| Name | trksnapshot JSON |
| Version |
0.1.5
JSON |
| download |
| home_page | None |
| Summary | Tractometry Visualization Tool |
| upload_time | 2025-09-05 23:15:48 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.10 |
| license | MIT License
Copyright (c) 2024, Yixue Feng
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE. |
| keywords |
tractometry
tractography
diffusion mri
white matter
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# trksnapshot
## Installation
`pip install trksnapshot` ([project page]([https://pypi.org/project/trksnapshot))
## Description
**trksnapshot** is a CLI for creating bundle visualizations (created using FURY and DIPY). It supports
1. Visualizing 3D bundles in an interactive window with custom color options and camera view. These include per-bundle color and along-tract color using BUAN (for tractometry results).
2. Plotting bundle with glass brain and pial surfaces.
3. Saving custom camera settings to produce consistent plots.
4. Saving snapshot images for publication-ready figures!
All bundle visualizations in our recent work [*Microstructural mapping of neural pathways in Alzheimer's disease using macrostructure-informed normative tractometry*](https://doi.org/10.1002/alz.14371) were created with this script. Here's one of the figures:
<img src="assets/atlas_bundles.jpg" alt="bundle_atlas" width="800">
## Usage
[**RECOMMENDED**] To visualization bundle(s) with default pial surfaces (in MNI space)
```bash
trksnapshot \
-i /path_to_tractogram/bundle*.trk \
-glass default_pial \
-show
```
You may also provide your own pial surface files
```bash
trksnapshot \
-i /path_to_tractogram/bundle*.trk \
-glass /path_to_surfaces/pial_left.nii /path_to_surfaces/pial_right.nii \
-show
```
To visualization bundle(s) with default glass brain (must be in MNI space)
```bash
trksnapshot \
-i /path_to_tractogram/bundle*.trk \
-glass default_glass \
-show
```
To visualization bundle with pial surfaces with BUAN output
```bash
trksnapshot \
-i /path_to_tractogram/bundle.trk \
-f /path_to_buan_results/pvals.npy \
-ctitle pvalues -auto -cbar /path_to_output_folder/cbar.png \
-glass /path_to_surfaces/pial_left.gii.gz /path_to_surfaces/pial_right.gii.gz
-show \
-o /path_to_output_folder/bundle.png
```
## Citations
1. [Microstructural mapping of neural pathways in Alzheimer's disease using macrostructure-informed normative tractometry
](https://doi.org/10.1002/alz.14371)
2. [FURY: advanced scientific visualization](10.21105/joss.03384)
Raw data
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"description": "# trksnapshot\n\n## Installation\n `pip install trksnapshot` ([project page]([https://pypi.org/project/trksnapshot))\n\n## Description\n**trksnapshot** is a CLI for creating bundle visualizations (created using FURY and DIPY). It supports \n1. Visualizing 3D bundles in an interactive window with custom color options and camera view. These include per-bundle color and along-tract color using BUAN (for tractometry results).\n2. Plotting bundle with glass brain and pial surfaces.\n3. Saving custom camera settings to produce consistent plots.\n4. Saving snapshot images for publication-ready figures!\n\nAll bundle visualizations in our recent work [*Microstructural mapping of neural pathways in Alzheimer's disease using macrostructure-informed normative tractometry*](https://doi.org/10.1002/alz.14371) were created with this script. Here's one of the figures:\n\n<img src=\"assets/atlas_bundles.jpg\" alt=\"bundle_atlas\" width=\"800\">\n\n## Usage\n\n[**RECOMMENDED**] To visualization bundle(s) with default pial surfaces (in MNI space)\n```bash\ntrksnapshot \\\n -i /path_to_tractogram/bundle*.trk \\\n -glass default_pial \\\n -show\n```\nYou may also provide your own pial surface files\n```bash\ntrksnapshot \\\n -i /path_to_tractogram/bundle*.trk \\\n -glass /path_to_surfaces/pial_left.nii /path_to_surfaces/pial_right.nii \\\n -show\n```\n\nTo visualization bundle(s) with default glass brain (must be in MNI space)\n```bash\ntrksnapshot \\\n -i /path_to_tractogram/bundle*.trk \\\n -glass default_glass \\\n -show\n```\n\nTo visualization bundle with pial surfaces with BUAN output\n```bash\ntrksnapshot \\\n -i /path_to_tractogram/bundle.trk \\\n -f /path_to_buan_results/pvals.npy \\\n -ctitle pvalues -auto -cbar /path_to_output_folder/cbar.png \\\n -glass /path_to_surfaces/pial_left.gii.gz /path_to_surfaces/pial_right.gii.gz\n -show \\\n -o /path_to_output_folder/bundle.png\n```\n\n## Citations\n1. [Microstructural mapping of neural pathways in Alzheimer's disease using macrostructure-informed normative tractometry\n](https://doi.org/10.1002/alz.14371)\n2. [FURY: advanced scientific visualization](10.21105/joss.03384)\n",
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