A meta-pipeline tool for tractography based on Nipype.
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TRAMPOLINO (TRActography Meta-Pipeline cOmmand LINe tOol) is a command line interface tool for brain tractography. 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 and support mainly MRtrix but the plan is to include as many software alternatives as possible.
- Free software: MIT license
- Documentation: https://trampolino.readthedocs.io.
- 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;
TRAMPOLINO requires the GraphViz_ visualization software and the MRtrix3_ tool.
TRAMPOLINO can be easily installed using pip::
pip install trampolino
To try TRAMPOLINO, you can download some example data using this script::
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!
This package was created with Cookiecutter_ and the
audreyr/cookiecutter-pypackage_ project template.
.. _GraphViz: http://www.graphviz.org
.. _MRtrix3: https://github.com/MRtrix3/mrtrix3
.. _DiPy: https://github.com/nipy/dipy
.. _Cookiecutter: https://github.com/audreyr/cookiecutter
- First release on PyPI.
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