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Custom values for brain_phantom #484

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Custom values for brain_phantom #484

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271d98f
Custom values for brain_phantom
gsahonero Sep 22, 2024
a67c5bd
Update Phantom.jl
gsahonero Sep 23, 2024
afbd05b
Introducing default brain phantom properties
gsahonero Sep 26, 2024
262bf14
Merge branch 'master' of https://github.com/gsahonero/KomaMRI.jl
gsahonero Sep 26, 2024
cf83a9e
Details on documentation
gsahonero Sep 26, 2024
f858ef1
Updating to remove unnecessary things
gsahonero Sep 26, 2024
0294f4b
Returning phantom to original code
gsahonero Sep 26, 2024
165b793
Resolving problems in brain phantom
gsahonero Sep 27, 2024
91d59f5
Merge branch 'master' of https://github.com/gsahonero/KomaMRI.jl
gsahonero Sep 27, 2024
6b990f4
Merge branch 'JuliaHealth:master' into master
gsahonero Sep 27, 2024
5b6e25d
Avoiding flat arrays.
gsahonero Oct 4, 2024
4020c3d
Merge branch 'JuliaHealth:master' into master
gsahonero Oct 4, 2024
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265 changes: 152 additions & 113 deletions KomaMRIBase/src/datatypes/Phantom.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,8 @@ a property value representing a spin. This struct serves as an input for the sim
- `Dλ2`: (`::AbstractVector{T<:Real}`) spin Dλ2 (diffusion) parameter vector
- `Dθ`: (`::AbstractVector{T<:Real}`) spin Dθ (diffusion) parameter vector
- `motion`: (`::AbstractMotion{T<:Real}`) motion
- `Mz`: (`::AbstractVector{ComplexF32}`) transverse magnetization parameter vector, only for storage purposes
- `Mxy`: (`::AbstractVector{ComplexF32}`) longitudinal magnetization parameter vector, only for storage purposes

# Returns
- `obj`: (`::Phantom`) Phantom struct
Expand All @@ -29,7 +31,7 @@ julia> obj = Phantom(x=[0.0])
julia> obj.ρ
```
"""
@with_kw mutable struct Phantom{T<:Real}
@with_kw mutable struct Phantom{T<:Number}
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name::String = "spins"
x :: AbstractVector{T}
y::AbstractVector{T} = zeros(eltype(x), size(x))
Expand All @@ -48,6 +50,8 @@ julia> obj.ρ
#Diff::Vector{DiffusionModel} #Diffusion map
#Motion
motion::AbstractMotion{T} = NoMotion{eltype(x)}()
Mxy::AbstractVector{ComplexF32} = zeros(eltype(x), size(x)) .+ 0im
Mz::AbstractVector{ComplexF32} = zeros(eltype(x), size(x)) .+ 0im
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end

const NON_STRING_PHANTOM_FIELDS = Iterators.filter(x -> fieldtype(Phantom, x) != String, fieldnames(Phantom))
Expand Down Expand Up @@ -195,6 +199,7 @@ function heart_phantom(;
return phantom
end


"""
phantom = brain_phantom2D(;axis="axial", ss=4)

Expand All @@ -212,7 +217,7 @@ Default ss=4 sample spacing is 2 mm. Original file (ss=1) sample spacing is .5 m
- `axis`: (`::String`, `="axial"`, opts=[`"axial"`, `"coronal"`, `"sagittal"`]) orientation of the phantom
- `ss`: (`::Integer or ::Vector{Integer}`, `=4`) subsampling parameter for all axes if scaler, per axis if 2 element vector [ssx, ssy]
- `us`: (`::Integer or ::Vector{Integer}`, `=1`) upsampling parameter for all axes if scaler, per axis if 2 element vector [usx, usy], if used ss is set to ss=1

- `tissue_properties`: (`::Dict`, `=nothing`) phantom tissue properties in ms and Hz considering the available tissues
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# Returns
- `obj`: (`::Phantom`) Phantom struct
Expand All @@ -223,11 +228,28 @@ julia> obj = brain_phantom2D(; axis="sagittal", ss=1)

julia> obj = brain_phantom2D(; axis="axial", us=[1, 2])

julia> phantom_values =
Dict(
# T1, T2, T2*, ρ, Δw
"CSF" => [2569, 329, 58, 1, 0],
"GM" => [1153, 83, 69, 0.86, 0],
"WM" => [746, 70, 61, 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])
julia> obj = brain_phantom2D(; tissue_properties=phantom_values)
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julia> plot_phantom_map(obj, :ρ)
```
"""
function brain_phantom2D(; axis="axial", ss=4, us=1)
function brain_phantom2D(; axis="axial", ss=4, us=1, tissue_properties = nothing)
# check and filter input
# check more spins
ssx, ssy, ssz, usx, usy, usz = check_phantom_arguments(2, ss, us)

