.00096875004, 0.0009765625, 0.000984375, 0.0009921875], 0.0f0, 0.001f0, 128, 128, 1, true, false), Trajectory{Float32}("Cartesian", Float32[-0.5 -0.4921875 … 0.484375 0.4921875; -0.5 -0.5 … 0.4921875 0.4921875], Float32[0.0, 7.8125f-6, 1.5625f-5, 2.34375f-5, 3.125f-5, 3.9062503f-5, 4.6875f-5, 5.46875f-5, 6.25f-5, 7.0312504f-5  …  0.00092187506, 0.0009296875, 0.00093750004, 0.00094531255, 0.00095312507, 0.0009609375, 0.00096875004, 0.0009765625, 0.000984375, 0.0009921875], 0.0f0, 0.001f0, 128, 128, 1, true, false), Trajectory{Float32}("Cartesian", Float32[-0.5 -0.4921875 … 0.484375 0.4921875; -0.5 -0.5 … 0.4921875 0.4921875], Float32[0.0, 7.8125f-6, 1.5625f-5, 2.34375f-5, 3.125f-5, 3.9062503f-5, 4.6875f-5, 5.46875f-5, 6.25f-5, 7.0312504f-5  …  0.00092187506, 0.0009296875, 0.00093750004, 0.00094531255, 0.00095312507, 0.0009609375, 0.00096875004, 0.0009765625, 0.000984375, 0.0009921875], 0.0f0, 0.001f0, 128, 128, 1, true, false), Trajectory{Float32}("Cartesian", Float32[-0.5 -0.4921875 … 0.484375 0.4921875; -0.5 -0.5 … 0.4921875 0.4921875], Float32[0.0, 7.8125f-6, 1.5625f-5, 2.34375f-5, 3.125f-5, 3.9062503f-5, 4.6875f-5, 5.46875f-5, 6.25f-5, 7.0312504f-5  …  0.00092187506, 0.0009296875, 0.00093750004, 0.00094531255, 0.00095312507, 0.0009609375, 0.00096875004, 0.0009765625, 0.000984375, 0.0009921875], 0.0f0, 0.001f0, 128, 128, 1, true, false), Trajectory{Float32}("Cartesian", Float32[-0.5 -0.4921875 … 0.484375 0.4921875; -0.5 -0.5 … 0.4921875 0.4921875], Float32[0.0, 7.8125f-6, 1.5625f-5, 2.34375f-5, 3.125f-5, 3.9062503f-5, 4.6875f-5, 5.46875f-5, 6.25f-5, 7.0312504f-5  …  0.00092187506, 0.0009296875, 0.00093750004, 0.00094531255, 0.00095312507, 0.0009609375, 0.00096875004, 0.0009765625, 0.000984375, 0.0009921875], 0.0f0, 0.001f0, 128, 128, 1, true, false), Trajectory{Float32}("Cartesian", Float32[-0.5 -0.4921875 … 0.484375 0.4921875; -0.5 -0.5 … 0.4921875 0.4921875], Float32[0.0, 7.8125f-6, 1.5625f-5, 2.34375f-5, 3.125f-5, 3.9062503f-5, 4.6875f-5, 5.46875f-5, 6.25f-5, 7.0312504f-5  …  0.00092187506, 0.0009296875, 0.00093750004, 0.00094531255, 0.00095312507, 0.0009609375, 0.00096875004, 0.0009765625, 0.000984375, 0.0009921875], 0.0f0, 0.001f0, 128, 128, 1, true, false)], Matrix{ComplexF32}[[-0.061319664f0 + 0.017328978f0im -0.060168564f0 - 0.08990121f0im 0.15327841f0 - 0.0001885891f0im -0.044200927f0 + 0.1044693f0im; 0.13910598f0 - 0.3327852f0im 0.32951653f0 - 0.069086686f0im 0.08607823f0 + 0.24484318f0im -0.2546804f0 - 0.11161268f0im; … ; -0.2469412f0 - 2.0783782f0im -0.19207834f0 - 1.8354934f0im -0.50140864f0 - 1.7342794f0im -0.5504193f0 - 2.0933352f0im; -0.39968485f0 - 1.7166488f0im -0.22616488f0 - 1.8982661f0im -0.116233066f0 - 1.6665893f0im -0.2668302f0 - 1.608389f0im]; [-0.03628423f0 + 0.002153933f0im -0.047774702f0 - 0.07336438f0im 0.10886579f0 - 0.014143705f0im -0.032712057f0 + 0.05882424f0im; 0.11176926f0 - 0.26732126f0im 0.25885093f0 - 0.07452397f0im 0.07931733f0 + 0.15332226f0im -0.16305706f0 - 0.10037924f0im; … ; -0.16288717f0 - 1.3709396f0im -0.12984529f0 - 1.2005954f0im -0.35099694f0 - 1.1324831f0im -0.37688038f0 - 1.3907237f0im; -0.25053963f0 - 1.3135548f0im -0.1369215f0 - 1.4281363f0im -0.070114344f0 - 1.2801168f0im -0.16514462f0 - 1.2434534f0im]; … ; [0.012780843f0 - 0.054939546f0im -0.01557029f0 - 0.059982f0im 0.009564942f0 - 0.06516403f0im -0.0056816936f0 - 0.061399773f0im; 0.043611184f0 - 0.11495465f0im 0.083025604f0 - 0.08596645f0im 0.053073376f0 - 0.053876266f0im 0.02885978f0 - 0.07771109f0im; … ; -8.274987f-5 + 0.07946415f0im -0.007975124f0 + 0.09075475f0im -0.031785965f0 + 0.09164592f0im -0.017845709f0 + 0.05942282f0im; 0.037896715f0 - 0.34353763f0im 0.029270597f0 - 0.3217612f0im 0.008714091f0 - 0.34047538f0im 0.023856364f0 - 0.35112888f0im]; [0.013366346f0 - 0.058309693f0im -0.013997305f0 - 0.061284862f0im 0.006546908f0 - 0.06791401f0im -0.004679367f0 - 0.06604436f0im; 0.04045324f0 - 0.10858832f0im 0.0751528f0 - 0.0852703f0im 0.05060865f0 - 0.059629396f0im 0.03289397f0 - 0.076442644f0im; … ; 0.002098024f0 + 0.1077297f0im -0.006123226f0 + 0.11456848f0im -0.023878727f0 + 0.114144534f0im -0.010111824f0 + 0.08896649f0im; 0.041279607f0 - 0.30421883f0im 0.030340124f0 - 0.28008235f0im 0.008398823f0 - 0.3014351f0im 0.025187712f0 - 0.31323624f0im];;;], [[1, 2, 3, 4, 5, 6, 7, 8, 9, 10  …  16375, 16376, 16377, 16378, 16379, 16380, 16381, 16382, 16383, 16384], [1, 2, 3, 4, 5, 6, 7, 8, 9, 10  …  16375, 16376, 16377, 16378, 16379, 16380, 16381, 16382, 16383, 16384], [1, 2, 3, 4, 5, 6, 7, 8, 9, 10  …  16375, 16376, 16377, 16378, 16379, 16380, 16381, 16382, 16383, 16384], [1, 2, 3, 4, 5, 6, 7, 8, 9, 10  …  16375, 16376, 16377, 16378, 16379, 16380, 16381, 16382, 16383, 16384], [1, 2, 3, 4, 5, 6, 7, 8, 9, 10  …  16375, 16376, 16377, 16378, 16379, 16380, 16381, 16382, 16383, 16384], [1, 2, 3, 4, 5, 6, 7, 8, 9, 10  …  16375, 16376, 16377, 16378, 16379, 16380, 16381, 16382, 16383, 16384], [1, 2, 3, 4, 5, 6, 7, 8, 9, 10  …  16375, 16376, 16377, 16378, 16379, 16380, 16381, 16382, 16383, 16384], [1, 2, 3, 4, 5, 6, 7, 8, 9, 10  …  16375, 16376, 16377, 16378, 16379, 16380, 16381, 16382, 16383, 16384], [1, 2, 3, 4, 5, 6, 7, 8, 9, 10  …  16375, 16376, 16377, 16378, 16379, 16380, 16381, 16382, 16383, 16384], [1, 2, 3, 4, 5, 6, 7, 8, 9, 10  …  16375, 16376, 16377, 16378, 16379, 16380, 16381, 16382, 16383, 16384]], (128, 128), (0.0, 0.0, 0.0))

