Finetune SAM on your customized medical imaging dataset

Authors: Hanxue Gu*, Haoyu Dong*, Jichen Yang, Maciej A. Mazurowski

Notice: 🥰Hi guys, since my github is not linked to my work email thus i might not reply to issues or questions quickly. Feel free to email me if you meet issues when using this repo, and i am glad to help. Here is my email: hanxue.gu@duke.edu.

This is the official code for our paper: How to build the best medical image segmentation algorithm using foundation models: a comprehensive empirical study with Segment Anything Model, where we explore three popular scenarios when fine-tuning foundation models to customized datasets in the medical imaging field: (1) only a single labeled dataset; (2) multiple labeled datasets for different tasks; and (3) multiple labeled and unlabeled datasets; and we design three common experimental setups, as shown in figure 1.

Our work summarizes and evaluates existing fine-tuning strategies with various backbone architectures, model components, and fine-tuning algorithms across 18 combinations, and 17 datasets covering all common radiology modalities.

Based on our extensive experiments, we found that:

1. fine-tuning SAM leads to slightly better performance than previous segmentation methods.
2. fine-tuning strategies that use parameter-efficient learning in both the encoder and decoder are superior to other strategies.
3. network architecture has a small impact on the final performance,
4. further training SAM with self-supervised learning can improve final model performance.

To use our codebase, we provide (a) codes to fine-tune your medical imaging dataset on either automatic/prompt-based setting, (b) pretrained weights we got from Setup 3 using task-agnostic self-supervised learning, which we found as good pretrained weights instead of initial SAM providing better performance for downstream tasks.

Bug fixes:

• May-10-2024, fixed the bug that when we updated the dataset.py at May 6th for multi class support, the mask resize processing was accidently forgotten.
• May-10-2024, fixed the bug that the provided demo for single gpu trianing only support updating decoder but the image encoder's gradients were not calculated.
• June-10-2024, fixed the bug that cfg.py was not updated as the same version of train.sh which didn't include two configs as 'train_img_list' and 'val_img_list'.

Updated functions:

• May-15-2024, add functions to auto save training args and load args for validation; save your time for manual definition.
• May-15-2024, add two jupyter-notebooks showing examples about how to make predictions on 3D volumes/2D pngs without ground truth; and for visualization.
• May-15-2024, provide two additional example demos.
• June-10-2024, add spatial transformation choice in dataset.py

a): fine-tune to one single task-specific dataset

Step 0: setup environment

If using conda enviroment:

conda env create -f environment.yml

If directly using pip

pip install -r requirements.txt

Step 1: dataset preparation.

Please prepare your images and mask pairs in 2D slices first. If your original dataset is in 3D format, please preprocess it and save images/masks as 2D slices.

There is no strict format for your dataset folder; you need first to identify your main dataset folder, for example:

args.img_folder = './datasets/'
args.mask_folder = './datasets/'

Then prepare your image/mask list file train/val/test.csv under args.img_folder/dataset_name/ in the following format: img_slice_path mask_slice_path, such as:

sa_xrayhip/images/image_044.ni_z001.png	sa_xrayhip/masks/image_044.ni_z001.png
sa_xrayhip/images/image_126.ni_z001.png	sa_xrayhip/masks/image_126.ni_z001.png
sa_xrayhip/images/image_034.ni_z001.png	sa_xrayhip/masks/image_034.ni_z001.png
sa_xrayhip/images/image_028.ni_z001.png	sa_xrayhip/masks/image_028.ni_z001.png

Step 2:

Configure your network architectures and other hyperparameters.

(1) Choose image encoder architecture.

args.arch = 'vit_b' # you can pick from  'vit_h','vit_b','vit_t'

#If load original sam's encoder, for example, if 'vit_b':
args.sam_ckpt = "sam_vit_b_01ec64.pth" 
# You can replace it with any other pretrained weights, such as 'medsam_vit_b.pth'

You need to download SAM's checkpoints of vit-h, and vit-b from SAM, and to use MobileSAM; you can download the checkpoints from MobileSAM

To be noticed** If pretrained weights are used as MedSAM, you need to use dataset normalization as [0-1] instead of the original SAM's mean/std normations.

# normalzie_type: 'sam' or 'medsam', if sam, using transforms.Normalize(mean=[0.485, 0.456, 0.406], std=[0.229, 0.224, 0.225]); if medsam, using [0,1] normalize.

args.normalize_type = 'medsam'

(2) Choose fine-tuning Methods.

(i) Vanilla fine-tuning

• If you want to update Encoder and Decoder both, just load the network and put:

args.if_update_encoder = True

• If you only want to update Mask Decoder, just load the network and put:

args.if_update_encoder = False

(2) fine-tuning using Adapter blocks

• If you want to add adapter blocks on the image encoder and mask decoder both:

args.if_mask_decoder_adapter=True

args.if_update_encoder = True
args.if_encoder_adapter=True
# You can pick the image encoder blocks by adding adapters
args.encoder_adapter_depths = range(0,12)

• If you want to add adapter blocks to the decoder only:

args.if_mask_decoder_adapter=True

(3) fine-tuning using LoRA blocks

• If you want to add LoRA blocks on the image encoder and mask decoder both:

