From 445ff8a109860c41bf528462f019870f10d27f98 Mon Sep 17 00:00:00 2001 From: Eva Oswald <106267274+evamariie@users.noreply.github.com> Date: Thu, 29 May 2025 16:26:40 +0200 Subject: [PATCH 1/7] added note Pre/Post Glioma segmentation with links + formated with blockquote - added Note with links regarding adult glioma segmentation Algothms Pre + Post Treatment - formated two Warning notes - using blockquote --- README.md | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 2c2431d..ebb3e08 100644 --- a/README.md +++ b/README.md @@ -74,6 +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) ### Python package Please have a look at `1_segmentation.py` in this repository for a demo application. @@ -88,8 +90,8 @@ 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: @@ -120,7 +122,8 @@ 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) From 747059fb9b0d08edd8e53696b1e0ecf8ecd5f443 Mon Sep 17 00:00:00 2001 From: Eva Oswald <106267274+evamariie@users.noreply.github.com> Date: Fri, 30 May 2025 21:54:42 +0200 Subject: [PATCH 2/7] added GlioMODA link into the note --- README.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/README.md b/README.md index ebb3e08..2af9b9f 100644 --- a/README.md +++ b/README.md @@ -75,8 +75,7 @@ BraTS Segmentor enables orchestration of BraTS brain tumor segmentation algorith 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) - +> 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).
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. From df898db8c4676d7758fa8a4af10f88b3a8b31d99 Mon Sep 17 00:00:00 2001 From: Eva Oswald <106267274+evamariie@users.noreply.github.com> Date: Mon, 22 Sep 2025 16:20:01 +0200 Subject: [PATCH 3/7] markdown-native line breakts istead of HTML tag - for more consistent format of the document --- README.md | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 2af9b9f..486eed1 100644 --- a/README.md +++ b/README.md @@ -67,15 +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. 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). > [!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).
If you're interested in Adult Glioma Segmentation [GlioMODA](https://github.com/BrainLesion/GlioMODA#gliomoda) may also be of interest. +> 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).
+
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. @@ -90,7 +94,7 @@ 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. +> 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: From 610e933ebc198012040bf347b81c98ab59ec5f20 Mon Sep 17 00:00:00 2001 From: Eva Oswald <106267274+evamariie@users.noreply.github.com> Date: Mon, 22 Sep 2025 16:29:59 +0200 Subject: [PATCH 4/7] small formating.md Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 486eed1..01398ef 100644 --- a/README.md +++ b/README.md @@ -78,7 +78,7 @@ You can preprocess your files using BrainLes preprocessing: https://github.com/B > 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).
-
If you're interested in Adult Glioma Segmentation (GlioMODA): https://github.com/BrainLesion/GlioMODA#gliomoda may also be of interest. +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. From f4ef503663e83f898700e9b60893ebff4a710d7e Mon Sep 17 00:00:00 2001 From: Eva Oswald <106267274+evamariie@users.noreply.github.com> Date: Mon, 22 Sep 2025 16:34:19 +0200 Subject: [PATCH 5/7] small formating2.md Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --- README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 01398ef..36597fd 100644 --- a/README.md +++ b/README.md @@ -75,10 +75,10 @@ BraTS Segmentor enables orchestration of BraTS brain tumor segmentation algorith 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).
-If you're interested in Adult Glioma Segmentation (GlioMODA): https://github.com/BrainLesion/GlioMODA#gliomoda may also be of interest. +> Algorithms are now available for Adult Glioma Segmentation: +> - [Pre-Treatment](https://github.com/BrainLesion/BraTS?tab=readme-ov-file#adult-glioma-segmentation-pre-treatment) +> - [Post-Treatment](https://github.com/BrainLesion/BraTS?tab=readme-ov-file#adult-glioma-segmentation-post-treatment) +> If you're interested in Adult Glioma Segmentation (GlioMODA): [https://github.com/BrainLesion/GlioMODA#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. From b95bf25d73de7bc37cbbc1b60321dba39afd0f72 Mon Sep 17 00:00:00 2001 From: Eva Oswald <106267274+evamariie@users.noreply.github.com> Date: Mon, 22 Sep 2025 16:48:40 +0200 Subject: [PATCH 6/7] Improve formatting in README.md Improve formatting in README.md --- README.md | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index 36597fd..454da5d 100644 --- a/README.md +++ b/README.md @@ -67,18 +67,16 @@ 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. 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). > [!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) -> - [Post-Treatment](https://github.com/BrainLesion/BraTS?tab=readme-ov-file#adult-glioma-segmentation-post-treatment) -> If you're interested in Adult Glioma Segmentation (GlioMODA): [https://github.com/BrainLesion/GlioMODA#gliomoda](https://github.com/BrainLesion/GlioMODA#gliomoda) may also be of interest. +> 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). +> 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. @@ -94,7 +92,7 @@ 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. +> 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: From 6a939fc64f2b4c3e44b81ecb8b4d336865bdf4f5 Mon Sep 17 00:00:00 2001 From: Eva Oswald <106267274+evamariie@users.noreply.github.com> Date: Mon, 22 Sep 2025 16:52:33 +0200 Subject: [PATCH 7/7] small gramma fix Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 454da5d..aa4df94 100644 --- a/README.md +++ b/README.md @@ -92,7 +92,7 @@ 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. +> BraTS Preprocessor is deprecated. It still works, but we recommend using [BrainLes preprocessing](https://github.com/BrainLesion/preprocessing) instead, which offers much more flexibility. ### Processing Modi BraTS Preprocessor offers the following preprocessing modes: