set the number of mip slices from the caller

korbinian90 · Sep 9, 2024 · f97751c · f97751c
1 parent f20c88e
commit f97751c
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Showing 3 changed files with 5 additions and 2 deletions.
diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "CLEARSWI"
 uuid = "06ae4d9b-ce5e-4813-a1b3-426e46312ec2"
 authors = ["Korbinian Eckstein"]
-version = "1.3.3"
+version = "1.3.4"
 
 [deps]
 ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"

diff --git a/ext/ClearswiApp/argparse.jl b/ext/ClearswiApp/argparse.jl
@@ -20,6 +20,9 @@ function getargs(args::AbstractVector, version)
                 specified in array or range syntax (eg. "[1.5,3.0]" or 
                 "3.5:3.5:14")."""
             nargs = '+'
+        "--mip-slices", "-s"
+            help = "The number of slices in the MIP image"
+            default = 7
         "--qsm"
             help = """When activated uses RTS QSM for phase weighting.
             """

diff --git a/ext/ClearswiApp/caller.jl b/ext/ClearswiApp/caller.jl
@@ -89,7 +89,7 @@ function CLEARSWI.clearswi_main(args; version="1.3.3")
     options = Options(;mag_combine, mag_sens, mag_softplus, phase_unwrap, phase_hp_sigma, phase_scaling_type, phase_scaling_strength, writesteps, qsm)
 
     swi = calculateSWI(data, options)
-    mip = createIntensityProjection(swi, minimum)
+    mip = createIntensityProjection(swi, minimum, settings["mip-slices"])
 
     savenii(swi, filename, writedir, hdr)
     savenii(mip, "mip", writedir, hdr)