Subsampling the kspace

We need to subsample the data. We generate a sampling mask which is different for each TE.

mask = zeros(Int32,(N,N,length(TEnum)))
for echo = 1:length(TEnum)
  mask_tmp = zeros(Int32,(N,N))
  cal_disk = sample_poissondisk((N,N),4.0;calsize = 14,seed=echo)

  mask_tmp[cal_disk] .= 1
  mask[:,:,echo] = mask_tmp
end

f=Figure()
ax = Axis(f[1,1],title = "mask TE n°1")
heatmap!(ax,mask[:,:,1])
ax = Axis(f[1,2],title = "mask TE n°2")
heatmap!(ax,mask[:,:,2])
f

Let's subsample the k-space in 2 different ways :

  • With the same mask along the temporal dimensions : acqData_u
  • With different masks along the temporal dimensions : acqData_u2
mask_multi2 = repeat(mask[:,:,1],1,1,1,nCh,nEchos,1);# same first mask along TE

kspace = kDataCart(acqData);
kspace = kspace .* mask_multi2;
acqData_u = AcquisitionData(kspace);

mask_multi = repeat(mask,1,1,1,nCh,1,1);
mask_multi = permutedims(mask_multi,(1,2,5,4,3,6));

kspace = kDataCart(acqData);
kspace = kspace .* mask_multi;
acqData_u2 = AcquisitionData(kspace);

Reconstruction of undersampled rawdata

params = Dict{Symbol,Any}()
params[:reconSize] = (N, N)
params[:reco] = "multiCoilMultiEcho"
params[:reg] = L2Regularization(1.e-3)
params[:iterations] = 1
params[:solver] = CGNR
params[:senseMaps] = reshape(coilsens, N, N, 1, nCh)

im_x = reconstruction(acqData, params).data # fully reconstruction
im_phant = abs.(im_x)

im_x_u = reconstruction(acqData_u, params).data # undersampling same mask
im_phant_u = abs.(im_x_u)

im_x_u2 = reconstruction(acqData_u2, params).data # undersampling different mask along TE
im_phant_u2 = abs.(im_x_u2)

p1 = (100, 45)
p2 = (40, 60)
echo=1
f = Figure()
ax = Axis(f[1, 1], aspect=1, title="Fully")
hidedecorations!(ax)
heatmap!(ax, im_phant[:, :, 1, echo, 1, 1])
scatter!(ax, p1,color=color[4])
scatter!(ax, p2,color=color[4])

ax = Axis(f[2, 1], aspect=1, title="CS same mask")
hidedecorations!(ax)
heatmap!(ax, im_phant_u[:, :, 1, echo, 1, 1])

ax = Axis(f[3, 1], aspect=1, title="CS different masks")
hidedecorations!(ax)
heatmap!(ax, im_phant_u2[:, :, 1, echo, 1, 1])

ax = Axis(f[:, 2],title = "T2₁=$(round(1/rmap[p1...],digits=0)) | T2₂=$(round(1/rmap[p2...],digits=0)) ms",xlabel = "TE [ms]",ylabel = "MR signal")
lines!(ax, im_phant[p1..., 1, :, 1, 1],color=:black,label = "fully")
lines!(ax, im_phant[p2..., 1, :, 1, 1],color=:black)

lines!(ax, im_phant_u[p1..., 1, :, 1, 1],color=color[2],label = "same mask")
lines!(ax, im_phant_u[p2..., 1, :, 1, 1],color=color[2],)

lines!(ax, im_phant_u2[p1..., 1, :, 1, 1],color=color[3],label = "different mask")
lines!(ax, im_phant_u2[p2..., 1, :, 1, 1],color=color[3])
axislegend(ax)
f

When the same mask is used along the temporal dimension, we see a standard decaying exponential curve. However the rate of decrease is biased by the PSF effect of the undersampling mask, corresponding by the same sum of others weigthed pixels.

