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@gsahonero
gsahonero committed Dec 11, 2024
1 parent ecc9bbe commit 1079053
Showing 1 changed file with 57 additions and 59 deletions.
116 changes: 57 additions & 59 deletions KomaMRIBase/src/datatypes/Phantom.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -225,18 +225,18 @@ julia> obj = brain_phantom2D(; axis="axial", us=[1, 2])
julia> phantom_values =
Dict(
# T1, T2, T2*, ρ, Δw
"CSF" => [2.569, 0.329, 0.058, 1, 0],
"GM" => [1.153, 0.083, 0.069, 0.86, 0],
"WM" => [0.746, 0.070, 0.061, 0.77, 0],
"FAT1" => [0, 0, 0, 0, 0],
"MUSCLE" => [0, 0, 0, 0, 0],
"SKIN/MUSCLE" => [0, 0, 0, 0, 0],
"SKULL" => [0, 0, 0, 0, 0],
"VESSELS" => [0, 0, 0, 0, 0],
"FAT2" => [0, 0, 0, 0, 0],
"DURA" => [0, 0, 0, 0, 0],
"MARROW" => [0, 0, 0, 0, 0])
# ρ, T1, T2, T2*, Δw
"CSF" => [1, 2.569, 0.329, 0.058, 0],
"GM" => [0.86, 0.833, 0.083, 0.069, 0],
"WM" => [0.77, 0.500, 0.070, 0.061, 0],
"FAT1" => [0, 0, 0, 0, 0],
"MUSCLE" => [0, 0, 0, 0, 0],
"SKIN/MUSCLE" => [0, 0, 0, 0, 0],
"SKULL" => [0, 0, 0, 0, 0],
"VESSELS" => [0, 0, 0, 0, 0],
"FAT2" => [0, 0, 0, 0, 0],
"DURA" => [0, 0, 0, 0, 0],
"MARROW" => [0, 0, 0, 0, 0])
julia> obj = brain_phantom2D(; tissue_properties=phantom_values)
julia> plot_phantom_map(obj, :ρ)
Expand Down Expand Up @@ -264,8 +264,8 @@ function brain_phantom2D(; axis="axial", ss=4, us=1, tissue_properties = Dict())
x, y = x .+ y' * 0, x * 0 .+ y' #grid points

# Get tissue properties
T1, T2, T2s, ρ, Δw = default_brain_tissue_properties(labels, tissue_properties)

ρ, T1, T2, T2s, Δw = default_brain_tissue_properties(labels, tissue_properties)
println("size of ", size(T1))
# Define and return the Phantom struct
obj = Phantom{Float64}(;
name="brain2D_" * axis,
Expand Down Expand Up @@ -311,18 +311,18 @@ julia> obj = brain_phantom3D(; us=[2, 2, 1])
julia> phantom_values =
Dict(
# T1, T2, T2*, ρ, Δw
"CSF" => [2.569, 0.329, 0.058, 1, 0],
"GM" => [1.153, 0.083, 0.069, 0.86, 0],
"WM" => [0.746, 0.070, 0.061, 0.77, 0],
"FAT1" => [0, 0, 0, 0, 0],
"MUSCLE" => [0, 0, 0, 0, 0],
"SKIN/MUSCLE" => [0, 0, 0, 0, 0],
"SKULL" => [0, 0, 0, 0, 0],
"VESSELS" => [0, 0, 0, 0, 0],
"FAT2" => [0, 0, 0, 0, 0],
"DURA" => [0, 0, 0, 0, 0],
"MARROW" => [0, 0, 0, 0, 0])
# ρ, T1, T2, T2*, Δw
"CSF" => [1, 2.569, 0.329, 0.058, 0],
"GM" => [0.86, 0.833, 0.083, 0.069, 0],
"WM" => [0.77, 0.500, 0.070, 0.061, 0],
"FAT1" => [0, 0, 0, 0, 0],
"MUSCLE" => [0, 0, 0, 0, 0],
"SKIN/MUSCLE" => [0, 0, 0, 0, 0],
"SKULL" => [0, 0, 0, 0, 0],
"VESSELS" => [0, 0, 0, 0, 0],
"FAT2" => [0, 0, 0, 0, 0],
"DURA" => [0, 0, 0, 0, 0],
"MARROW" => [0, 0, 0, 0, 0])
julia> obj = brain_phantom3D(; tissue_properties=phantom_values)
julia> plot_phantom_map(obj, :ρ)
Expand Down Expand Up @@ -357,7 +357,7 @@ function brain_phantom3D(; ss=4, us=1, start_end=[160, 200], tissue_properties=D
z = 0 * xx .+ 0 * yy .+ 1 * zz

# Get tissue properties
T1, T2, T2s, ρ, Δw = default_brain_tissue_properties(labels, tissue_properties)
ρ, T1, T2, T2s, Δw = default_brain_tissue_properties(labels, tissue_properties)

# Define and return the Phantom struct
obj = Phantom{Float64}(;
Expand Down Expand Up @@ -540,56 +540,54 @@ function check_phantom_arguments(nd, ss, us)
end

