Trekker

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/.

Installation

Stand-alone executables: Please find the stand-alone executables under Releases.

Building from Source

Trekker relies on nibrary. To compile Trekker from source, ensure that nibrary is installed first. Then follow these steps to compile Trekker:

Step 1: Download the Source Code

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

Step 2: Modify and run the build script

• For Linux: Edit build_Linux.sh

Note: Trekker binaries can be compiled using the following version matching with nibrary:

Trekker version	nibrary version
master	main
v1.0.0-rc2	v0.2.0
v1.0.0-rc1	v0.1.0
v1.0-beta	v0.0.0

Usage

Simply run trekker on the terminal. This will display help and the commands, which are listed below:

Command	Description
info	displays information about input file
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)
dMRI	dMRI commands

Examples

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.vtk

Fiber 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.vtk

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