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app.py
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@@ -18,9 +18,27 @@ BUNDLE_PATH = os.path.join(torch.hub.get_dir(), 'bundle', BUNDLE_NAME)
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title = "Segment Brain Tumors with MONAI!"
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description = """
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A pre-trained model for volumetric (3D) segmentation of brain tumor subregions from multimodal MRIs based on BraTS 2018 data.
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"""
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#examples = 'examples/'
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title = "Segment Brain Tumors with MONAI!"
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description = """
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## Brain Tumor Segmentation 🧠
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A pre-trained model for volumetric (3D) segmentation of brain tumor subregions from multimodal MRIs based on BraTS 2018 data.
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The model is trained to segment 3 nested subregions of primary brain tumors (gliomas): the "enhancing tumor" (ET), the "tumor core" (TC), the "whole tumor" (WT) based on 4 aligned input MRI scans (T1c, T1, T2, FLAIR).
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- The ET is described by areas that show hyper intensity in T1c when compared to T1, but also when compared to "healthy" white matter in T1c.
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- The TC describes the bulk of the tumor, which is what is typically resected. The TC entails the ET, as well as the necrotic (fluid-filled) and the non-enhancing (solid) parts of the tumor.
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- The WT describes the complete extent of the disease, as it entails the TC and the peritumoral edema (ED), which is typically depicted by hyper-intense signal in FLAIR.
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## To run 🚀
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Upload a image file in the format: 4 channel MRI (4 aligned MRIs T1c, T1, T2, FLAIR at 1x1x1 mm)
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## Disclaimer ⚠️
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This is an example, not to be used for diagnostic purposes.
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## References 👀
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[1] Myronenko, Andriy. "3D MRI brain tumor segmentation using autoencoder regularization." International MICCAI Brainlesion Workshop. Springer, Cham, 2018. https://arxiv.org/abs/1810.11654.
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[2] Menze BH, et al. "The Multimodal Brain Tumor Image Segmentation Benchmark (BRATS)", IEEE Transactions on Medical Imaging 34(10), 1993-2024 (2015) DOI: 10.1109/TMI.2014.2377694
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[3] Bakas S, et al. "Advancing The Cancer Genome Atlas glioma MRI collections with expert segmentation labels and radiomic features", Nature Scientific Data, 4:170117 (2017) DOI:10.1038/sdata.2017.117
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"""
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#examples = 'examples/'
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