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Aug 28, 2020
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Update URLs #11

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2 changes: 1 addition & 1 deletion 3d_image_transforms.ipynb
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"\n",
"This notebook introduces you MONAI's transformation module for 3D images.\n",
"\n",
"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Project-MONAI/MONAI/blob/master/examples/notebooks/3d_image_transforms.ipynb)"
"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Project-MONAI/Tutorials/blob/master/3d_image_transforms.ipynb)"
]
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{
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2 changes: 1 addition & 1 deletion automatic_mixed_precision.ipynb
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"\n",
"The Spleen dataset can be downloaded from http://medicaldecathlon.com/.\n",
"\n",
"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Project-MONAI/MONAI/blob/master/examples/notebooks/automatic_mixed_precision.ipynb)"
"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Project-MONAI/Tutorials/blob/master/automatic_mixed_precision.ipynb)"
]
},
{
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2 changes: 1 addition & 1 deletion brats_segmentation_3d.ipynb
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"1. the enhancing tumor structures (light blue) visible in T1Gd, surrounding the cystic/necrotic components of the core (green) (Fig. C).\n",
"1. The segmentations are combined to generate the final labels of the tumor sub-regions (Fig.D): edema (yellow), non-enhancing solid core (red), necrotic/cystic core (green), enhancing core (blue).\n",
"\n",
"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Project-MONAI/MONAI/blob/master/examples/notebooks/brats_segmentation_3d.ipynb)"
"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Project-MONAI/Tutorials/blob/master/brats_segmentation_3d.ipynb)"
]
},
{
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2 changes: 1 addition & 1 deletion cache_dataset_speed.ipynb
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"This tutorial shows how to accelerate PyTorch medical DL program based on MONAI CacheDataset. \n",
"It's modified from the Spleen 3D segmentation tutorial notebook.\n",
"\n",
"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Project-MONAI/MONAI/blob/master/examples/notebooks/cache_dataset_speed.ipynb)"
"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Project-MONAI/Tutorials/blob/master/cache_dataset_speed.ipynb)"
]
},
{
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2 changes: 1 addition & 1 deletion integrate_3rd_party_transforms.ipynb
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"This tutorial shows how to integrate 3rd party transforms into a MONAI program. \n",
"Mainly showing transforms from `BatchGenerator`, `TorchIO`, `Rising` and `ITK`.\n",
"\n",
"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Project-MONAI/MONAI/blob/master/examples/notebooks/integrate_3rd_party_transforms.ipynb)"
"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Project-MONAI/Tutorials/blob/master/integrate_3rd_party_transforms.ipynb)"
]
},
{
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4 changes: 2 additions & 2 deletions mednist_GAN_tutorial.ipynb
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"* Defining the networks\n",
"* Training and evaluation\n",
"\n",
"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Project-MONAI/MONAI/blob/master/examples/notebooks/mednist_GAN_tutorial.ipynb)"
"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Project-MONAI/Tutorials/blob/master/mednist_GAN_tutorial.ipynb)"
]
},
{
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"\n",
"\n",
"If you use the MedNIST dataset, please acknowledge the source, e.g. \n",
"https://github.com/Project-MONAI/MONAI/blob/master/examples/notebooks/mednist_tutorial.ipynb."
"https://github.com/Project-MONAI/Tutorials/blob/master/mednist_tutorial.ipynb."
]
},
{
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6 changes: 3 additions & 3 deletions mednist_GAN_workflow.ipynb
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"The MONAI framework can be used to easily design, train, and evaluate generative adversarial networks.\n",
"This notebook exemplifies using MONAI components to design and train a simple GAN model to reconstruct images of Hand CT scans.\n",
"\n",
"Read the [MONAI Mednist GAN Tutorial](https://github.com/Project-MONAI/MONAI/blob/master/examples/notebooks/mednist_GAN_tutorial.ipynb) for details about the network architecture and loss functions.\n",
"Read the [MONAI Mednist GAN Tutorial](https://github.com/Project-MONAI/Tutorials/blob/master/mednist_GAN_tutorial.ipynb) for details about the network architecture and loss functions.\n",
"\n",
"**Table of Contents**\n",
"\n",
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"3. Run Training\n",
"4. Evaluate Results\n",
"\n",
"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Project-MONAI/MONAI/blob/master/examples/notebooks/mednist_GAN_workflow.ipynb)"
"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Project-MONAI/Tutorials/blob/master/mednist_GAN_workflow.ipynb)"
]
},
{
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"\n",
"\n",
"If you use the MedNIST dataset, please acknowledge the source, e.g. \n",
"https://github.com/Project-MONAI/MONAI/blob/master/examples/notebooks/mednist_tutorial.ipynb."
"https://github.com/Project-MONAI/Tutorials/blob/master/mednist_tutorial.ipynb."
