Exporting Tractography Results

After computing a tractogram, you can export streamlines to the TCK file format for use with other neuroimaging tools like MRtrix3, TrackVis, etc.

Saving to TCK Format

The TCK format is a widely-used binary format for storing tractography streamlines. Tractography.jl provides a convenience function save_streamlines that uses the Python library nibabel via PythonCall.jl to export streamlines.

Prerequisites

Ensure you have PythonCall.jl installed and nibabel available in your Python environment:

using Pkg
Pkg.add("PythonCall")

Then install nibabel in Python (this typically happens automatically via PythonCall).

Basic Example

using Tractography
using PythonCall
const TG = Tractography

# ... model definition skipped
streamlines, tract_length = TG.sample(model, alg_tracking, seeds)

# Export to TCK file
TG.save_streamlines("my_tractogram.tck", streamlines, tract_length)

Output Format

The saved TCK file contains:

• Streamline coordinates: 3D positions of points along each fiber tract

The file can be visualized and analyzed using standard tractography software.