# Get data from .mat file
Expand All @@ -247,59 +269,8 @@ function brain_phantom2D(; axis="axial", ss=4, us=1)
y = (-FOVy / 2):Δy:(FOVy / 2) #spin coordinates
x, y = x .+ y' * 0, x * 0 .+ y' #grid points

# Define spin property vectors
T2 =
(class .== 23) * 329 .+ #CSF
(class .== 46) * 83 .+ #GM
(class .== 70) * 70 .+ #WM
(class .== 93) * 70 .+ #FAT1
(class .== 116) * 47 .+ #MUSCLE
(class .== 139) * 329 .+ #SKIN/MUSCLE
(class .== 162) * 0 .+ #SKULL
(class .== 185) * 0 .+ #VESSELS
(class .== 209) * 70 .+ #FAT2
(class .== 232) * 329 .+ #DURA
(class .== 255) * 70 #MARROW
T2s =
(class .== 23) * 58 .+ #CSF
(class .== 46) * 69 .+ #GM
(class .== 70) * 61 .+ #WM
(class .== 93) * 58 .+ #FAT1
(class .== 116) * 30 .+ #MUSCLE
(class .== 139) * 58 .+ #SKIN/MUSCLE
(class .== 162) * 0 .+ #SKULL
(class .== 185) * 0 .+ #VESSELS
(class .== 209) * 61 .+ #FAT2
(class .== 232) * 58 .+ #DURA
(class .== 255) * 61 #MARROW
T1 =
(class .== 23) * 2569 .+ #CSF
(class .== 46) * 833 .+ #GM
(class .== 70) * 500 .+ #WM
(class .== 93) * 350 .+ #FAT1
(class .== 116) * 900 .+ #MUSCLE
(class .== 139) * 569 .+ #SKIN/MUSCLE
(class .== 162) * 0 .+ #SKULL
(class .== 185) * 0 .+ #VESSELS
(class .== 209) * 500 .+ #FAT2
(class .== 232) * 2569 .+ #DURA
(class .== 255) * 500 #MARROW
ρ =
(class .== 23) * 1 .+ #CSF
(class .== 46) * 0.86 .+ #GM
(class .== 70) * 0.77 .+ #WM
(class .== 93) * 1 .+ #FAT1
(class .== 116) * 1 .+ #MUSCLE
(class .== 139) * 1 .+ #SKIN/MUSCLE
(class .== 162) * 0 .+ #SKULL
(class .== 185) * 0 .+ #VESSELS
(class .== 209) * 0.77 .+ #FAT2
(class .== 232) * 1 .+ #DURA
(class .== 255) * 0.77 #MARROW
Δw_fat = -220 * 2π
Δw =
(class .== 93) * Δw_fat .+ #FAT1
(class .== 209) * Δw_fat #FAT2
# Get tissue properties
T1, T2, T2s, ρ, Δw = default_brain_tissue_properties(class, tissue_properties)
T1 = T1 * 1e-3
T2 = T2 * 1e-3
T2s = T2s * 1e-3
Expand Down Expand Up @@ -336,6 +307,7 @@ Default ss=4 sample spacing is 2 mm. Original file (ss=1) sample spacing is .5 m
- `ss`: (`::Integer or ::Vector{Integer}`, `=4`) subsampling parameter for all axes if scaler, per axis if 3 element vector [ssx, ssy, ssz]
- `us`: (`::Integer or ::Vector{Integer}`, `=1`) upsampling parameter for all axes if scaler, per axis if 3 element vector [usx, usy, usz]
- `start_end`: (`::Vector{Integer}`, `=[160,200]`) z index range of presampled phantom, 180 is center
- `tissue_properties`: (`::Dict`, `=nothing`) phantom tissue properties in ms and Hz considering the available tissues

