TRAMPOLINO
TRAMPOLINO (TRActography Meta-Pipeline cOmmand LINe tOol) is a command line interface tool for brain tractography, written in Python. It leverages the Nipype Python package to offer an immediate way to reconstruct an orientation distribution function, use it to track the streamlines and eventually filter them, all using existing software toolboxes.
At the moment it is under active development but supports already several software packages and the plan is to include as many software alternatives as possible.
- Free software: MIT license
- Documentation: https://trampolino.readthedocs.io.
Features
- Composable command line interfaces built using the Click Python package;
- One-command generation of multiple results using different parameters (e.g. angular thresholds, tracking algorithm);
- Ensemble tractography implementation;
- Short-cut workflows to rapidly generate results from sample data;
- Native support to containers (through the Docker API);
Requirements
TRAMPOLINO requires Python 3 and the GraphViz visualization software. The Python packages required are listed in the [requirements.txt]{.title-ref} file.
At the moment, TRAMPOLINO can be used to run the following tools:
The current container image supports MRtrix3 (3.0.0) and Trekker (0.7).
To run those workflows directly in a container, you need to install the Docker API:
pip install docker
Installing TRAMPOLINO
TRAMPOLINO can be easily installed using pip:
pip install trampolino
Running TRAMPOLINO
To try TRAMPOLINO, you can download some example data using this script:
get_example_data
It will download the Sherbrooke multi-shell dataset from dipy. Then you can run:
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
And you have your first results!
Contributors
Matteo Mancini
Bastian David - https://github.com/bastiandavid
Want to contribute? Have suggestions/crazy ideas/evil plans? Get in touch!
Credits
TRAMPOLINO is built on top of the amazing Nipype 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 and dipy, currently used respectively for conversion and fetching data. Be sure to check them out!
TRAMPOLINO has started its life during Brainhack School (Montreal, August 2019) and has been first extended during the OHBM Brainhack in 2020 (virtual event). Therefore, TRAMPOLINO would not exist if it wasn't for Brainhack!
This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.
