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Sep 23, 2025
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added note Pre/Post Glioma segmentation with links + formated links #66

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added note Pre/Post Glioma segmentation with links + formated with bl…
evamariie May 29, 2025
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10 changes: 6 additions & 4 deletions README.md
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Expand Up @@ -74,7 +74,8 @@ Further, have a look at the Python examples in this repository for preprocessing
BraTS Segmentor enables orchestration of BraTS brain tumor segmentation algorithms for generation of fully-automated segmentations.
For segmentation, your files should be `preprocessed`, meaning they should be co-registered and skullstripped in SRI-24 space.
You can preprocess your files using [BrainLes preprocessing](https://github.com/BrainLesion/preprocessing) (recommended) or the deprecated preprocessor of BraTS Toolkit (see below).

> [!NOTE]
> Algorithms are now available for Adult Glioma Segmentation [Pre-Treatment](https://github.com/BrainLesion/BraTS?tab=readme-ov-file#adult-glioma-segmentation-pre-treatment) and [Post-Treatment](https://github.com/BrainLesion/BraTS?tab=readme-ov-file#adult-glioma-segmentation-post-treatment).<br> If you're interested in Adult Glioma Segmentation [GlioMODA](https://github.com/BrainLesion/GlioMODA#gliomoda) may also be of interest.
### Python package
Please have a look at `1_segmentation.py` in this repository for a demo application.

Expand All @@ -88,8 +89,8 @@ Please have a look at `2_fusion.py` in this repository for a demo application.

## Brats Preprocessor (deprecated)
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.

> WARNING: BraTS Preprocessor is deprecated. It still works, but we recommended using [BrainLes preprocessing](https://github.com/BrainLesion/preprocessing) instead, which offers much more flexibility.
> [!WARNING]
> BraTS Preprocessor is deprecated. It still works, but we recommended using [BrainLes preprocessing](https://github.com/BrainLesion/preprocessing) instead, which offers much more flexibility.

### Processing Modi
BraTS Preprocessor offers the following preprocessing modes:
Expand Down Expand Up @@ -120,7 +121,8 @@ Type `brats-batch-preprocess -h` after installing the Python package to see avai

### 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.
> [!WARNING]
> The GUI is not nicely maintained. We encourage you to use the Python package or the CLI instead.


### Command Line Interface (CLI)
Expand Down