# Returns
- `obj`: (`::Phantom`) 3D Phantom struct
Expand All @@ -346,13 +318,29 @@ julia> obj = brain_phantom3D(; ss=5)

julia> obj = brain_phantom3D(; us=[2, 2, 1])

julia> phantom_values =
Dict(
# T1, T2, T2*, ρ, Δw
"CSF" => [2569, 329, 58, 1, 0],
"GM" => [1153, 83, 69, 0.86, 0],
"WM" => [746, 70, 61, 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])
julia> obj = brain_phantom3D(; tissue_properties=phantom_values)

julia> plot_phantom_map(obj, :ρ)
```
"""
function brain_phantom3D(; ss=4, us=1, start_end=[160, 200])
function brain_phantom3D(; ss=4, us=1, start_end=[160, 200], tissue_properties=nothing)
# check and filter input
ssx, ssy, ssz, usx, usy, usz = check_phantom_arguments(3, ss, us)

# Get data from .mat file
path = @__DIR__
data = MAT.matread(path * "/phantom/brain3D.mat")
Expand All @@ -377,60 +365,9 @@ function brain_phantom3D(; ss=4, us=1, start_end=[160, 200])
x = 1 * xx .+ 0 * yy .+ 0 * zz
y = 0 * xx .+ 1 * yy .+ 0 * zz
z = 0 * xx .+ 0 * yy .+ 1 * zz

# Define spin property vectors
T2 =
(class .== 23) * 329 .+ #CSF
(class .== 46) * 83 .+ #GM
(class .== 70) * 70 .+ #WM
(class .== 93) * 70 .+ #FAT1
(class .== 116) * 47 .+ #MUSCLE
(class .== 139) * 329 .+ #SKIN/MUSCLE
(class .== 162) * 0 .+ #SKULL
(class .== 185) * 0 .+ #VESSELS
(class .== 209) * 70 .+ #FAT2
(class .== 232) * 329 .+ #DURA
(class .== 255) * 70 #MARROW
T2s =
(class .== 23) * 58 .+ #CSF
(class .== 46) * 69 .+ #GM
(class .== 70) * 61 .+ #WM
(class .== 93) * 58 .+ #FAT1
(class .== 116) * 30 .+ #MUSCLE
(class .== 139) * 58 .+ #SKIN/MUSCLE
(class .== 162) * 0 .+ #SKULL
(class .== 185) * 0 .+ #VESSELS
(class .== 209) * 61 .+ #FAT2
(class .== 232) * 58 .+ #DURA
(class .== 255) * 61 #MARROW
T1 =
(class .== 23) * 2569 .+ #CSF
(class .== 46) * 833 .+ #GM
(class .== 70) * 500 .+ #WM
(class .== 93) * 350 .+ #FAT1
(class .== 116) * 900 .+ #MUSCLE
(class .== 139) * 569 .+ #SKIN/MUSCLE
(class .== 162) * 0 .+ #SKULL
(class .== 185) * 0 .+ #VESSELS
(class .== 209) * 500 .+ #FAT2
(class .== 232) * 2569 .+ #DURA
(class .== 255) * 500 #MARROW
ρ =
(class .== 23) * 1 .+ #CSF
(class .== 46) * 0.86 .+ #GM
(class .== 70) * 0.77 .+ #WM
(class .== 93) * 1 .+ #FAT1
(class .== 116) * 1 .+ #MUSCLE
(class .== 139) * 1 .+ #SKIN/MUSCLE
(class .== 162) * 0 .+ #SKULL
(class .== 185) * 0 .+ #VESSELS
(class .== 209) * 0.77 .+ #FAT2
(class .== 232) * 1 .+ #DURA
(class .== 255) * 0.77 #MARROW
Δw_fat = -220 * 2π
Δw =
(class .== 93) * Δw_fat .+ #FAT1
(class .== 209) * Δw_fat #FAT2

# Get tissue properties
T1, T2, T2s, ρ, Δw = default_brain_tissue_properties(class, tissue_properties)
T1 = T1 * 1e-3
T2 = T2 * 1e-3
T2s = T2s * 1e-3
Expand Down Expand Up @@ -482,7 +419,7 @@ function pelvis_phantom2D(; ss=4, us=1)

# subsample or upsample the phantom data
class = repeat(data["pelvis3D_slice"][1:ssx:end, 1:ssy:end]; inner=[usx, usy])

# Define spin position vectors
Δx = .5e-3 * ssx / usx
Δy = .5e-3 * ssy / usy
Expand Down Expand Up @@ -612,5 +549,107 @@ function check_phantom_arguments(nd, ss, us)
ssy = ss[2]
end
end

return ssx, ssy, ssz, usx, usy, usz
end

"""
T1, T2, T2s, ρ, Δw = default_brain_tissue_properties(class, tissue_properties = nothing)

This function returns the default brain tissue properties using a class identifier Matrix
# Arguments
- `class` : (`::Matrix`) the class identifier matrix of the phantom
- `tissue_properties` : (`::Dict`, `=nothing`) phantom tissue properties in ms and Hz considering the available tissues

# Returns
- `T1, T2, T2s, ρ, Δw`: (`::Matrix`) matrices of the same size of class with the tissues properties information

# Examples
```julia-repl
julia> T1, T2, T2s, ρ, Δw = default_brain_tissue_properties(class, tissue_properties)

