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https://github.com/cbica/dlicv

A repository that allows users to apply the DLICV method to their brain imaging data.

https://github.com/cbica/dlicv

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
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    DOI references
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    Academic publication links
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    Academic email domains
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    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.7%) to scientific vocabulary

Keywords

deeplearning imagesegmentation medical-image-analysis medical-image-processing nnunet
Last synced: 5 months ago · JSON representation

Repository

A repository that allows users to apply the DLICV method to their brain imaging data.

Basic Info
  • Host: GitHub
  • Owner: CBICA
  • License: other
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 19.4 MB
Statistics
  • Stars: 2
  • Watchers: 1
  • Forks: 0
  • Open Issues: 1
  • Releases: 3
Topics
deeplearning imagesegmentation medical-image-analysis medical-image-processing nnunet
Created over 2 years ago · Last pushed 6 months ago
Metadata Files
Readme Contributing License

README.md

DLICV - Deep Learning Intra Cranial Volume

Overview

DLICV uses a trained nnUNet model to compute the intracranial volume from structural MRI scans in the nifti image format, oriented in LPS orientation.

Installation

As a python package

bash pip install DLICV

Directly from this repository

bash git clone https://github.com/CBICA/DLICV cd DLICV 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 hugging face account. Feel free to use it under the package's licence bash DLICV -i "input_folder" -o "output_folder" -device cpu

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 DLICV 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

CBICA focuses on the development and application of advanced computation techniques.

GitHub Events

Total
  • Issue comment event: 5
  • Push event: 268
  • Pull request event: 5
  • Fork event: 3
  • Create event: 4
Last Year
  • Issue comment event: 5
  • Push event: 268
  • Pull request event: 5
  • Fork event: 3
  • Create event: 4

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 0
  • Total pull requests: 2
  • Average time to close issues: N/A
  • Average time to close pull requests: 2 months
  • Total issue authors: 0
  • Total pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 1.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 2
  • Average time to close issues: N/A
  • Average time to close pull requests: 2 months
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 1.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • gurayerus (3)
  • euroso97 (1)
Pull Request Authors
  • AlexanderGetka-cbica (3)
  • spirosmaggioros (2)
  • euroso97 (2)
Top Labels
Issue Labels
Pull Request Labels
bug (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 69 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 6
  • Total maintainers: 2
pypi.org: dlicv

DLICV - Deep Learning Intra Cranial Volume.

  • Versions: 6
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 69 Last month
Rankings
Dependent packages count: 9.8%
Forks count: 29.9%
Average: 36.6%
Stargazers count: 38.9%
Dependent repos count: 67.9%
Maintainers (2)
AlexanderGetka gaidinis
Last synced: 6 months ago

Dependencies

requirements-dev.txt pypi
  • nnunet >=1.7.0 development
  • torch >2.0,<2.1 development
requirements-test.txt pypi
  • nnunet >=1.7.0 test
  • pytest >=7.0.0 test
  • torch >2.0,<2.1 test
requirements.txt pypi
  • nnunet >=1.7.0
  • torch >2.0,<2.1
setup.py pypi