From a32cc2cd6637b96b34e37bbf40292ab55452b36e Mon Sep 17 00:00:00 2001
From: Korbinian Eckstein <korbinian90@gmail.com>
Date: Tue, 12 Apr 2022 13:35:03 +0200
Subject: [PATCH] update romeo version

---
 Project.toml          | 4 ++--
 src/mcpc3ds.jl        | 2 ++
 src/romeofunctions.jl | 4 ++--
 3 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/Project.toml b/Project.toml
index 5486318..1670ac8 100644
--- 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
index c78d265..eacbec9 100644
--- 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
index e9a3db5..6e3253d 100644
--- 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