julia> T1, T2, T2s, ρ, Δw = default_brain_tissue_properties(class)
```
"""
function default_brain_tissue_properties(class, tissue_properties = nothing)
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if isnothing(tissue_properties)
# Load default tissue properties
tissue_properties = Dict(
# T1, T2, T2*, ρ, Δw
"CSF" => [2569, 329, 58, 1, 0],
"GM" => [833, 83, 69, 0.86, 0],
"WM" => [500, 70, 61, 0.77, 0],
"FAT1" => [350, 70, 58, 1, -220],
"MUSCLE" => [900, 47, 30, 1, 0],
"SKIN/MUSCLE" => [569, 329, 58, 1, 0],
"SKULL" => [0, 0, 0, 0, 0],
"VESSELS" => [0, 0, 0, 0, 0],
"FAT2" => [500, 70, 61, 0.77, -220],
"DURA" => [2569, 329, 58, 1, 0],
"MARROW" => [500, 70, 61, 0.77, 0])
# Define spin property vectors
end
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T1 =
(class .== 23) * tissue_properties["CSF"][1] .+ #CSF
(class .== 46) * tissue_properties["GM"][1] .+ #GM
(class .== 70) * tissue_properties["WM"][1] .+ #WM
(class .== 93) * tissue_properties["FAT1"][1] .+ #FAT1
(class .== 116) * tissue_properties["MUSCLE"][1] .+ #MUSCLE
(class .== 139) * tissue_properties["SKIN/MUSCLE"][1] .+ #SKIN/MUSCLE
(class .== 162) * tissue_properties["SKULL"][1] .+ #SKULL
(class .== 185) * tissue_properties["VESSELS"][1] .+ #VESSELS
(class .== 209) * tissue_properties["FAT2"][1] .+ #FAT2
(class .== 232) * tissue_properties["DURA"][1] .+ #DURA
(class .== 255) * tissue_properties["MARROW"][1] #MARROW
T2 =
(class .== 23) * tissue_properties["CSF"][2] .+ #CSF
(class .== 46) * tissue_properties["GM"][2] .+ #GM
(class .== 70) * tissue_properties["WM"][2] .+ #WM
(class .== 93) * tissue_properties["FAT1"][2] .+ #FAT1
(class .== 116) * tissue_properties["MUSCLE"][2] .+ #MUSCLE
(class .== 139) * tissue_properties["SKIN/MUSCLE"][2] .+ #SKIN/MUSCLE
(class .== 162) * tissue_properties["SKULL"][2] .+ #SKULL
(class .== 185) * tissue_properties["VESSELS"][2] .+ #VESSELS
(class .== 209) * tissue_properties["FAT2"][2] .+ #FAT2
(class .== 232) * tissue_properties["DURA"][2] .+ #DURA
(class .== 255) * tissue_properties["MARROW"][2] #MARROW
