baranaydogan / trekker

dMRI based fiber tracking using parallel transport tractography

Trekker

Trekker implements a state-of-the-art tractography algorithm, parallel transport tractography (PTT). PTT is capable of reconstructing geometrically smooth and topographically organized fiber bundles.

Trekker software has the following features:

• Clean probabilistic tractography with PTT.
• Pathway rules that offer flexible options to reconstruct intricate connections.
• Time limiting enables tracking for a given length of duration, specification of streamline count is optional.
• Multithreading reconstructs streamlines using multiple cores of a CPU.
• Support for asymmetric FODs provides a more flexible option for fiber tracking.
• Command line interface, an essential requirement to write scripts for processing big data in computer grids.
• Python package, wrapped using Cython from Trekker's C/C++ code which provides easy access to PTT algorithm for python lovers.
• .vtk output, that is compatible with a large number of third party 3D rendering software, for easy and high quality visualizations.

For complete documentation, tutorials and examples, visit https://dmritrekker.github.io/.

Example:

#Clean whole brain tractography with intuitive options

./trekker -fod FOD.nii.gz \
          -seed_image WHITEMATTER.nii.gz \
          -seed_count 100000 \
          -pathway=discard_if_ends_inside WHITEMATTER.nii.gz \
          -pathway=discard_if_enters CSF.nii.gz \
          -minLength 20 \
          -maxLength 300 \
          -output OUTPUT.vtk

Installation

Stand-alone executables:

Latest binaries are under: https://github.com/baranaydogan/trekker/tree/master/binaries

Building from source:

Step 1. Download the source code:

git clone https://github.com/dmritrekker/trekker

Step 2. Modify the first few lines in the build script (make sure to have cmake-3.15 or newer):

• For Linux -> build_Linux.sh
• For Windows -> build_Windows.bat

Step 3. Run the build script. This will build Trekker under:

• For Linux -> /build/Linux/install
• For Windows -> /build/Windows/install

Python package:

A python package can be built from source. You can also download a built distributions (.whl) from the /binaries folder.

To install the python package use:

pip install Trekker-<VERSION>.whl

Demo

To test your installation, please use the scripts under -> /demo

Publications:

If you use Trekker, please cite [Aydogan2021], which provides a detailed explanation of the algorithm and the results obtained from extensive experiments. A precursory abstract was initially published during ISMRM 2019, Montreal [Aydogan2019], which can additionally be cited:

• [Aydogan2021] Aydogan D.B., Shi Y., "Parallel transport tractography", in IEEE Transactions on Medical Imaging, vol. 40, no. 2, pp. 635-647, Feb. 2021, doi: 10.1109/TMI.2020.3034038.

• [Aydogan2019] Aydogan D.B., Shi Y., "A novel fiber tracking algorithm using parallel transport frames", Proceedings of the 27th Annual Meeting of the International Society of Magnetic Resonance in Medicine (ISMRM) 2019