update romeo version

korbinian90 · Apr 12, 2022 · a32cc2c · a32cc2c · korbinian90 · Apr 12, 2022
1 parent 886e746
commit a32cc2c
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Showing 3 changed files with 6 additions and 4 deletions.
diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "MriResearchTools"
 uuid = "557dad86-b9bd-4533-8525-1a39684d020f"
 authors = ["Korbinian Eckstein"]
-version = "0.6.3"
+version = "0.7.0"
 
 [deps]
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
@@ -20,5 +20,5 @@ Interpolations = "0.12 - 0.13"
 NIfTI = "0.4 - 0.5"
 PaddedViews = "0.5"
 Requires = "1"
-ROMEO = "0.2.5"
+ROMEO = "0.3"
 julia = "1.5"
diff --git a/src/mcpc3ds.jl b/src/mcpc3ds.jl
@@ -65,6 +65,8 @@ function combinewithPO(compl, po)
     return combined ./ sqrt.(abs.(combined))
 end
 
+## Bipolar correction
+# see https://doi.org/10.34726/hss.2021.43447, page 53, 3.1.3 Bipolar Corrections
 function bipolar_correction!(image; TEs, σ, mask)
     fG = artefact(image, TEs)
     fG .= gaussiansmooth3d_phase(fG, σ; mask)

diff --git a/src/romeofunctions.jl b/src/romeofunctions.jl
@@ -14,11 +14,11 @@ julia> mask = mask_from_voxelquality(qmap);
 
 See also [`romeovoxelquality`](@ref), [`romeo`](@ref), [`robustmask`](@ref)
 """
-function mask_from_voxelquality(qmap::AbstractArray, threshold=0.5)
+function mask_from_voxelquality(qmap::AbstractArray, threshold=0.2, th2=0.8)
     qmap_bin = qmap .> threshold # NaN defaults to false (0)
     max_hole_size = length(qmap) / 20
     qmap_bin = .!imfill(.!qmap_bin, (1, max_hole_size)) # fills all holes up to max_hole_size (uses 6 connectivity as default)
-    return gaussiansmooth3d(qmap_bin, (1,1,1)) .> 0.8 # hardcoded final threshold
+    return gaussiansmooth3d(qmap_bin, (1,1,1)) .> th2
 end
 
 function ROMEO.calculateweights(phase::AbstractArray{T,4}; TEs, template=2, p2ref=1, keyargs...) where T