From 64a4b33f8b5ae664d579489c671c3b1f2525e72a Mon Sep 17 00:00:00 2001
From: korbi <korbinian90@gmail.com>
Date: Mon, 23 Mar 2020 12:07:32 +0100
Subject: [PATCH] improve readme

---
 README.md | 67 ++++++++++++++++++++++++++++++++++++++++++-------------
 1 file changed, 52 insertions(+), 15 deletions(-)

diff --git a/README.md b/README.md
index 429c6b0..dc81699 100644
--- a/README.md
+++ b/README.md
@@ -5,12 +5,12 @@
 [![Codecov](https://codecov.io/gh/korbinian90/MriResearchTools.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/korbinian90/MriResearchTools.jl)
 [![Coveralls](https://coveralls.io/repos/github/korbinian90/MriResearchTools.jl/badge.svg?branch=master)](https://coveralls.io/github/korbinian90/MriResearchTools.jl?branch=master)
 
-### Prerequisites
+## Prerequisites
 A Julia installation v1.x is required.
 
 Magnitude and Phase images in NIfTI fileformat (4D images with echoes in the 4th dimension)
 
-### Installing
+## Installing
 Open the Julia REPL and type
 
 ```julia
@@ -20,25 +20,62 @@ julia> ] # enter julia package manager
 julia>
 ```
 
-### Included Functionality
+## Quick Start
+Open multi-echo 4D NIfTI phase and magnitude files and perform ROMEO phase unwrapping.
 
-ROMEO 3D/4D Phase Unwrapping
+```julia
+using MriResearchTools
+# input images
+TEs = [4,8,12]
+nifti_folder = joinpath("test", "data", "small")
+magfile = joinpath(nifti_folder, "Mag.nii") # Path to the magnitude image in nifti format, must be .nii or .hdr
+phasefile = joinpath(nifti_folder, "Phase.nii") # Path to the phase image
+# load images
+mag = readmag(magfile)
+phase = readphase(phasefile)
+# unwrap
+unwrapped = romeo(phase; mag=mag, TEs=TEs)
+# save unwrapped image
+outputfolder = "outputFolder"
+mkpath(outputfolder)
+savenii(unwrapped, "unwrapped", outputfolder, header(phase))
+```
+
+## Included Functionality
+
+ROMEO 3D/4D Phase Unwrapping\
+`romeo` `unwrap` `unwrap_individual`
+
+Reading, writing and other functions for NIfTI files (adapted from JuliaIO/NIfTI)\
+`readphase` `readmag` `niread` `savenii` `header`
+
+Magnitude homogeneity correction ([example](https://github.com/korbinian90/Magnitude-Intensity-Correction/blob/master/Intensity%20Correction.ipynb))\
+`makehomogeneous`
+
+Simple robust masking (threshold)\
+`robustmask`
 
-Reading and writing NIfTI files (adapted from JuliaIO/NIfTI)
+Combine multiple echoes\
+`RSS`
 
-Magnitude homogeneity correction ([example](https://github.com/korbinian90/Magnitude-Intensity-Correction/blob/master/Intensity%20Correction.ipynb))
+Laplacian unwrapping\
+`laplacianunwrap`
 
-Simple robust masking (threshold)
+Unwarping of B0 dependent shifts\
+`getVSM` `thresholdforward` `unwarp`
 
-Combine multiple echoes
+Fast gaussian smoothing\
+`gaussiansmooth3d`
+  - standard
+  - weighted
+  - with missing values
 
-Laplacian unwrapping
+Other functions
+`robustrescale` `getHIP` `getsensitivity` `getscaledimage` `estimatequantile`
 
-Unwarping of B0 dependent shifts
+## License
+This project is licensed under the MIT License - see the [LICENSE](https://github.com/korbinian90/MriResearchTools.jl/blob/master/LICENSE) for details
 
-Fast gaussian smoothing
-- standard
-- weighted
-- with missing values
 
-TODO: Tests and Examples
+## TODO
+Tests, Examples and Documentation