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Fixing brain phantom values #465

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merged 2 commits into from
Aug 20, 2024
Merged

Fixing brain phantom values #465

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33821c9
Marrow's T2* and Skin/Muscle's PD fixed using Aubert-Broche et al. (2…
gsahonero Aug 19, 2024
e74ae5b
Update Phantom.jl
gsahonero Aug 20, 2024
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14 changes: 6 additions & 8 deletions KomaMRIBase/src/datatypes/Phantom.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -204,7 +204,7 @@ Default ss=4 sample spacing is 2 mm. Original file (ss=1) sample spacing is .5 m
digital brain phantom" NeuroImage, in review - 2006
- B. Aubert-Broche, M. Griffin, G.B. Pike, A.C. Evans and D.L. Collins: "20 new digital
brain phantoms for creation of validation image data bases" IEEE TMI, in review - 2006
- https://brainweb.bic.mni.mcgill.ca/brainweb
- https://brainweb.bic.mni.mcgill.ca/brainweb/tissue_mr_parameters.txt
# Keywords
- `axis`: (`::String`, `="axial"`, opts=[`"axial"`, `"coronal"`, `"sagittal"`]) orientation of the phantom
Expand Down Expand Up @@ -269,8 +269,7 @@ function brain_phantom2D(; axis="axial", ss=4, us=1)
(class .== 185) * 0 .+ #VESSELS
(class .== 209) * 61 .+ #FAT2
(class .== 232) * 58 .+ #DURA
(class .== 255) * 61 .+#MARROW
(class .== 255) * 70 #MARROW
(class .== 255) * 61 #MARROW
T1 =
(class .== 23) * 2569 .+ #CSF
(class .== 46) * 833 .+ #GM
Expand All @@ -289,7 +288,7 @@ function brain_phantom2D(; axis="axial", ss=4, us=1)
(class .== 70) * 0.77 .+ #WM
(class .== 93) * 1 .+ #FAT1
(class .== 116) * 1 .+ #MUSCLE
(class .== 139) * 0.7 .+ #SKIN/MUSCLE
(class .== 139) * 1 .+ #SKIN/MUSCLE
(class .== 162) * 0 .+ #SKULL
(class .== 185) * 0 .+ #VESSELS
(class .== 209) * 0.77 .+ #FAT2
Expand Down Expand Up @@ -329,7 +328,7 @@ Default ss=4 sample spacing is 2 mm. Original file (ss=1) sample spacing is .5 m
digital brain phantom" NeuroImage, in review - 2006
- B. Aubert-Broche, M. Griffin, G.B. Pike, A.C. Evans and D.L. Collins: "20 new digital
brain phantoms for creation of validation image data bases" IEEE TMI, in review - 2006
- https://brainweb.bic.mni.mcgill.ca/brainweb
- https://brainweb.bic.mni.mcgill.ca/brainweb/tissue_mr_parameters.txt
# Keywords
- `ss`: (`::Integer or ::Vector{Integer}`, `=4`) subsampling parameter for all axes if scaler, per axis if 3 element vector [ssx, ssy, ssz]
Expand Down Expand Up @@ -401,8 +400,7 @@ function brain_phantom3D(; ss=4, us=1, start_end=[160, 200])
(class .== 185) * 0 .+ #VESSELS
(class .== 209) * 61 .+ #FAT2
(class .== 232) * 58 .+ #DURA
(class .== 255) * 61 .+#MARROW
(class .== 255) * 70 #MARROW
(class .== 255) * 61 #MARROW
T1 =
(class .== 23) * 2569 .+ #CSF
(class .== 46) * 833 .+ #GM
Expand All @@ -421,7 +419,7 @@ function brain_phantom3D(; ss=4, us=1, start_end=[160, 200])
(class .== 70) * 0.77 .+ #WM
(class .== 93) * 1 .+ #FAT1
(class .== 116) * 1 .+ #MUSCLE
(class .== 139) * 0.7 .+ #SKIN/MUSCLE
(class .== 139) * 1 .+ #SKIN/MUSCLE
(class .== 162) * 0 .+ #SKULL
(class .== 185) * 0 .+ #VESSELS
(class .== 209) * 0.77 .+ #FAT2
Expand Down