Skip to content
TRActography Meta-Pipeline cOmmand LINe tOol
Python Makefile
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
.github
docs
tests
trampolino
.editorconfig
.gitignore
.travis.yml
AUTHORS.rst
CONTRIBUTING.rst
HISTORY.rst
LICENSE
MANIFEST.in
Makefile
README.rst
requirements.txt
setup.cfg
setup.py
tox.ini

README.rst

TRAMPOLINO

Documentation Status

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.

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;

Requirements

TRAMPOLINO requires the GraphViz visualization software and the MRtrix3 tool.

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!

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.

You can’t perform that action at this time.