diff --git a/README.md b/README.md index 3ac272d..dfb5072 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,5 @@ # MRI Tools -![made-with-python](http://ForTheBadge.com/images/badges/made-with-python.svg) ![license](https://img.shields.io/github/license/abdrysdale/mri-tools.svg) ![size](https://badge-size.herokuapp.com/abdrysdale/mri-tools/main/README.md) +![license](https://img.shields.io/github/license/abdrysdale/mri-tools.svg) A collection of free and open-source software software tools for use in MRI. Free is meant as in free beer (gratis) and freedom (libre). @@ -23,8 +23,8 @@ tags = ["repo-tag-1", "repo-tag-2"] - [analysis](#analysis) - [processing](#processing) - [simulation](#simulation) - - [visualisation](#visualisation) - [segmentation](#segmentation) + - [visualisation](#visualisation) - [fetal](#fetal) - [data](#data) - [brain](#brain) @@ -40,11 +40,10 @@ tags = ["repo-tag-1", "repo-tag-2"] - [c](#c) - [javascript](#javascript) - [r](#r) - - [mathematica](#mathematica) - [jupyter](#jupyter) ## Stats -- Total repos: 61 +- Total repos: 60 - Languages: | Language | Count | @@ -55,7 +54,6 @@ tags = ["repo-tag-1", "repo-tag-2"] | c | 5 | | javascript | 4 | | r | 2 | -| mathematica | 1 | | jupyter | 1 | - Tags: @@ -64,10 +62,10 @@ tags = ["repo-tag-1", "repo-tag-2"] |---|---| | reconstruction | 17 | | analysis | 15 | -| processing | 14 | -| simulation | 13 | -| visualisation | 7 | +| processing | 13 | +| simulation | 12 | | segmentation | 7 | +| visualisation | 6 | | fetal | 6 | | data | 5 | | brain | 4 | @@ -82,8 +80,8 @@ tags = ["repo-tag-1", "repo-tag-2"] | Licence | Count | |---|---| | mit | 22 | -| bsd | 11 | | apache | 11 | +| bsd | 10 | | gplv3 | 8 | | agplv3 | 2 | | lgplv3 | 2 | @@ -301,12 +299,6 @@ tags = ["repo-tag-1", "repo-tag-2"] >- Tags: simulation, reconstruction, processing >- Multi Modal Acquisition Software, Which Allows Individualizable, Modular And Cloud-Based Processing Of Functional And Anatomical Medical Images. -- [qmritools](https://github.com/mfroeling/QMRITools) ->- Languages: mathematica ->- License: BSD ->- Tags: simulation, processing, visualisation ->- Collection Of Tools And Functions For Processing Quantitative Mri Data. - - [spinal-chord-toolbox](https://github.com/spinalcordtoolbox/spinalcordtoolbox) >- Languages: python >- License: LGPLv3 @@ -410,12 +402,6 @@ tags = ["repo-tag-1", "repo-tag-2"] >- Tags: simulation, analysis, visualisation >- Open Source Software Package For Visualization And Image Analysis. -- [qmritools](https://github.com/mfroeling/QMRITools) ->- Languages: mathematica ->- License: BSD ->- Tags: simulation, processing, visualisation ->- Collection Of Tools And Functions For Processing Quantitative Mri Data. - - [pypulseq](https://github.com/imr-framework/pypulseq/) >- Languages: python >- License: AGPLv3 @@ -452,49 +438,6 @@ tags = ["repo-tag-1", "repo-tag-2"] >- Tags: processing, analysis, simulation >- Specialized Tools For Mri -### Visualisation -- [slicer](https://github.com/Slicer/Slicer) ->- Languages: python, c++ ->- License: BSD ->- Tags: simulation, analysis, visualisation ->- Open Source Software Package For Visualization And Image Analysis. - -- [qmritools](https://github.com/mfroeling/QMRITools) ->- Languages: mathematica ->- License: BSD ->- Tags: simulation, processing, visualisation ->- Collection Of Tools And Functions For Processing Quantitative Mri Data. - -- [ukf-tractography](https://github.com/pnlbwh/ukftractography) ->- Languages: c, c++ ->- License: BSD ->- Tags: visualisation, brain ->- Framework Which Uses An Unscented Kalman Filter For Performing Tractography - -- [freesurfer](https://github.com/freesurfer/freesurfer) ->- Languages: c++, c, python ->- License: GPLv3 ->- Tags: analysis, visualisation, brain ->- Analysis And Visualization Of Neuroimaging Data From Cross-Sectional And Longitudinal Studies - -- [gif_your_nifti](https://github.com/miykael/gif_your_nifti) ->- Languages: python ->- License: