update sensitivity correction:

more robust default estimation for smaller FoV sizes;
expose setting to options

Project.toml

@@ -1,7 +1,7 @@
 name = "CLEARSWI"
 uuid = "06ae4d9b-ce5e-4813-a1b3-426e46312ec2"
 authors = ["Korbinian Eckstein"]
-version = "1.3.1"
+version = "1.3.2"
 
 [deps]
 ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"
@@ -16,6 +16,6 @@ ClearswiApp = "ArgParse"
 
 [compat]
 ArgParse = "1"
-MriResearchTools = "3.1"
+MriResearchTools = "3.1.4"
 Statistics = "1"
 julia = "1.7"

README.md

@@ -105,7 +105,7 @@ qsm=false
   * `(:closest => 15.3)` to select the echo that is closest to 15.3 ms 
   * `(:SE => 15.3)` to simulate the contrast that would be achieved using a corresponding single-echo scan with 15.3 ms echo time.
 
-* If `mag_sens` is set to an array, it is used instead of CLEAR-SWI sensitivity estimation. This can also be set to `mag_sens=[1]` to use the constant sensitivity of 1 and effectively avoid sensitivity correction.
+* If `mag_sens` is set to an array, it is used instead of CLEAR-SWI sensitivity estimation. This can also be set to `mag_sens=[1]` to use the constant sensitivity of 1 and effectively avoid sensitivity correction. To change the sigma_mm value of the expected bias field size, set it to i.e. `mag_sens=(:sigma_mm => 7)`. The default is 7mm.
 
 * To deactivate scaling of the combined magnitude with the softplus function, use `mag_softplus=false`.
 

src/magnitude_processing.jl

@@ -13,7 +13,9 @@ end
 function sensitivity_correction(combined_mag, data, options)
     sensitivity = options.mag_sens
     if isnothing(sensitivity)
-        sensitivity = getsensitivity(data.mag[:,:,:,1], getpixdim(data))
+        sensitivity = getsensitivity(data.mag, getpixdim(data))
+    elseif sensitivity isa Pair && first(sensitivity) == :sigma_mm
+        sensitivity = getsensitivity(data.mag, getpixdim(data); sigma_mm=last(sensitivity))
     end
     savenii(sensitivity, "sensitivity", options.writesteps, data.header)
     return combined_mag ./ sensitivity

src/utility.jl

@@ -36,7 +36,7 @@ end
     * `(:closest => 15.3)` to select the echo that is closest to 15.3 ms 
     * `(:SE => 15.3)` to simulate the contrast that would be achieved using a corresponding single-echo scan with 15.3 ms echo time.
 
-* If `mag_sens` is set to an array, it is used instead of CLEAR-SWI sensitivity estimation. This can also be set to `mag_sens=[1]` to use the constant sensitivity of 1 and effectively avoid sensitivity correction.
+* If `mag_sens` is set to an array, it is used instead of CLEAR-SWI sensitivity estimation. This can also be set to `mag_sens=[1]` to use the constant sensitivity of 1 and effectively avoid sensitivity correction. To change the sigma_mm value of the expected bias field size, set it to i.e. `mag_sens=(:sigma_mm => 7)`. The default is 7mm.
 
 * To deactivate scaling of the combined magnitude with the softplus function, use `mag_softplus=false`.
 
@@ -54,7 +54,7 @@ end
 """
 struct Options
     mag_combine
-    mag_sens::Union{AbstractArray, Nothing}
+    mag_sens::Union{AbstractArray, Nothing, Pair}
     mag_softplus
     phase_unwrap::Symbol
     phase_hp_sigma::AbstractArray

test/functions_test.jl

@@ -47,6 +47,7 @@ options = [
     Options(mag_combine=:last) # 3
     Options(mag_softplus=false)
     Options(mag_sens=[1])
+    Options(mag_sens=(:sigma_mm => 3))
 ]
 # TODO
 wrong_options = [