Merge branch 'main' into dynamic_print

Author: Hendrik-code

.github/workflows/release.yml

@@ -0,0 +1,54 @@
+# Tutorials for the AURORA package
+This folder contains several Jupyter notebooks to showcase different possible use cases of the [AURORA package](https://github.com/BrainLesion/AURORA).
+Please have a look at the Jupyter notebooks.
+
+
+## Citation
+Please support our development by citing the following manuscripts:
+
+[Identifying core MRI sequences for reliable automatic brain metastasis segmentation](https://www.sciencedirect.com/science/article/pii/S016781402389795X)
+
+```
+@article{buchner2023identifying,
+  title={Identifying core MRI sequences for reliable automatic brain metastasis segmentation},
+  author={Buchner, Josef A and Peeken, Jan C and Etzel, Lucas and Ezhov, Ivan and Mayinger, Michael and Christ, Sebastian M and Brunner, Thomas B and Wittig, Andrea and Menze, Bjoern H and Zimmer, Claus and others},
+  journal={Radiotherapy and Oncology},
+  volume={188},
+  pages={109901},
+  year={2023},
+  publisher={Elsevier}
+}
+```
+
+also consider citing the original AURORA manuscript, especially when using the `vanilla` model:
+
+[Development and external validation of an MRI-based neural network for brain metastasis segmentation in the AURORA multicenter study](https://www.sciencedirect.com/science/article/pii/S0167814022045625)
+
+```
+@article{buchner2022development,
+  title={Development and external validation of an MRI-based neural network for brain metastasis segmentation in the AURORA multicenter study},
+  author={Buchner, Josef A and Kofler, Florian and Etzel, Lucas and Mayinger, Michael and Christ, Sebastian M and Brunner, Thomas B and Wittig, Andrea and Menze, Bj{\"o}rn and Zimmer, Claus and Meyer, Bernhard and others},
+  journal={Radiotherapy and Oncology},
+  year={2022},
+  publisher={Elsevier}
+}
+```
+
+
+## Licensing
+
+This project is licensed under the terms of the [GNU Affero General Public License v3.0](https://www.gnu.org/licenses/agpl-3.0.de.html).
+
+Contact us regarding licensing.
+
+## Contact / Feedback / Questions
+
+If possible please open a GitHub issue [here](https://github.com/neuronflow/AURORA/issues).
+
+For inquiries not suitable for GitHub issues:
+
+Florian Kofler
+florian.kofler [at] tum.de
+
+Josef Buchner
+j.buchner [at] tum.de

AURORA/README.md

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+import os
+import matplotlib.pyplot as plt
+import nibabel as nib
+
+DATA_FOLDER = "data"
+
+
+def visualize_data(data_folder: str = DATA_FOLDER, slice_index: int = 75):
+    """Visualize the MRI modalities for a given slice index
+
+    Args:
+        data_folder (str, optional): Path to the folder containing the t1, t1c, t2 & flair file. Defaults to DATA_FOLDER.
+        slice_index (int, optional): Slice to be visualized (first index in data of shape (155, 240, 240)). Defaults to 75.
+    """
+    _, axes = plt.subplots(1, 4, figsize=(12, 10))
+
+    modalities = ["t1", "t1c", "t2", "flair"]
+    for i, mod in enumerate(modalities):
+        modality_file = os.path.join(data_folder, f"{mod}.nii.gz")
+        modality_np = nib.load(modality_file).get_fdata().transpose(2, 1, 0)
+        axes[i].set_title(mod)
+        axes[i].imshow(modality_np[slice_index, :, :], cmap="gray")
+        axes[i].axis("off")
+
+
+def visualize_segmentation(modality_file: str, segmentation_file: str):
+    """Visualize the MRI modality and the segmentation
+
+    Args:
+        modality_file (str): Path to the desired modality file
+        segmentation_file (str): Path to the segmentation file
+    """
+    modality_np = nib.load(modality_file).get_fdata().transpose(2, 1, 0)
+    seg_np = nib.load(segmentation_file).get_fdata().transpose(2, 1, 0)
+    _, ax = plt.subplots(1, 2, figsize=(8, 4))
+
+    slice_index = modality_np.shape[0] // 2  # You can choose any slice here
+    ax[0].imshow(modality_np[slice_index, :, :], cmap="gray")
+    ax[1].imshow(modality_np[slice_index, :, :], cmap="gray")
+    ax[1].imshow(seg_np[slice_index, :, :], cmap="plasma", alpha=0.3)
+    for ax in ax:
+        ax.axis("off")
+    plt.tight_layout()

AURORA/data/flair.nii.gz

@@ -1 +1,4 @@
-# tutorials
+# Tutorials
+<!-- TODO should such tutorial readmes also get badges? -->
+
+This repository provides tutorials showcasing the functionality and usage of our BrainLes packages.