BSD ->- Tags: visualisation ->- Create Nice Looking Gifs From Your Nifti (.Nii Or .Nii.Gz) Files With A Simple Command - -- [brainchop](https://github.com/neuroneural/brainchop) ->- Languages: javascript, python ->- License: MIT ->- Tags: segmentation, visualisation ->- In-Browser 3D Mri Rendering And Segmentation - -- [mri-viewer](https://github.com/epam/mriviewer) ->- Languages: javascript ->- License: Apache ->- Tags: visualisation ->- High Performance Web Tool For Advanced Visualization (Both In 2D And 3D Modes) Medical Volumetric Data, Provided In Popular File Formats: Dicom, Nifti, Ktx, Hdr - ### Segmentation - [dl-direct](https://github.com/SCAN-NRAD/DL-DiReCT) >- Languages: python @@ -538,6 +481,43 @@ tags = ["repo-tag-1", "repo-tag-2"] >- Tags: segmentation, visualisation >- In-Browser 3D Mri Rendering And Segmentation +### Visualisation +- [slicer](https://github.com/Slicer/Slicer) +>- Languages: python, c++ +>- License: BSD +>- Tags: simulation, analysis, visualisation +>- Open Source Software Package For Visualization And Image Analysis. + +- [ukf-tractography](https://github.com/pnlbwh/ukftractography) +>- Languages: c, c++ +>- License: BSD +>- Tags: visualisation, brain +>- Framework Which Uses An Unscented Kalman Filter For Performing Tractography + +- [freesurfer](https://github.com/freesurfer/freesurfer) +>- Languages: c++, c, python +>- License: GPLv3 +>- Tags: analysis, visualisation, brain +>- Analysis And Visualization Of Neuroimaging Data From Cross-Sectional And Longitudinal Studies + +- [gif_your_nifti](https://github.com/miykael/gif_your_nifti) +>- Languages: python +>- License: BSD +>- Tags: visualisation +>- Create Nice Looking Gifs From Your Nifti (.Nii Or .Nii.Gz) Files With A Simple Command + +- [brainchop](https://github.com/neuroneural/brainchop) +>- Languages: javascript, python +>- License: MIT +>- Tags: segmentation, visualisation +>- In-Browser 3D Mri Rendering And Segmentation + +- [mri-viewer](https://github.com/epam/mriviewer) +>- Languages: javascript +>- License: Apache +>- Tags: visualisation +>- High Performance Web Tool For Advanced Visualization (Both In 2D And 3D Modes) Medical Volumetric Data, Provided In Popular File Formats: Dicom, Nifti, Ktx, Hdr + ### Fetal - [nesvor](https://github.com/daviddmc/NeSVoR) >- Languages: python @@ -1137,13 +1117,6 @@ tags = ["repo-tag-1", "repo-tag-2"] >- Tags: analysis >- R Package For Performing Graph Theory Analyses Of Brain Mri Data -### Mathematica -- [qmritools](https://github.com/mfroeling/QMRITools) ->- Languages: mathematica ->- License: BSD ->- Tags: simulation, processing, visualisation ->- Collection Of Tools And Functions For Processing Quantitative Mri Data. - ### Jupyter - [openmorph](https://github.com/cMadan/openMorph) >- Languages: jupyter diff --git a/make.py b/make.py index e1bdb62..e7bab9f 100644 --- a/make.py +++ b/make.py @@ -85,7 +85,7 @@ def make(repos: list[dict], out: str = "README.md") -> bool: intro = ( "# MRI Tools\n" - "![license](https://img.shields.io/github/license/abdrysdale/mri-tools.svg) " + "![license](https://img.shields.io/github/license/abdrysdale/mri-tools.svg)\n\n" "A collection of free and open-source software software tools for use in MRI.\n" "Free is meant as in free beer (gratis) and freedom (libre).\n\n" "To add a project edit the repos.toml file and submit a pull request.\n" diff --git a/repos.toml b/repos.toml index 0359a37..71c2b26 100644 --- a/repos.toml +++ b/repos.toml @@ -40,13 +40,6 @@ license = "BSD" description = "open source software package for visualization and image analysis." tags = ["simulation", "analysis", "visualisation"] -[qmritools] -languages = ["mathematica"] -link = "https://github.com/mfroeling/QMRITools" -license = "BSD" -description = "collection of tools and functions for processing quantitative MRI data." -tags = ["simulation", "processing", "visualisation"] - [eptlib] languages = ["c++", "python"] link = "https://github.com/eptlib/eptlib"