When the mask is not the same along the temporal dimension, we observed a noisy curve close to the real exponential.

Implementation of a subspace reconstruction

Build the dictionary

We build a signal dictionary using the analytical equation :

\[S(TE) = \frac{-TE}{T2}\]

with a range of T2 from 1:1:2000 ms

function createExpBasis(TE_vec::AbstractVector{T}, T2_vec::AbstractVector{T}) where {T<:Real}
  nTE = length(TE_vec)
  nSimu = length(T2_vec)
  expSignal = zeros(T, nSimu, nTE)

  for (i, T2) in enumerate(T2_vec)
    expSignal[i, :] = exp.(-TE_vec / T2_vec[i])
  end

  return expSignal
end

T2_vec = (1:1:2000)
sDict = createExpBasis(Float32.(TEnum), Float32.(T2_vec))
2000×10 Matrix{Float32}:
 0.000911882  8.31529f-7   7.58256f-10  …  4.35961f-28  3.97545f-31
 0.0301974    0.000911882  2.75364f-5      2.08797f-14  6.30512f-16
 0.096972     0.00940356   0.000911882     7.58256f-10  7.35295f-11
 0.173774     0.0301974    0.00524752      1.44498f-7   2.511f-8
 0.246597     0.0608101    0.0149956       3.37201f-6   8.31529f-7
 0.311403     0.096972     0.0301974    …  2.75364f-5   8.57494f-6
 0.367879     0.135335     0.0497871       0.00012341   4.53999f-5
 0.416862     0.173774     0.0724398       0.000380129  0.000158461
 0.459426     0.211072     0.096972        0.000911882  0.000418942
 0.496585     0.246597     0.122456        0.0018363    0.000911882
 ⋮                                      ⋱               
 0.996492     0.992997     0.989513        0.968868     0.96547
 0.996494     0.993        0.989518        0.968884     0.965487
 0.996496     0.993004     0.989524        0.968899     0.965504
 0.996497     0.993007     0.989529        0.968914     0.965521
 0.996499     0.993011     0.989534     …  0.96893      0.965538
 0.996501     0.993014     0.989539        0.968945     0.965555
 0.996503     0.993017     0.989545        0.96896      0.965572
 0.996504     0.993021     0.98955         0.968976     0.965589
 0.996506     0.993024     0.989555        0.968991     0.965605

For real application with stimulated echo we have to remove the 1st echo from the dictionary and the rawdata

Extract the subspace temporal basis

Now we can perform an svd decomposition of the signal dictionnary in order to extract the temporal basis in order to use them during the reconstruction

svd_obj = svd(sDict)
basis = Complex.(svd_obj.V)[:, 1:5]
10×5 Matrix{ComplexF32}:
 -0.333034+0.0im    0.593633+0.0im  …     0.378921+0.0im  -0.164077+0.0im
  -0.32883+0.0im    0.390348+0.0im       -0.525306+0.0im   0.568116+0.0im
 -0.324832+0.0im    0.227168+0.0im       -0.342704+0.0im   -0.21721+0.0im
 -0.321005+0.0im   0.0917305+0.0im     -0.00770928+0.0im   -0.42247+0.0im
 -0.317326+0.0im  -0.0231925+0.0im        0.235677+0.0im  -0.209906+0.0im
 -0.313777+0.0im   -0.122277+0.0im  …     0.335603+0.0im   0.105224+0.0im
 -0.310345+0.0im   -0.208751+0.0im        0.297942+0.0im   0.318067+0.0im
 -0.307018+0.0im   -0.284943+0.0im        0.144373+0.0im   0.325537+0.0im
 -0.303787+0.0im   -0.352601+0.0im       -0.101426+0.0im  0.0891638+0.0im
 -0.300644+0.0im   -0.413064+0.0im       -0.418202+0.0im  -0.392987+0.0im

In this example, we will use the 5 first basis.

f=Figure()
ax = Axis(f[1,1])
for i = 1:size(basis,2)
  lines!(ax,real.(svd_obj.V[:,i]))
end
f

Our supposition for the subspace reconstruction is that the MESE signal can be approximated by a linear combinaison of the 5 basis corresponding to the temporal curve.

