trampolino 0.1.9

A meta-pipeline tool for tractography based on Nipype.

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:

• MRtrix3
• DiffusionToolkit
• DSI_Studio
• dMRI Trekker
• TractSeg

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.

History

0.1.9 (2021-02-01)

• Fixed issue with missing file in manifest;

0.1.8 (2021-02-01)

• Fixed issue with pip installation requirements;

0.1.7 (2021-02-01)

• TractSeg interface and workflow;
• Trekker interface and workflow;
• Added support for containers;
• Refactored command line interface code;

0.1.6 (2020-07-21)

• Added "force" feature;
• Added conversion command;
• Nibabel interface and workflows;

0.1.5 (2019-11-05)

• Diffusion Toolkit workflows
• DSI Studio interface and workflows;

0.1.4 (2019-10-11)

• Added exclusion criteria;
• Script to retrieve sample data;

0.1.3 (2019-09-12)

• Minimum length parameter;
• Length-based ensembling;

0.1.2 (2019-09-11)

• Added angle-range feature;
• Improved folder naming and seed selection;

0.1.1 (2019-09-10)

• Added workflow-specific options;
• Added documentation;
• Fixed minor issues with paths;

0.1.0 (2019-08-30)

• First release on PyPI!
• Dynamic workflow loading;
• Meta-workflow assembly line;
• MRtrix3 interface and workflows;