T2s =
(class .== 23) * tissue_properties["CSF"][3] .+ #CSF
(class .== 46) * tissue_properties["GM"][3] .+ #GM
(class .== 70) * tissue_properties["WM"][3] .+ #WM
(class .== 93) * tissue_properties["FAT1"][3] .+ #FAT1
(class .== 116) * tissue_properties["MUSCLE"][3] .+ #MUSCLE
(class .== 139) * tissue_properties["SKIN/MUSCLE"][3] .+ #SKIN/MUSCLE
(class .== 162) * tissue_properties["SKULL"][3] .+ #SKULL
(class .== 185) * tissue_properties["VESSELS"][3] .+ #VESSELS
(class .== 209) * tissue_properties["FAT2"][3] .+ #FAT2
(class .== 232) * tissue_properties["DURA"][3] .+ #DURA
(class .== 255) * tissue_properties["MARROW"][3] #MARROW

ρ =
(class .== 23) * tissue_properties["CSF"][4] .+ #CSF
(class .== 46) * tissue_properties["GM"][4] .+ #GM
(class .== 70) * tissue_properties["WM"][4] .+ #WM
(class .== 93) * tissue_properties["FAT1"][4] .+ #FAT1
(class .== 116) * tissue_properties["MUSCLE"][4] .+ #MUSCLE
(class .== 139) * tissue_properties["SKIN/MUSCLE"][4] .+ #SKIN/MUSCLE
(class .== 162) * tissue_properties["SKULL"][4] .+ #SKULL
(class .== 185) * tissue_properties["VESSELS"][4] .+ #VESSELS
(class .== 209) * tissue_properties["FAT2"][4] .+ #FAT2
(class .== 232) * tissue_properties["DURA"][4] .+ #DURA
(class .== 255) * tissue_properties["MARROW"][4] #MARROW

Δw =
(class .== 23) * tissue_properties["CSF"][5] .+ #CSF
(class .== 46) * tissue_properties["GM"][5] .+ #GM
(class .== 70) * tissue_properties["WM"][5] .+ #WM
(class .== 93) * tissue_properties["FAT1"][5] .+ #FAT1
(class .== 116) * tissue_properties["MUSCLE"][5] .+ #MUSCLE
(class .== 139) * tissue_properties["SKIN/MUSCLE"][5] .+ #SKIN/MUSCLE
(class .== 162) * tissue_properties["SKULL"][5] .+ #SKULL
(class .== 185) * tissue_properties["VESSELS"][5] .+ #VESSELS
(class .== 209) * tissue_properties["FAT2"][5] .+ #FAT2
(class .== 232) * tissue_properties["DURA"][5] .+ #DURA
(class .== 255) * tissue_properties["MARROW"][5] #MARROW
return T1, T2, T2s, ρ, Δw
end
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