trk_to_annotation
This repository provides utilities for converting .trk tractography files into Neuroglancer precomputed annotation format, and serving them locally with HTTP requests.
Install
python -m build
pip install .
Usage
python -m trk_to_annotation <trk_file> \
--annotation_output_dir ./precomputed_annotations \
--segmentation_output_dir ./precomputed_segmentations \
--grid_densities 1 2 4 8 16
Arguments
| Argument | Required | Default | Description |
|---|---|---|---|
| trk_file | ✅ | — | Path to the input .trk file |
| --annotation_output_dir | ❌ | ./precomputed_annotations | Output directory for precomputed annotations |
| --segmentation_output_dir | ❌ | ./precomputed_annotations/precomputed_segmentations | Output directory for precomputed segmentations |
| --grid_densities | ❌ | [1, 2, 4, 8, 16] | Grid densities (powers of two, ascending order) |
Running server for neuroglancer
Run the following command in the directory with your outputted folders
python -m trk_to_annotation.http_server
You should now be able to access the annotation and segmentation layers on neuroglancer via http://localhost:8000/
1 maintainer
Metadata
1 maintainer
Release files for trk-to-annotation 0.0.2
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Total release size: 34.7 kB
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