diff --git a/Project.toml b/Project.toml index 583b81c..917fa74 100644 --- a/Project.toml +++ b/Project.toml @@ -1,12 +1,11 @@ name = "CLEARSWI" uuid = "06ae4d9b-ce5e-4813-a1b3-426e46312ec2" authors = ["Korbinian Eckstein"] -version = "1.2.0" +version = "1.3.0" [deps] ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63" MriResearchTools = "557dad86-b9bd-4533-8525-1a39684d020f" -QuantitativeSusceptibilityMappingTGV = "bd393529-335a-4aed-902f-5de61cc7ff49" Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" [weakdeps] @@ -18,5 +17,4 @@ ClearswiApp = "ArgParse" [compat] ArgParse = "1" MriResearchTools = "3.1" -QuantitativeSusceptibilityMappingTGV = "0.2" julia = "1.7" diff --git a/README.md b/README.md index 6f0d307..6ad0371 100644 --- a/README.md +++ b/README.md @@ -93,6 +93,7 @@ phase_hp_sigma=[4,4,0] phase_scaling_type=:tanh phase_scaling_strength=4 writesteps=nothing +qsm=false ``` * `mag_combine` selects the echo combination for the magnitude. Options are @@ -118,6 +119,8 @@ writesteps=nothing * Set `writesteps` to the path, where intermediate steps should be saved, e.g. `writesteps="/tmp/clearswi_steps"`. If set to `nothing`, intermediate steps won't be saved. +* [Experimental] Set `qsm` to true to use QSM processing for the phase contrast. This requires the additional use of a QSM package. Supported are either [`QSM`](https://github.com/kamesy/QSM.jl) or [`QuantitativeSusceptibilityMappingTGV`](https://github.com/korbinian90/QuantitativeSusceptibilityMappingTGV.jl). Before setting this option, you need load one of these packages with `using`. + ### Calculating T2* and B0 maps on multi-echo datasets T2* and B0 maps can be calculated using the package [MriResearchTools](https://github.com/korbinian90/MriResearchTools.jl): @@ -161,7 +164,7 @@ usage: [-m MAGNITUDE] [-p PHASE] [-o OUTPUT] [-e ECHOES [ECHOES...]] [-N] [--no-phase-rescale] [--writesteps WRITESTEPS] [-v] [--version] [-h] -3.6.4 +4.0.4 optional arguments: -m, --magnitude MAGNITUDE @@ -173,7 +176,7 @@ optional arguments: The echo times are required for multi-echo datasets specified in array or range syntax (eg. "[1.5,3.0]" or "3.5:3.5:14"). - --qsm When activated uses TGV-QSM for phase weighting + --qsm When activated uses RTS QSM for phase weighting --mag-combine MAG-COMBINE [MAG-COMBINE...] SNR | average | echo | SE . Magnitude combination algorithm. echo selects a diff --git a/clearswi.jl b/clearswi.jl index 56218bc..9987e47 100644 --- a/clearswi.jl +++ b/clearswi.jl @@ -1,10 +1,10 @@ import Pkg Pkg.activate(@__DIR__) try - using CLEARSWI, ArgParse + using CLEARSWI, QSM, ArgParse catch - Pkg.add(["CLEARSWI", "ArgParse"]) - using CLEARSWI, ArgParse + Pkg.add(["CLEARSWI", "QSM", "ArgParse"]) + using CLEARSWI, QSM, ArgParse end @time msg = clearswi_main(ARGS) diff --git a/ext/ClearswiApp/argparse.jl b/ext/ClearswiApp/argparse.jl index c812d43..403378f 100644 --- a/ext/ClearswiApp/argparse.jl +++ b/ext/ClearswiApp/argparse.jl @@ -21,7 +21,7 @@ function getargs(args::AbstractVector, version) "3.5:3.5:14").""" nargs = '+' "--qsm" - help = """When activated uses TGV-QSM for phase weighting + help = """When activated uses RTS QSM for phase weighting. """ action = :store_true "--mag-combine" diff --git a/src/CLEARSWI.jl b/src/CLEARSWI.jl index 6d98492..c2ea48d 100644 --- a/src/CLEARSWI.jl +++ b/src/CLEARSWI.jl @@ -1,7 +1,6 @@ module CLEARSWI using MriResearchTools -using QuantitativeSusceptibilityMappingTGV using Statistics include("tissue.jl")