"""
T1, T2, T2s, ρ, Δw = default_brain_tissue_properties(labels, tissue_properties = nothing)
ρ, T1, T2, T2s, Δw = default_brain_tissue_properties(labels, tissue_properties = nothing)
This function returns the default brain tissue properties using a labels identifier Matrix
# Arguments
- `labels` : (`::Matrix`) the labels identifier matrix of the phantom
- `tissue_properties` : (`::Dict`, `=Dict()`) phantom tissue properties in ms and Hz considering the available tissues
# Returns
- `T1, T2, T2s, ρ, Δw`: (`::Matrix`) matrices of the same size of labels with the tissues properties information
- `ρ, T1, T2, T2s, Δw`: (`::Matrix`) matrices of the same size of labels with the tissues properties information
# Examples
```julia-repl
julia> T1, T2, T2s, ρ, Δw = default_brain_tissue_properties(labels, tissue_properties)
julia> ρ, T1, T2, T2s, Δw = default_brain_tissue_properties(labels, tissue_properties)
julia> T1, T2, T2s, ρ, Δw = default_brain_tissue_properties(labels)
julia> ρ, T1, T2, T2s, Δw = default_brain_tissue_properties(labels)
```
"""
function default_brain_tissue_properties(labels, tissue_properties = Dict())
# Load default tissue properties
default_properties = Dict(
# T1, T2, T2*, ρ, Δw
"CSF" => [2.569, 0.329, 0.058, 1, 0],
"GM" => [0.833, 0.083, 0.069, 0.86, 0],
"WM" => [0.500, 0.070, 0.061, 0.77, 0],
"FAT1" => [0.350, 0.070, 0.058, 1, -3.84], #-220 Hz
"MUSCLE" => [0.900, 0.047, 0.030, 1, 0],
"SKIN/MUSCLE" => [0.569, 0.329, 0.058, 1, 0],
"SKULL" => [0, 0, 0, 0, 0],
"VESSELS" => [0, 0, 0, 0, 0],
"FAT2" => [0.500, 0.070, 0.061, 0.77, -3.84], #-220 Hz
"DURA" => [2.569, 0.329, 0.058, 1, 0],
"MARROW" => [0.500, 0.070, 0.061, 0.77, 0])
# ρ, T1, T2, T2*, Δw
"CSF" => [1, 2.569, 0.329, 0.058, 0],
"GM" => [0.86, 0.833, 0.083, 0.069, 0],
"WM" => [0.77, 0.500, 0.070, 0.061, 0],
"FAT1" => [1, 0.350, 0.070, 0.058, -220*2π], #-220 Hz
"MUSCLE" => [1, 0.900, 0.047, 0.030, 0],
"SKIN/MUSCLE" => [1, 0.569, 0.329, 0.058, 0],
"SKULL" => [0, 0, 0, 0, 0],
"VESSELS" => [0, 0, 0, 0, 0],
"FAT2" => [0.77, 0.500, 0.070, 0.061, -220*2π], #-220 Hz
"DURA" => [1, 2.569, 0.329, 0.058, 0],
"MARROW" => [0.77, 0.500, 0.070, 0.061, 0])

tissue_properties = merge(default_properties, tissue_properties)
properties = []
for i=1:5
temp =
(labels .== 23) * tissue_properties["CSF"][i] .+ #CSF
(labels .== 46) * tissue_properties["GM"][i] .+ #GM
(labels .== 70) * tissue_properties["WM"][i] .+ #WM
(labels .== 93) * tissue_properties["FAT1"][i] .+ #FAT1
(labels .== 116) * tissue_properties["MUSCLE"][i] .+ #MUSCLE
(labels .== 139) * tissue_properties["SKIN/MUSCLE"][i] .+ #SKIN/MUSCLE
(labels .== 162) * tissue_properties["SKULL"][i] .+ #SKULL
(labels .== 185) * tissue_properties["VESSELS"][i] .+ #VESSELS
(labels .== 209) * tissue_properties["FAT2"][i] .+ #FAT2
(labels .== 232) * tissue_properties["DURA"][i] .+ #DURA
(labels .== 255) * tissue_properties["MARROW"][i] #MARROW
push!(properties, temp)
props = ["ρ", "T1", "T2", "T2s", "Δw"]
Nproperties = length(props)
tissue_labels = [23, 46, 70, 93, 116, 139, 162, 185, 209, 232, 255]
tissue_texts = ["CSF", "GM", "WM", "FAT1", "MUSCLE", "SKIN/MUSCLE", "SKULL", "VESSELS", "FAT2", "DURA", "MARROW"]
data_properties = zeros(Nproperties, size(labels)...)
dims = size(data_properties)
for i=1:Nproperties
for (label, tissue) in zip(tissue_labels, tissue_texts)
data_properties[i, ntuple(j -> 1:dims[j+1], length(dims)-1)...] += (labels .== label)*tissue_properties[tissue][i]
end
end

# To make it a tuple of five elements
properties = Tuple(data_properties[i, :, :, :] for i in 1:size(data_properties, 1))
# To avoid singleton dimensions
properties = Tuple(reshape(item, filter(d -> d>1, size(item))...) for item in properties)
return properties
end

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