Trekker offers state-of-the-art tractography tools to study the structural connectivity of the brain. Trekker aims to improve fiber tracking pipelines by offering features like:
- Well-organized, clean, probabilistic streamline tractography using the parallel transport tractography (PTT) algorithm.
- A comprehensive set of tractogram filtering options, including support for anatomical constraints using surface meshes.
- Compatibility with .vtk format, to enable the use of powerful third-party 3D rendering software, such as Paraview, for easy and high-quality visualizations.
- Support for asymmetric FODs, providing greater flexibility in fiber tracking.
- Several features designed for high-performance computing (HPC), including multithreading, time-limited tracking, and a user-friendly command line interface.
🏆 Awards and Recognitions:
Tractography pipelines based on Trekker have earned awards in every international tractography challenge since 2017. Click here to read more about Trekker's awards.
For complete documentation, tutorials and examples, visit https://dmritrekker.github.io/.
Stand-alone executables: Please find the stand-alone executables under Releases.
Trekker relies on nibrary. To compile Trekker from source, ensure that nibrary is installed first. Then follow these steps to compile Trekker:
git clone https://github.com/dmritrekker/trekker- For Linux: Edit
build_Linux.sh - For Windows: Edit
build_Windows.bat
Simply run trekker on the terminal. This will display help and the commands, which are listed below:
| Command | Description |
|---|---|
| track | performs fiber tracking using parallel transport tractography (PTT) algorithm. PTT excels in reconstructing geometrically smooth and topographically organized fiber bundles. |
| filter | Trekker employs an intuitive set of pathway rules to filter tractograms. The rules can be specified with surface meshes, as well as with spheres, image masks and partial volume fractions. |
| track2img | maps tractogram features on an image |
| track2surf | maps tractogram features on a surface |
| img2track | maps image values on a tractogram |
| select | selects streamlines from a tractogram |
| resample | resamples streamlines in a tractogram |
| convert | converts tractogram file formats (.vtk, .tck, .trk) |
| transform | applies a transform on an input tractogram |
| diff | finds different streamlines between two tractograms |
| merge | merges two tractograms, optionally ignoring duplicates |
| addColor | adds colors to streamlines (.vtk only) |
| fieldExport | exports a selected vtk field from a tractogram (.vtk only) |
| fieldImport | adds a new vtk field with values read from a file (.vtk only) |
| fieldRemove | removes a vtk field from a tractogram (.vtk only) |
Fiber tracking example:
./trekker track \
FOD.nii.gz \
--seed WHITE_MATTER_SURFACE.gii \
--seed_surf_useSurfNorm \
--seed_count 100000 \
--pathway discard_if_ends_inside WHITE_MATTER.nii.gz \
--pathway discard_if_enters CSF.nii.gz \
--minLength 20 \
--maxLength 300 \
--output OUT_TRACK.vtkFiber filtering example:
# You can use the --seed option when filtering too.
./trekker filter \
INP_TRACK.vtk \
--seed WHITE_MATTER_SURFACE.gii \
--pathway require_end_inside LEFT_THAL.nii.gz \
OUT_TRACK.vtkIf 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:
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[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.
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[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