https://github.com/cbica/dlwmls
Science Score: 26.0%
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○Scientific vocabulary similarity
Low similarity (16.4%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: CBICA
- License: other
- Language: Python
- Default Branch: main
- Size: 1000 KB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 2
- Releases: 0
Metadata Files
README.md
DLWMLS - Deep Learning White Matter Lesion Segmentation
Overview
DLWMLS uses a trained nnUNet model to segment White Matter Lesions (WML) from ICV-segmented (see DLICV method) and LPS oriented brain images (Nifti/.nii.gz format).
Installation
As a python package
Directly from this repository
bash
git clone https://github.com/CBICA/DLWMLS
cd DLWMLS
pip install -e .
Installing PyTorch
Depending on your system configuration and supported CUDA version, you may need to follow the PyTorch Installation Instructions.
Usage
A pre-trained nnUNet model can be found at our HuggingFace account. Feel free to use it under the package's license.
From command line (CUDA is recommended)
bash
DLWMLS -i "input_folder" -o "output_folder" -device cuda
The files in the input folder must have "FLLPS.nii.gz" as prefix.
In-code usage
python
from DLWMLS import run_dlwmls_pipeline
...
run_dlwmls_pipeline(in_dir, out_dir, device)
For more details, please refer to
bash
DLWMLS -h
[Windows Users] Troubleshooting model download failures
Our model download process creates several deep directory structures. If you are on Windows and your model download process fails, it may be due to Windows file path limitations.
To enable long path support in Windows 10, version 1607, and later, the registry key HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\FileSystem LongPathsEnabled (Type: REG_DWORD) must exist and be set to 1.
If this affects you, we recommend re-running DLWMLS with the --clear_cache flag set on the first run.
Contact
For more information, please contact CBICA Software.
For Developers
Contributions are welcome! Please refer to our CONTRIBUTING.md for more information on how to report bugs, suggest enhancements, and contribute code. Please make sure to write tests for new code and run them before submitting a pull request.
Owner
- Name: Center for Biomedical Image Computing & Analytics (CBICA)
- Login: CBICA
- Kind: organization
- Email: software@cbica.upenn.edu
- Location: Philadelphia, PA
- Website: https://www.med.upenn.edu/cbica/
- Twitter: CBICAannounce
- Repositories: 21
- Profile: https://github.com/CBICA
CBICA focuses on the development and application of advanced computation techniques.
GitHub Events
Total
- Issues event: 1
- Delete event: 1
- Push event: 19
- Public event: 1
- Pull request event: 12
- Create event: 2
Last Year
- Issues event: 1
- Delete event: 1
- Push event: 19
- Public event: 1
- Pull request event: 12
- Create event: 2
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 2
- Total pull requests: 6
- Average time to close issues: 11 days
- Average time to close pull requests: 8 days
- Total issue authors: 2
- Total pull request authors: 3
- Average comments per issue: 0.0
- Average comments per pull request: 0.0
- Merged pull requests: 3
- Bot issues: 0
- Bot pull requests: 2
Past Year
- Issues: 2
- Pull requests: 6
- Average time to close issues: 11 days
- Average time to close pull requests: 8 days
- Issue authors: 2
- Pull request authors: 3
- Average comments per issue: 0.0
- Average comments per pull request: 0.0
- Merged pull requests: 3
- Bot issues: 0
- Bot pull requests: 2
Top Authors
Issue Authors
- spirosmaggioros (1)
- euroso97 (1)
Pull Request Authors
- spirosmaggioros (2)
- dependabot[bot] (2)
- euroso97 (2)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- argparse *
- huggingface_hub *
- nnunetv2 >=2.2.1
- pathlib *
- torch >=2.2.1