{"id":13689128,"url":"https://github.com/matteomancini/trampolino","last_synced_at":"2025-05-01T23:32:20.438Z","repository":{"id":35090428,"uuid":"204799104","full_name":"matteomancini/trampolino","owner":"matteomancini","description":"TRAMPOLINO (TRActography Meta-Pipeline cOmmand LINe tOol) is a CLI for brain tractography. 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It leverages the Nipype\nPython package to offer an immediate way to reconstruct an orientation\ndistribution function, use it to track the streamlines and eventually\nfilter them, all using existing software toolboxes.\n\nAt the moment it is under active development but supports already several\nsoftware packages and the plan is to include as many software alternatives as possible.\n\n-   Free software: MIT license\n-   Documentation: \u003chttps://trampolino.readthedocs.io\u003e.\n\n\nFeatures\n========\n\n-   Composable command line interfaces built using the Click Python\n    package;\n-   One-command generation of multiple results using different\n    parameters (e.g. angular thresholds, tracking algorithm);\n-   Ensemble tractography implementation;\n-   Short-cut workflows to rapidly generate results from sample data;\n-   Native support to containers (through the Docker API);\n\n\nRequirements\n============\n\nTRAMPOLINO requires Python 3 and the [GraphViz](http://www.graphviz.org)\nvisualization software. The Python packages required are listed in the\n[requirements.txt]{.title-ref} file.\n\nAt the moment, TRAMPOLINO can be used to run the following tools:\n\n-   [MRtrix3](https://github.com/MRtrix3/mrtrix3)\n-   [DiffusionToolkit](http://trackvis.org/dtk/)\n-   [DSI\\_Studio](http://dsi-studio.labsolver.org)\n-   [dMRI Trekker](https://dmritrekker.github.io/)\n-   [TractSeg](https://github.com/MIC-DKFZ/TractSeg)\n\nThe current container image supports MRtrix3 (`3.0.0`) and Trekker (`0.7`).\nTo run those workflows directly in a container, you need to install the Docker API:\n\n    pip install docker\n\n\n\nInstalling TRAMPOLINO\n=====================\n\nTRAMPOLINO can be easily installed using pip:\n\n    pip install trampolino\n\n\nRunning TRAMPOLINO\n==================\n\nTo try TRAMPOLINO, you can download some example data using this script:\n\n    get_example_data\n\nIt will download the Sherbrooke multi-shell dataset from\n[dipy](https://github.com/nipy/dipy). Then you can run:\n\n    trampolino -n msmt_csd -r example_results recon -i sherbrooke_3shell/dwi.nii.gz -v sherbrooke_3shell/bvec.txt -b sherbrooke_3shell/bval.txt mrtrix_msmt_csd track --angle 30,45 --algorithm iFOD2,SD_Stream mrtrix_tckgen\n\nAnd you have your first results!\n\n\nContributors\n------------\n\nMatteo Mancini\n\nBastian David - \u003chttps://github.com/bastiandavid\u003e\n\nWant to contribute? Have suggestions/crazy ideas/evil plans? [Get in touch](mailto:ingmatteomancini@gmail.com)!\n\n\nCredits\n-------\n\nTRAMPOLINO is built on top of the amazing [Nipype](https://nipype.readthedocs.io/en/latest/) toolkit. At the moment, some of the interfaces already available in Nipype are included in order to fix and/or add features for the sake of compatibility with modern tools. This is only temporary, and once those features are merge in Nipype, TRAMPOLINO will use directly the native interfaces. Other important tools for TRAMPOLINO are [nibabel](https://nipy.org/nibabel/) and [dipy](https://dipy.org), currently used respectively for conversion and fetching data. Be sure to check them out!\n\nTRAMPOLINO has started its life during [Brainhack School](https://brainhackmtl.github.io/school2019/index.html) (Montreal, August 2019) and has been first extended during the [OHBM Brainhack](https://ohbm.github.io/hackathon2020/) in 2020 (virtual event). Therefore, TRAMPOLINO would not exist if it wasn't for [Brainhack](https://brainhack.org)!\n\nThis package was created with\n[Cookiecutter](https://github.com/audreyr/cookiecutter) and the\n[audreyr/cookiecutter-pypackage](https://github.com/audreyr/cookiecutter-pypackage)\nproject template.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmatteomancini%2Ftrampolino","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmatteomancini%2Ftrampolino","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmatteomancini%2Ftrampolino/lists"}