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Remove air tissue from pelvis phantom example #331

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Mar 27, 2024
Merged

Remove air tissue from pelvis phantom example #331

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cd63f2d
Remove air tissue from pelvis phantom exaple
beorostica Mar 22, 2024
c619e6e
Add some blank spaces
beorostica Mar 27, 2024
b31466d
Merge branch 'master' into pelvis-phantom
cncastillo Mar 27, 2024
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12 changes: 4 additions & 8 deletions KomaMRIBase/src/datatypes/Phantom.jl
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Expand Up @@ -433,23 +433,19 @@ function pelvis_phantom2D(; ss=4, us=1)
x, y = x .+ y'*0, x*0 .+ y' # grid points

# Define spin property vectors
ρ = (class.==51)*.001 .+ # Air
(class.==102)*.86 .+ # Fat
ρ = (class.==102)*.86 .+ # Fat
(class.==153)*.9 .+ # SoftTissue
(class.==204)*.4 .+ # SpongyBone
(class.==255)*.2 # CorticalBone
T1 = (class.==51)*.001 .+ # Air
(class.==102)*366 .+ # Fat
T1 = (class.==102)*366 .+ # Fat
(class.==153)*1200 .+ # SoftTissue
(class.==204)*381 .+ # SpongyBone
(class.==255)*100 # CorticalBone
T2 = (class.==51)*.001 .+ # Air
(class.==102)*70 .+ # Fat
T2 = (class.==102)*70 .+ # Fat
(class.==153)*80 .+ # SoftTissue
(class.==204)*52 .+ # SpongyBone
(class.==255)*.3 # CorticalBone
T2s = (class.==51)*.001 .+ # Air
(class.==102)*70 .+ # Fat
T2s = (class.==102)*70 .+ # Fat
(class.==153)*80 .+ # SoftTissue
(class.==204)*52 .+ # SpongyBone
(class.==255)*.3 # CorticalBone
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12 changes: 4 additions & 8 deletions docs/src/create-your-own-phantom.md
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Expand Up @@ -78,29 +78,25 @@ x, y = x .+ y'*0, x*0 .+ y' # x and y grid points
Now, let's define the arrays for the properties. It's essential to have prior knowledge of the property values for different tissue classes. For example, for soft tissue, we use `ρ = 0.9`, `T1 = 1200 * 1e-3`, `T2 = 80 * 1e-3`, and `T2s = 80 * 1e-3`. Additionally, we create an array mask to identify the location of a tissue's ID. For soft tissue with ID = 153, the mask is `(class .== 153)`. Finally, to obtain a property, sum all the masks with values for all tissue classes. This process is illustrated below:
```julia
# Define the proton density array
ρ = (class.==51)*.001 .+ # Air
(class.==102)*.86 .+ # Fat
ρ = (class.==102)*.86 .+ # Fat
(class.==153)*.9 .+ # SoftTissue
(class.==204)*.4 .+ # SpongyBone
(class.==255)*.2 # CorticalBone

# Define the T1 decay array
T1 = (class.==51)*.001 .+ # Air
(class.==102)*366 .+ # Fat
T1 = (class.==102)*366 .+ # Fat
(class.==153)*1200 .+ # SoftTissue
(class.==204)*381 .+ # SpongyBone
(class.==255)*100 # CorticalBone

# Define the T2 decay array
T2 = (class.==51)*.001 .+ # Air
(class.==102)*70 .+ # Fat
T2 = (class.==102)*70 .+ # Fat
(class.==153)*80 .+ # SoftTissue
(class.==204)*52 .+ # SpongyBone
(class.==255)*.3 # CorticalBone

# Define the T2s decay array
T2s = (class.==51)*.001 .+ # Air
(class.==102)*70 .+ # Fat
T2s = (class.==102)*70 .+ # Fat
(class.==153)*80 .+ # SoftTissue
(class.==204)*52 .+ # SpongyBone
(class.==255)*.3 # CorticalBone
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