MONAI example updates (NVIDIA#1506)

* update instructions & paths * remove virtualenv folders * fix links
siomvas · Mar 14, 2023 · 67c8a58 · 67c8a58
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diff --git a/integration/monai/README.md b/integration/monai/README.md
@@ -29,6 +29,9 @@ For an example of using [NVIDIA FLARE](https://nvflare.readthedocs.io/en/main/in
 
 ## Requirements
 
+We recommend following the instructions for setting up a [virtual environment](../../examples/README.md#set-up-a-virtual-environment),
+and using it in [JupyterLab](../../examples/README.md#notebooks) for running the notebooks the MONAI integration examples.
+
 Install MONAI-NVFlare integration from [PyPI](https://pypi.org/):
 ```
 pip install monai_nvflare

diff --git a/integration/monai/examples/spleen_ct_segmentation_real-world/README.md b/integration/monai/examples/spleen_ct_segmentation_real-world/README.md
@@ -20,26 +20,10 @@ And go to the folder containing this tutorial
 ## Setup environment
 
 To execute the below commands, please open a terminal
-and go to the folder containing this tutorial:
+and go to the folder containing this tutorial.
 
-#### (Optional) Set up a virtual environment
-```
-python3 -m pip install --user --upgrade pip
-python3 -m pip install --user virtualenv
-```
-(If needed) make all shell scripts executable using
-```
-find . -name ".sh" -exec chmod +x {} \;
-```
-initialize virtual environment.
-```
-source ./virtualenv/set_env.sh
-```
-install required packages for training
-```
-pip install --upgrade pip
-pip install -r virtualenv/requirements.txt
-```
+We recommend following the instructions for setting up a [virtual environment](../../../../examples/README.md#set-up-a-virtual-environment),
+and using it in [JupyterLab](../../../../examples/README.md#notebooks) for running the notebooks the MONAI integration examples.
 
 ### 1. Download the Spleen Bundle
 

diff --git a/...on_real-world/virtualenv/requirements.txt → ..._segmentation_real-world/requirements.txt b/...on_real-world/virtualenv/requirements.txt → ..._segmentation_real-world/requirements.txt
diff --git a/integration/monai/examples/spleen_ct_segmentation_real-world/virtualenv/set_env.sh b/integration/monai/examples/spleen_ct_segmentation_real-world/virtualenv/set_env.sh
diff --git a/integration/monai/examples/spleen_ct_segmentation_sim/README.md b/integration/monai/examples/spleen_ct_segmentation_sim/README.md
@@ -7,26 +7,10 @@ For an example with real-world deployment settings, see [here](../spleen_ct_segm
 ## Setup environment
 
 To execute the below commands, please open a terminal
-and go to the folder containing this tutorial:
+and go to the folder containing this tutorial.
 
-#### (Optional) Set up a virtual environment
-```
-python3 -m pip install --user --upgrade pip
-python3 -m pip install --user virtualenv
-```
-(If needed) make all shell scripts executable using
-```
-find . -name ".sh" -exec chmod +x {} \;
-```
-initialize virtual environment.
-```
-source ./virtualenv/set_env.sh
-```
-install required packages for training
-```
-pip install --upgrade pip
-pip install -r virtualenv/requirements.txt
-```
+We recommend following the instructions for setting up a [virtual environment](../../../../examples/README.md#set-up-a-virtual-environment),
+and using it in [JupyterLab](../../../../examples/README.md#notebooks) for running the notebooks the MONAI integration examples.
 
 ### 1. Download the Spleen Bundle
 

diff --git a/...mentation_sim/virtualenv/requirements.txt → ...leen_ct_segmentation_sim/requirements.txt b/...mentation_sim/virtualenv/requirements.txt → ...leen_ct_segmentation_sim/requirements.txt
diff --git a/integration/monai/examples/spleen_ct_segmentation_sim/stats_demo/stats_demo.ipynb b/integration/monai/examples/spleen_ct_segmentation_sim/stats_demo/stats_demo.ipynb
diff --git a/integration/monai/examples/spleen_ct_segmentation_sim/virtualenv/set_env.sh b/integration/monai/examples/spleen_ct_segmentation_sim/virtualenv/set_env.sh