]
},
{
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2 changes: 1 addition & 1 deletion mednist_tutorial.ipynb
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"* Train the model with a PyTorch program\n",
"* Evaluate on test dataset\n",
"\n",
"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Project-MONAI/MONAI/blob/master/examples/notebooks/mednist_tutorial.ipynb)"
"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Project-MONAI/Tutorials/blob/master/mednist_tutorial.ipynb)"
]
},
{
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2 changes: 1 addition & 1 deletion models_ensemble.ipynb
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"MONAI provides `EnsembleEvaluator` and `MeanEnsemble`, `VoteEnsemble` post transforms. \n",
"This tutorial shows how to leverage ensemble modules in MONAI to set up ensemble program.\n",
"\n",
"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Project-MONAI/MONAI/blob/master/examples/notebooks/models_ensemble.ipynb)"
"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Project-MONAI/Tutorials/blob/master/models_ensemble.ipynb)"
]
},
{
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2 changes: 1 addition & 1 deletion multi_gpu_test.ipynb
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"source": [
"# Multi GPU Test\n",
"\n",
"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Project-MONAI/MONAI/blob/master/examples/notebooks/multi_gpu_test.ipynb)"
"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Project-MONAI/Tutorials/blob/master/multi_gpu_test.ipynb)"
]
},
{
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2 changes: 1 addition & 1 deletion nifti_read_example.ipynb
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"\n",
"The purpose of this notebook is to illustrate reading Nifti files and iterating over patches of the volumes loaded from them.\n",
"\n",
"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Project-MONAI/MONAI/blob/master/examples/notebooks/nifti_read_example.ipynb)"
"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Project-MONAI/Tutorials/blob/master/nifti_read_example.ipynb)"
]
},
{
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2 changes: 1 addition & 1 deletion persistent_dataset_speed.ipynb
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"\n",
"It's modified from the Spleen 3D segmentation tutorial notebook.\n",
"\n",
"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Project-MONAI/MONAI/blob/master/examples/notebooks/persistent_dataset_speed.ipynb)"
"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Project-MONAI/Tutorials/blob/master/persistent_dataset_speed.ipynb)"
]
},
{
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2 changes: 1 addition & 1 deletion post_transforms.ipynb
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"\n",
"This tutorial shows several of above post transforms based on the model output of spleen segmentation.\n",
"\n",
"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Project-MONAI/MONAI/blob/master/examples/notebooks/post_transforms.ipynb)"
"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Project-MONAI/Tutorials/blob/master/post_transforms.ipynb)"
]
},
{
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2 changes: 1 addition & 1 deletion public_datasets.ipynb
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"* Create training experiment with DecathlonDataset and workflow\n",
"* Share other public data and add Dataset in MONAI\n",
"\n",
"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Project-MONAI/MONAI/blob/master/examples/notebooks/public_datasets.ipynb)"
"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Project-MONAI/Tutorials/blob/master/public_datasets.ipynb)"
]
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{
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2 changes: 1 addition & 1 deletion spleen_segmentation_3d.ipynb
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"Source: Memorial Sloan Kettering Cancer Center \n",
"Challenge: Large ranging foreground size\n",
"\n",
"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Project-MONAI/MONAI/blob/master/examples/notebooks/spleen_segmentation_3d.ipynb)"
"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Project-MONAI/Tutorials/blob/master/spleen_segmentation_3d.ipynb)"
]
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{
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2 changes: 1 addition & 1 deletion spleen_segmentation_3d_lightning.ipynb
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"Source: Memorial Sloan Kettering Cancer Center \n",
"Challenge: Large ranging foreground size\n",
"\n",
"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Project-MONAI/MONAI/blob/master/examples/notebooks/spleen_segmentation_3d_lightning.ipynb)"
"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Project-MONAI/Tutorials/blob/master/spleen_segmentation_3d_lightning.ipynb)"
]
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{
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2 changes: 1 addition & 1 deletion transform_speed.ipynb
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"\n",
"The purpose of this notebook is to illustrate reading Nifti files and test speed of different methods.\n",
"\n",
"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Project-MONAI/MONAI/blob/master/examples/notebooks/transform_speed.ipynb)"
"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Project-MONAI/Tutorials/blob/master/transform_speed.ipynb)"
]
},
{
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2 changes: 1 addition & 1 deletion transforms_demo_2d.ipynb
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" \n",
"Find out more in MONAI's wiki page: https://github.com/Project-MONAI/MONAI/wiki\n",
"\n",
"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Project-MONAI/MONAI/blob/master/examples/notebooks/transforms_demo_2d.ipynb)"
"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Project-MONAI/Tutorials/blob/master/transforms_demo_2d.ipynb)"
]
},
{
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4 changes: 2 additions & 2 deletions unet_segmentation_3d_catalyst.ipynb
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"* Sliding window inference method.\n",
"* Deterministic training for reproducibility.\n",
"\n",
"This tutorial is based on [unet_training_dict.py](https://github.com/Project-MONAI/MONAI/blob/master/examples/segmentation_3d/unet_training_dict.py) and [spleen_segmentation_3d.ipynb](https://github.com/Project-MONAI/MONAI/blob/master/examples/notebooks/spleen_segmentation_3d.ipynb).\n",
"This tutorial is based on [unet_training_dict.py](https://github.com/Project-MONAI/MONAI/blob/master/examples/segmentation_3d/unet_training_dict.py) and [spleen_segmentation_3d.ipynb](https://github.com/Project-MONAI/Tutorials/blob/master/spleen_segmentation_3d.ipynb).\n",
"\n",
"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Project-MONAI/MONAI/blob/master/examples/notebooks/unet_segmentation_3d_catalyst.ipynb)"
"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Project-MONAI/Tutorials/blob/master/unet_segmentation_3d_catalyst.ipynb)"
]
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{
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2 changes: 1 addition & 1 deletion unet_segmentation_3d_ignite.ipynb
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"source": [
"# 3D Segmentation with UNet\n",
"\n",
"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Project-MONAI/MONAI/blob/master/examples/notebooks/unet_segmentation_3d_ignite.ipynb)"
"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Project-MONAI/Tutorials/blob/master/unet_segmentation_3d_ignite.ipynb)"
]
},
{
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