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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
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Merge branch 'master' into master
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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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Removing a println
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223 changes: 101 additions & 122 deletions KomaMRIBase/src/datatypes/Phantom.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -212,7 +212,7 @@ 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`, `=Dict()`) phantom tissue properties in SI units considering the available tissues

# Returns
- `obj`: (`::Phantom`) Phantom struct
Expand All @@ -223,10 +223,26 @@ 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" => [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])
julia> obj = brain_phantom2D(; tissue_properties=phantom_values)

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 = Dict())
# check and filter input
ssx, ssy, ssz, usx, usy, usz = check_phantom_arguments(2, ss, us)

Expand All @@ -235,74 +251,20 @@ function brain_phantom2D(; axis="axial", ss=4, us=1)
data = MAT.matread(path * "/phantom/brain2D.mat")

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

# Define spin position vectors
Δx = .5e-3 * ssx / usx
Δy = .5e-3 * ssy / usy
M, N = size(class)
M, N = size(labels)
FOVx = (M - 1) * Δx #[m]
FOVy = (N - 1) * Δy #[m]
x = (-FOVx / 2):Δx:(FOVx / 2) #spin coordinates
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
T1 = T1 * 1e-3
T2 = T2 * 1e-3
T2s = T2s * 1e-3
# Get tissue properties
T1, T2, T2s, ρ, Δw = default_brain_tissue_properties(labels, tissue_properties)

# Define and return the Phantom struct
obj = Phantom{Float64}(;
Expand Down Expand Up @@ -336,6 +298,7 @@ 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`, `=Dict()`) phantom tissue properties in SI units considering the available tissues

# Returns
- `obj`: (`::Phantom`) 3D Phantom struct
Expand All @@ -346,19 +309,34 @@ julia> obj = brain_phantom3D(; ss=5)

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])
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=Dict())
# 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")

# subsample or upsample the phantom data
class = repeat(
labels = repeat(
data["data"][1:ssx:end, 1:ssy:end, start_end[1]:ssz:start_end[2]];
inner=[usx, usy, usz],
)
Expand All @@ -367,7 +345,7 @@ function brain_phantom3D(; ss=4, us=1, start_end=[160, 200])
Δx = .5e-3 * ssx / usx
Δy = .5e-3 * ssy / usy
Δz = .5e-3 * ssz / usz
M, N, Z = size(class)
M, N, Z = size(labels)
FOVx = (M - 1) * Δx #[m]
FOVy = (N - 1) * Δy #[m]
FOVz = (Z - 1) * Δz #[m]
Expand All @@ -377,63 +355,9 @@ 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
T1 = T1 * 1e-3
T2 = T2 * 1e-3
T2s = T2s * 1e-3

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

# Define and return the Phantom struct
obj = Phantom{Float64}(;
Expand Down Expand Up @@ -482,7 +406,6 @@ 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 +535,61 @@ 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(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

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

julia> T1, T2, T2s, ρ, 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])
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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)
end
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return properties
end
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