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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
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Merge branch 'master' of https://github.com/gsahonero/KomaMRI.jl
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Details on documentation
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Updating to remove unnecessary things
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Returning phantom to original code
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Resolving problems in brain phantom
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Merge branch 'master' of https://github.com/gsahonero/KomaMRI.jl
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Merge branch 'JuliaHealth:master' into master
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Avoiding flat arrays.
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Merge branch 'JuliaHealth:master' into master
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Merge branch 'master' into master
cncastillo Nov 1, 2024
3689518
Update Phantom.jl
gsahonero Nov 9, 2024
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Merge branch 'master' into master
cncastillo Nov 13, 2024
9cc9d29
Update KomaMRIBase/src/datatypes/Phantom.jl
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Update KomaMRIBase/src/datatypes/Phantom.jl
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Update KomaMRIBase/src/datatypes/Phantom.jl
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Update KomaMRIBase/src/datatypes/Phantom.jl
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Update KomaMRIBase/src/datatypes/Phantom.jl
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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


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"""
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
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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)

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# 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])

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# 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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