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monai_uf_tutorials

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# monai_uf_tutorials
This repository hosts tutorials for using [MONAI](https://monai.io/) on UF HiperGator.

## Download this repository on HiperGator
Log in to HiperGator, change `hju` to your HiperGator username

```
ssh hju@hpg.rc.ufl.edu
```

Go to your home directory

```
cd ~
```

Download this repository into a local directory. The default name of the directory is `monai_uf_tutorials`.

```
git clone https://github.com/hw-ju/monai_uf_tutorials.git
```

Make all files in the directory executable

```
chmod -R +x monai_uf_tutorials/
```

## Contents
1. [use MONAI Core for single-GPU training](./monaicore_singlegpu/)
2. [use MONAI Core for multi-GPU training](./monaicore_multigpu/)
3. [use MONAI Core for Swin UNETR training & evaluation for BRATS21](./monaicore_swinUNETR/)
4. [use MONAI Core for Swin UNETR self-supervised pretraining for BTCV](./pretrain_modify/)
5. [use MONAI Core for Swin UNETR training & evaluation for BTCV](./btcv_modify/)
6. [use MONAI Core for dynunet(nnUnet) training](./monaicore_dynunet/)
7. [use Datasets accelerated by caching in MONAI Core](./caching/)
8. [performance profiling of MONAI Core training by NVIDIA Nsight Systems](./profile/)
9. [Use Clara Parabricks on HiperGator](./clara_parabricks/)
10. [Run GPU-Accelerated Single-Cell Genomics Analysis with RAPIDS on HiperGator](./rapids-single-cell/)

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