Subspace reconstruction

In order to perform the subspace reconstruction we are using a dedicated pipeline name : params[:reco] = "multiCoilMultiEchoSubspace" and we also need to pass the basis params[:basis] = basis

Here, we also have added a Wavelet spatial regularization that will be applied on the basis coefficient maps.

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

params[:reg] = L1Regularization(0.001)
params[:sparseTrafo] = "Wavelet" #sparse trafo
params[:solver] = ADMM
params[:senseMaps] = reshape(coilsens, N, N, 1, nCh)
params[:basis] = basis

params[:iterations] = 1
α = reconstruction(acqData, params)
im_sub = abs.(applySubspace(α, basis))

params[:iterations] = 100
α = reconstruction(acqData_u, params)
im_sub_2 = abs.(applySubspace(α, basis))

α = reconstruction(acqData_u2, params)
im_sub_3 = abs.(applySubspace(α, basis));
nothing #hide

Coefficient maps

The reconstruction returns the coefficient maps :

f = Figure()
for i = 1:size(basis,2)
  ax = Axis(f[1,i],aspect=1,title = "Basis n°$i")
  heatmap!(abs.(α[:,:,1,i,1,1]),colormap=:plasma)
  hidedecorations!(ax)
end
f

Virtual echo images

We need to multiply the subspace basis to the coefficient maps in order to get the virtual TE images

\[im_{TE}(i,j) = \sum_{basis=1}^{5} \alpha(i,j) \times basis'\]

which gives the following results :

begin
p1 = (100, 45)
p2 = (40, 60)
echo = 1
f = Figure()
ax = Axis(f[1, 1], aspect=1, title="Fully standard")
hidedecorations!(ax)
heatmap!(ax, im_phant[:, :, 1, echo, 1, 1])
scatter!(ax, p1,color=:red)
scatter!(ax, p2,color=:red)

ax = Axis(f[1, 2], aspect=1, title="Fully with subspace reco")
hidedecorations!(ax)
heatmap!(ax, im_sub[:, :, 1, echo, 1, 1])

ax = Axis(f[1, 3], aspect=1, title="CS same mask")
hidedecorations!(ax)
heatmap!(ax, im_sub_2[:, :, 1, echo, 1, 1])

ax = Axis(f[1, 4], aspect=1, title="CS different masks")
hidedecorations!(ax)
heatmap!(ax, im_sub_3[:, :, 1, 1, 1, 1])

ax = Axis(f[2, :],title = "T2₁=$(round(1/rmap[p1...],digits=0)) | T2₂=$(round(1/rmap[p2...],digits=0)) ms",xlabel = "TE [ms]",ylabel = "MR signal")
function scale_T2(T2vect)
  return T2vect/T2vect[1]
end
lines!(ax, scale_T2(im_phant[p1..., 1, :, 1, 1]),color=:black,label = "fully")
lines!(ax, scale_T2(im_phant[p2..., 1, :, 1, 1]),color=:black)

lines!(ax, scale_T2(im_sub[p1..., 1, :, 1, 1]),color=color[1],label = "fully subspace")
lines!(ax, scale_T2(im_sub[p2..., 1, :, 1, 1]),color=color[1])

lines!(ax, scale_T2(im_sub_2[p1..., 1, :, 1, 1]),color=color[2],label = "same mask")
lines!(ax, scale_T2(im_sub_2[p2..., 1, :, 1, 1]),color=color[2])

lines!(ax, scale_T2(im_sub_3[p1..., 1, :, 1, 1]),color=color[3],label = "different mask")
lines!(ax, scale_T2(im_sub_3[p2..., 1, :, 1, 1]),color=color[3])
axislegend(ax)
f
end

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 1.10.3"
 "Commit 0b4590a5507 (2024-04-30 10:59 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 v0.12.0
⌃ [e30172f5] Documenter v0.25.2
  [8ad4436d] ImageUtils v0.2.11
  [98b081ad] Literate v2.18.0
  [f7771a9a] MRIBase v0.4.2 `/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 v0.3.0 `/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.