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BraTS-Toolkit
1.0.4
One-liner (summary)
Description
[](https://brats-toolkit.readthedocs.io/en/latest/?badge=latest) [](https://pypi.python.org/pypi/BraTS-Toolkit/)
____ _____ ____ _____ _ _ _ __ | '__/ _` || | ___ | |/ _ \ / _ \| | |/ / | __||_) | | | (_| || | ___) | | | (_) | (_) | | <| | |_|____/|_| __,_||_| |____/ |_|___/ ___/|_|_|__|__|
# BraTS Toolkit: What is it and what can I use it for? Abstract: >BraTS Toolkit is a holistic approach to brain tumor segmentation and consists out of out of three components:
First, the BraTS Preprocessor facilitates data standardization and preprocessing for researchers and clinicians alike. It covers the entire image analysis workflow prior to tumor segmentation, from image conversion and registration to brain extraction. Second, BraTS Segmentor enables orchestration of BraTS brain tumor segmentation algorithms for generation of fully-automated segmentations. Finally, BraTS Fusionator can combine the resulting candidate segmentations into consensus segmentations using fusion methods such as majority voting and iterative SIMPLE fusion. The capabilities of our tools are illustrated with a practical example to enable easy translation to clinical and scientific practice.
## Installation To install the most up to date version from the master branch please use the following pip install command: ` pip install BraTS-Toolkit `
We recommended installation in a virtual environment based on Python 3.10 .
Further, NVIDIA Docker Toolkit needs to be installed (installation instructions here: https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/install-guide.html#docker and here: https://neuronflow.github.io/BraTS-Preprocessor/#dockerinstallation ).
## Issues When running into issues please use the issue tracker here on Github: https://github.com/neuronflow/BraTS-Toolkit/issues So others can profit and contribute as well.
## Citation If you use BraTS Toolkit please cite:
https://www.frontiersin.org/articles/10.3389/fnins.2020.00125/full
Kofler, F., Berger, C., Waldmannstetter, D., Lipkova, J., Ezhov, I., Tetteh, G., Kirschke, J., Zimmer, C., Wiestler, B., & Menze, B. H. (2020). BraTS Toolkit: Translating BraTS Brain Tumor Segmentation Algorithms Into Clinical and Scientific Practice. Frontiers in neuroscience, 14, 125. https://doi.org/10.3389/fnins.2020.00125
``` @article{kofler2020brats,
title={BraTS toolkit: translating BraTS brain tumor segmentation algorithms into clinical and scientific practice}, author={Kofler, Florian and Berger, Christoph and Waldmannstetter, Diana and Lipkova, Jana and Ezhov, Ivan and Tetteh, Giles and Kirschke, Jan and Zimmer, Claus and Wiestler, Benedikt and Menze, Bjoern H}, journal={Frontiers in neuroscience}, pages={125}, year={2020}, publisher={Frontiers}
}
Please also cite the following original authors of the algorithms who make this repository and tool possible:
## Brats Preprocessor BraTS Preprocessor facilitates data standardization and preprocessing for researchers and clinicians alike. It covers the entire image analysis workflow prior to tumor segmentation, from image conversion and registration to brain extraction.
### Processing Modi BraTS Preprocessor offers the following preprocessing modes: #### GPU brain extraction: "gpu" Activates HD-BET in CUDA mode. Only supported when using NVIDIA docker (Linux operating systems only for the moment). #### CPU brain extraction: "cpu" Activates HD-BET or ROBEX in CPU mode depending on available RAM. #### ROBEX brain extraction: "robex" Activates Robex brain extraction. #### GPU defacing: "gpu_defacing" Activates GPU defacing - not implemented yet falls back to cpu_defacing for the moment. #### CPU defacing: "cpu_defacing" Activates mri-deface to deface using CPU.
- ### Single vs. batch processing
BraTS preprocessor offers processing files in batch or single mode. Please have a look at the respective example scripts / CLI commands for information how to use them.
For faster computation we strictly recommend the batch processing mode, which avoids additional overhead of spawning and shutting down multiple docker containers and instead does all the processing in one container.
### Python package Please have a look at 0_preprocessing_batch.py and 0_preprocessing_single.py in this repository for a demo application. You can download the example data by cloning this repository.
### Command Line Interface (CLI) #### single file processing Type brats-preprocess -h after installing the python package to see available options. #### batch file processing Type brats-batch-preprocess -h after installing the python package to see available options.
### Graphical User Interface (GUI) You can find instructions to use and download the GUI variant here: https://neuronflow.github.io/BraTS-Preprocessor/ > WARNING: The GUI is not nicely maintained. We encourage you to use the python package or the CLI instead.
## Brats Segmentor BraTS Segmentor enables orchestration of BraTS brain tumor segmentation algorithms for generation of fully-automated segmentations. ### Python package Please have a look at 1_segmentation.py in this repository for a demo application.
### Command Line Interface (CLI) Type brats-segment -h after installing the python package to see available options.
## Brats Fusionator BraTS Fusionator can combine the resulting candidate segmentations into consensus segmentations using fusion methods such as majority voting and iterative SIMPLE fusion. ### Python package Please have a look at 2_fusion.py in this repository for a demo application.
### Command Line Interface (CLI) Type brats-fuse -h after installing the python package to see available options.
## Contact / Feedback / Questions Open an issue in this git repository or contact us per email.
| Status | Completed |
|---|---|
| Checksum (MD5) | fbb277fa81b64c7d7f48d79e66ef1c20 |
| Checksum (SHA-1) | 7c1e3ea8886ee333141c1771a50368b8c677e7b6 |
| Checksum (SHA-256) | 2cd6a450d9dedb11c88bc4858b8351b092d90dff87daa8ed1e0b8e305b41c269 |
| Checksum (SHA-512) | dfdcfc2ef4a286bb8c35f3bcef96df1de381878dd37a5fc339e60250be960c45ef… |
| GPG Signature | |
| GPG Fingerprint | 6811684bac0b8895434e97bdd4391b8fb999e537 |
| Storage Region | Dublin, Ireland |
| Type | Binary (contains binaries and binary artifacts) |
| Uploaded At | 4 months, 3 weeks ago |
| Uploaded By |
|
| Slug Id | brats_toolkit-104-py3-none-anywhl-2gh4 |
| Unique Id | coJTSWGLcFuP79se |
| Version (Raw) | 1.0.4 |
| Version (Parsed) |
|
| extended metadata | |
| Author | Unset |
| Classifiers | License :: OSI Approved :: GNU Affero General Public License v3 | Operating System :: OS Independent | Programming Language :: Python :: 3 |
| Keywords | brain tumor,glioma,BraTS,segmentation,fusion,skullstripping,brain extraction |
| Maintainer | Unset |
| Metadata Version | 2.1 |
| Project Urls | repository, https://github.com/neuronflow/BraTS-Toolkit |
| Py Filetype | bdist_wheel |
| Py Version | py3 |
| Requires Dist | SimpleITK (==2.1.1.2) | numpy (==1.22.0) | pytest ; extra == 'dev' | python-engineio (==3.14.2) | python-socketio (==4.6.1) | requests (==2.24.0) |
| pkg | BraTS_Toolkit-1.0.4-py3-none-an… |
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Last scanned
4 months, 3 weeks ago
Scan result
Clean
Vulnerability count
0
Max. severity
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BraTS-Toolkit==1.0.4
](https://pypi.python.org/pypi/BraTS-Toolkit/){kind=link}