v1.0

2023-01-30 23:50:20 +00:00
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-# RETFound_MAE
-RETFound - A foundation model for retinal image
+## RETFound - A foundation model for retinal image
+
+
+This is official repo for RETFound, which heavily bases on [MAE](https://github.com/facebookresearch/mae):
+
+
+### Key features
+
+- RETFound was trained on 1.6 million retinal images
+- RETFound has been validated in multiple disease detection tasks
+- RETFound can be efficiently adapted to customised task
+
+
+### Install enviroment
+
+Create enviroment with conda:
+
+```
+conda create -n retfound python=3.6.15 -y
+```
+
+Install Pytorch 1.81 (cuda 11.1)
+```
+pip install torch==1.8.1+cu111 torchvision==0.9.1+cu111 torchaudio==0.8.1 -f https://download.pytorch.org/whl/torch_stable.html
+```
+
+Install others
+```
+pip install -r requirement.txt
+```
+
+
+### Fine-tuning with RETFound weights
+
+- RETFound pre-trained weights
+<table><tbody>
+<!-- START TABLE -->
+<!-- TABLE HEADER -->
+<th valign="bottom"></th>
+<th valign="bottom">ViT-Large</th>
+<!-- TABLE BODY -->
+<tr><td align="left">Colour fundus image</td>
+<td align="center"><a href="https://dl.fbaipublicfiles.com/mae/pretrain/mae_pretrain_vit_large.pth">download</a></td>
+</tr>
+<!-- TABLE BODY -->
+<tr><td align="left">OCT</td>
+<td align="center"><a href="https://dl.fbaipublicfiles.com/mae/pretrain/mae_pretrain_vit_large.pth">download</a></td>
+</tr>
+</tbody></table>
+
+- Organise data (use IDRiD as example)
+
+<p align="left">
+  <img src="https://user-images.githubusercontent.com/11435359/146857310-f258c86c-fde6-48e8-9cee-badd2b21bd2c.png" width="480">
+</p>
+
+
+- Start fine-tuning (use IDRiD as example). A fine-tuned checkpoint will be saved during training. Evaluation will be run after training.
+
+
+```
+python -m torch.distributed.launch --nproc_per_node=1 --master_port=48798 main_finetune.py  
+    --batch_size 16 \
+    --world_size 1 \
+    --model vit_large_patch16 \
+    --epochs 50 \
+    --blr 5e-3 --layer_decay 0.65 \
+    --weight_decay 0.05 --drop_path 0.2 \
+    --nb_classes 5 \
+    --data_path ./IDRiD_data/ \
+    --task ./finetune_IDRiD/ \
+    --finetune ./RETFound_cfp_weights.pth
+
+```
+
+
+- For evaluation only
+
+
+```
+python -m torch.distributed.launch --nproc_per_node=1 --master_port=48798 main_finetune.py 
+    --eval --batch_size 16 \
+    --world_size 1 \
+    --model vit_large_patch16 \
+    --epochs 40 \
+    --blr 5e-3 --layer_decay 0.65 \
+    --weight_decay 0.05 --drop_path 0.2 \
+    --nb_classes 5 \
+    --data_path ./IDRiD_data/ \
+    --task ./internal_IDRiD/ \
+    --resume ./finetune_IDRiD/checkpoint-best.pth
+
+```
+
+