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added note Pre/Post Glioma segmentation with links + formated links #66

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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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18 changes: 12 additions & 6 deletions README.md
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Expand Up @@ -67,14 +67,19 @@ Please also cite the following original authors of the algorithms who make this


## Usage
BrainLes features [Jupyter notebook tutorials](https://github.com/BrainLesion/tutorials/tree/main/BraTS-Toolkit) for glioma segmentation with BraTS Toolkit.
BrainLes features (Jupyter notebook tutorials: https://github.com/BrainLesion/tutorials/tree/main/BraTS-Toolkit) for glioma segmentation with BraTS Toolkit.
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Copilot AI Sep 22, 2025

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The parentheses around the link description create awkward formatting. Consider using proper markdown link syntax: [Jupyter notebook tutorials](https://github.com/BrainLesion/tutorials/tree/main/BraTS-Toolkit) for better readability and consistency with markdown conventions.

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BrainLes features (Jupyter notebook tutorials: https://github.com/BrainLesion/tutorials/tree/main/BraTS-Toolkit) for glioma segmentation with BraTS Toolkit.
BrainLes features [Jupyter notebook tutorials](https://github.com/BrainLesion/tutorials/tree/main/BraTS-Toolkit) for glioma segmentation with BraTS Toolkit.

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Further, have a look at the Python examples in this repository for preprocessing (`0_preprocessing_single.py`), segmentation (`1_segmentation.py`) and fusion (`2_fusion.py`).

## Brats Segmentor
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).

You can preprocess your files using BrainLes preprocessing: https://github.com/BrainLesion/preprocessing (recommended) or the deprecated preprocessor of BraTS Toolkit (see below).
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Copilot AI Sep 22, 2025

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The link formatting is inconsistent with markdown conventions. Consider using proper markdown link syntax: [BrainLes preprocessing](https://github.com/BrainLesion/preprocessing) for better readability and consistency.

Suggested change
You can preprocess your files using BrainLes preprocessing: https://github.com/BrainLesion/preprocessing (recommended) or the deprecated preprocessor of BraTS Toolkit (see below).
You can preprocess your files using [BrainLes preprocessing](https://github.com/BrainLesion/preprocessing) (recommended) or the deprecated preprocessor of BraTS Toolkit (see below).

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> [!NOTE]
> Algorithms are now available for Adult Glioma Segmentation <br>
Pre-Treatment: https://github.com/BrainLesion/BraTS?tab=readme-ov-file#adult-glioma-segmentation-pre-treatment <br>
and Post-Treatment: https://github.com/BrainLesion/BraTS?tab=readme-ov-file#adult-glioma-segmentation-post-treatment). <br>
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There's an extra closing parenthesis on line 80 after the URL that should be removed.

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and Post-Treatment: https://github.com/BrainLesion/BraTS?tab=readme-ov-file#adult-glioma-segmentation-post-treatment). <br>
and Post-Treatment: https://github.com/BrainLesion/BraTS?tab=readme-ov-file#adult-glioma-segmentation-post-treatment. <br>

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<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 +93,8 @@ 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.
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The link formatting is inconsistent with markdown conventions. Consider using proper markdown link syntax: [BrainLes preprocessing](https://github.com/BrainLesion/preprocessing) for better readability and consistency.

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

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### Processing Modi
BraTS Preprocessor offers the following preprocessing modes:
Expand Down Expand Up @@ -120,7 +125,8 @@ 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