From 371d44a468ab17fba300708831483dcfa732499a Mon Sep 17 00:00:00 2001
From: Korbinian Eckstein <korbinian.eckstein@gmail.com>
Date: Tue, 10 Oct 2023 14:04:01 +1000
Subject: [PATCH] add masking commets

---
 README.md  | 14 ++++++++++++++
 src/tgv.jl |  2 +-
 2 files changed, 15 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index cd97483..295dbe0 100644
--- a/README.md
+++ b/README.md
@@ -140,3 +140,17 @@ For Mac GPU:
 using Metal
 chi = qsm_tgv(phase, mask, res; TE, fieldstrength, gpu=Metal);
 ```
+
+## Masking for QSM
+
+Masking for QSM is a challenge, since including corrupted phase areas can cause global artefacts in the QSM result. See the publications [QSMxT](https://doi.org/10.1002%2Fmrm.29048) and [phase based masking](https://doi.org/10.1002/mrm.29368).
+
+A simple solution is to remove areas based on phase quality using [ROMEO](https://onlinelibrary.wiley.com/doi/10.1002/mrm.28563)
+
+```julia
+using MriResearchTools
+mask_phase = robustmask(romeovoxelquality(phase; mag))
+mask_combined = mask_phase .& mask_brain
+```
+
+The mask might contain holes, and a more sophisticated approach is taken in the [QSMxT toolbox](https://qsmxt.github.io/QSMxT/).
diff --git a/src/tgv.jl b/src/tgv.jl
index 2dd115e..26c0319 100644
--- a/src/tgv.jl
+++ b/src/tgv.jl
@@ -35,7 +35,7 @@ function qsm_tgv(phase, mask, res; TE, B0_dir=[0, 0, 1], fieldstrength=3, regula
         ret = nothing
     end
 
-    @showprogress dt=0.5 desc="Running $max_iterations TGV iterations..." for k in 1:max_iterations
+    @showprogress dt=1 desc="Running $max_iterations TGV iterations..." for k in 1:max_iterations
         #############
         # dual update
         KernelAbstractions.synchronize(device)