From 40fc26e8e853f4a950c5e6fa6404771cfb36b5a1 Mon Sep 17 00:00:00 2001 From: Korbinian Eckstein Date: Thu, 10 Mar 2022 14:31:04 +0100 Subject: [PATCH] Update README.md --- README.md | 25 +++++++++++++------------ 1 file changed, 13 insertions(+), 12 deletions(-) diff --git a/README.md b/README.md index ea58f5f..d638860 100644 --- a/README.md +++ b/README.md @@ -1,15 +1,13 @@ # ROMEO Unwrapping Unwrapping of 3D and 4D datasets. -Coil combination of 5D datasets. +Coil combination of 5D datasets. ![ROMEO](https://user-images.githubusercontent.com/1307522/144416428-0c51a0e5-cb07-4b7d-8571-9fa2dc33f580.png) ## Download ROMEO Ordered from simple to more involved approaches. ### Option 1: [Download Executables for Linux and Windows (mritools)](https://github.com/korbinian90/CompileMRI.jl/releases) - -**Download link for mritools: https://github.com/korbinian90/CompileMRI.jl/releases** - +**Download link for mritools: https://github.com/korbinian90/CompileMRI.jl/releases** *For a compiled MacOS version, see [MacOS](https://github.com/korbinian90/ROMEO/edit/master/README.md#macos), but the suggested way is Option 4* ### Option 2: Run in [Neurodesk](https://neurodesk.github.io/) (every OS) @@ -32,10 +30,6 @@ https://github.com/korbinian90/ROMEO.jl **MCPC-3D-S Coil Combination**: Eckstein, K., Dymerska, B., Bachrata, B., Bogner, W., Poljanc, K., Trattnig, S., Robinson, S.D., 2018. Computationally Efficient Combination of Multi-channel Phase Data From Multi-echo Acquisitions (ASPIRE). Magnetic Resonance in Medicine 79, 2996–3006. https://doi.org/10.1002/mrm.26963 -## Related Repositories -The sourcecode is available under [ROMEO.jl](https://github.com/korbinian90/ROMEO.jl). -The binaries are a standalone compiled version of [RomeoApp.jl](https://github.com/korbinian90/RomeoApp.jl). The compilation scripts and recent releases are in [CompileMRI.jl](https://github.com/korbinian90/CompileMRI.jl). - ## Getting Started ### Prerequisites Phase (and optionally Magnitude) images in NIfTI fileformat. @@ -43,13 +37,16 @@ For multi-echo/multi-timepoint data, 4D-NIfTI files are used with echoes/timepoi Individual 3D files can be merged into 4D files using [fslmerge](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Fslutils). If 5D-NIfTI datasets with channels in the 5th dimension are given, coil combination can be performed as first step. -### [Compiled Version](https://github.com/korbinian90/ROMEO/releases) -ROMEO is a command line application. +### Run ROMEO +ROMEO is a command line application. The binary is in the folder `mritools/bin` -Example usage for single-echo or multiple time points with identical echo time (fMRI): +Example usage for single-echo data: `$ romeo ph.nii -m mag.ii -k nomask -o outputdir` -Example usage for a 3-echo Scan with TE = [3,6,9] ms: +Example for multiple time points with identical echo time (fMRI): +`$ romeo ph.nii -m mag.ii -k nomask -t epi -o outputdir` + +Example usage for a 3-echo scan with TE = [3,6,9] ms: `$ romeo ph.nii -m mag.ii -k nomask -t [3,6,9] -o outputdir` Note that echo times are required for unwrapping multi-echo data. @@ -182,6 +179,10 @@ optional arguments: -h, --help show this help message and exit ``` +## Related Repositories +The sourcecode is available under [ROMEO.jl](https://github.com/korbinian90/ROMEO.jl). +The binaries are a standalone compiled version of [RomeoApp.jl](https://github.com/korbinian90/RomeoApp.jl). The compilation scripts and recent releases are in [CompileMRI.jl](https://github.com/korbinian90/CompileMRI.jl). + ## Known issues ### v1.4 - single echo unwrapping with magnitude and default mask leads to ReadOnlyMemory error. Fixed in v1.4.1