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README.md

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# Raidionics 3D Slicer plugin
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Plugin developed to perform automatic segmentation and clinical reporting using custom models.
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Plugin developed to perform automatic segmentation and clinical reporting (RADS) using custom models.
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Please cite the following article if you use the plugin:
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>`@misc{,`
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`primaryClass=`
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`}`
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## 1. Method background
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## 1. Methodological background
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More information about the different models provided and architectures used can be accessed from those previous publications:
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More information about the different models provided and architectures used can be accessed from the below-listed publications.
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## 1.1 Neuro
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* AGUNet neural network architecture => [Meningioma Segmentation in T1-Weighted MRI Leveraging Global Context and Attention Mechanisms](https://www.frontiersin.org/articles/10.3389/fradi.2021.711514/full)
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* Standardized reporting and Data System (RADS) => [Glioblastoma Surgery Imaging—Reporting and Data System: Standardized Reporting of Tumor Volume, Location, and Resectability Based on Automated Segmentations ](https://www.mdpi.com/2072-6694/13/12/2854)
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* Segmentation performance => [Glioblastoma Surgery Imaging–Reporting and Data System: Validation and Performance of the Automated Segmentation Task ](https://www.mdpi.com/2072-6694/13/18/4674)
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## 1.2 Mediastinum
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* Mediastinum organs segmentation => [Semantic segmentation and detection of mediastinal lymph nodes and anatomical structures in CT data for lung cancer staging](https://link.springer.com/article/10.1007/s11548-019-01948-8)
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* Lymph nodes segmentation => [Mediastinal lymph nodes segmentation using 3D convolutional neural network ensembles and anatomical priors guiding](https://www.tandfonline.com/doi/pdf/10.1080/21681163.2022.2043778)
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>`@article{bouget2021mediastinal,`
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`title={Mediastinal lymph nodes segmentation using 3D convolutional neural network ensembles and anatomical priors guiding},`
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`author={Bouget, David and Pedersen, Andr{\'e} and Vanel, Johanna and Leira, Haakon O and Lang{\o}, Thomas},`
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`journal={arXiv preprint arXiv:2102.06515},`
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`year={2021}`
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`}`
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## 2. Plugin installation
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2.1 Download 3DSlicer for your running Operating System at https://download.slicer.org/ (running on stable 4.11).
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2.2 Download the Raidionics plugin code:
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* release candidate with name .... on the right-hand panel (Github repo).
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* (Or git clone --single-branch --branch master https://github.com/dbouget/Slicer-Raidionics.git /path/to/folder/).
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Or
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* git clone --single-branch --branch master https://github.com/dbouget/Slicer-Raidionics.git /path/to/folder/.
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2.3 Download and install Docker (see Section 3).
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2.3 Load the plugin into 3DSlicer:
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∘ All Modules > Extension Wizard.

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