# define which blocks you would like to add LoRAs, if [] is empty, it will be added at **each** block.
args.if_update_encoder = True
args.if_encoder_lora_layer = True
args.encoder_lora_layer = []
args.if_decoder_lora_layer = True  

• If you only want to add LoRA blocks on the mask decoder:

args.if_decoder_lora_layer = True  

Other configurations

1. If you want to enable warmup:

# If you want to use warmup
args.if_warmup = True
args.warmup_period = 200

2. If you want to use DDP training for multiple GPUs, use

python DDP_train_xxx.py

Otherwise, use:

python SingleGPU_train_xxx.py

if the network is large and you cannot fit into one single GPU, you can use our DDP_train_xxx.py as well as split the image encoder into 2 GPUs:

args.if_split_encoder_gpus = True
args.gpu_fractions = [0.5,0.5] # the fraction of image encoder on each GPU

Multi-cls segmentation VS. binary segmentation

1. if you want to do binary segmentation:

# set the output channels as 2 (background, object)
args.num_cls = 2

If your target objects actually have multiple labels but you want to combine them as binary:

# put the dataset's parameter for 'target' as 'combine_all', for example:
Public_dataset(args,args.img_folder, args.mask_folder, train_img_list,phase='train',targets=['combine_all'],normalize_type='sam',if_prompt=False)

2. if you want to do multi-cls segmentation:

# set the output channels as num_of_target_objects + 1 (background, object1, object2,...)
args.num_cls = n+1

# put the dataset's parameter for 'target' as 'multi_all', for example:
Public_dataset(args,args.img_folder, args.mask_folder, train_img_list,phase='train',targets=['multi_all'],normalize_type='sam',if_prompt=False)

3. if you actually have multiple different targets but you want to select a subset, such as one target from your mask for trianing:

Todo

Example bash file for running the training

Here is one example (train_singlegpu_demo.sh) of running the training on a demo dataset using vit-b with Adapter and updating Mask Decoder only.

#!/bin/bash

# Set CUDA device
export CUDA_VISIBLE_DEVICES="5"

# Define variables
arch="vit_b"  # Change this value as needed
finetune_type="adapter"
dataset_name="MRI-Prostate"  # Assuming you set this if it's dynamic
targets='combine_all' # make it as binary segmentation 'multi_all' for multi cls segmentation
# Construct train and validation image list paths
img_folder="./datasets"  # Assuming this is the folder where images are stored
train_img_list="${img_folder}/${dataset_name}/train_5shot.csv"
val_img_list="${img_folder}/${dataset_name}/val_5shot.csv"


# Construct the checkpoint directory argument
dir_checkpoint="2D-SAM_${arch}_decoder_${finetune_type}_${dataset_name}_noprompt"

# Run the Python script
python SingleGPU_train_finetune_noprompt.py \
    -if_warmup True \
    -finetune_type "$finetune_type" \
    -arch "$arch" \
    -if_mask_decoder_adapter True \
    -img_folder "$img_folder" \
    -mask_folder "$img_folder" \
    -sam_ckpt "sam_vit_b_01ec64.pth" \
    -dataset_name "$dataset_name" \
    -dir_checkpoint "$dir_checkpoint" \
    -train_img_list "$train_img_list" \
    -val_img_list "$val_img_list"

To run the training, just use the command:

bash train_singlegpu_demo.sh
or 
bash train_ddpgpu_demo.sh

Visualization of the loss

You can visualize your training logs using tensorboard; in a terminal, just type:

tensorboard --logdir args.dir_checkpoint/log --ip 0.0.0.0

Then, open the browser to visualize the loss.

Additional interactive modes

if you want to use prompt_based training, just edit the dataset into prompt_type='point' or prompt_type='box' or prompt_type='hybrid', for example:

train_dataset = Public_dataset(args,args.img_folder, args.mask_folder, train_img_list,phase='train',targets=['all'],normalize_type='sam',prompt_type='point')
eval_dataset = Public_dataset(args,args.img_folder, args.mask_folder, val_img_list,phase='val',targets=['all'],normalize_type='sam',prompt_type='point')

And you need to edit the block for the prompt encoder input accordingly:

sparse_emb, dense_emb = sam_fine_tune.prompt_encoder(
            points=points,
            boxes=None,
            masks=None,
        )

Step 3: Validation of the model

bash val_singlegpu_demo.sh

Additional model inference mode and prediction visualization

Refer to 2D_predictions_with_vis.ipynb and 3D_predictions_with_vis.ipynb.

b): fine-tune from task-expansive pretrained weights

If you want to use MedSAM as pretrained weights, please refer to MedSAM and download their checkpoints as 'medsam_vit_b.pth'.

c): fine-tune from task-agnostic self-supervised pre-trained weights

In our paper, we found that training in Setup 3, which starts from self-supervised weights and then fine-tuning to one customized dataset using Parameter Efficient Learning to fine-tune both Encoder/Decoder, provides the best model. To use our self-supervised pretrained weights, please refer to SSLSAM.

ToDOlist:

• add the branch of codes for automatic multi-cls segmentation
• add the branch of codes for prompt-based multi-cls segmentation. output has two channels and random select one target at one time during training.

Acknowledgement

This work was supported by Duke Univeristy. We built these codes based on the following:

1. SAM
2. MobileSAM
3. MedSAM
4. Medical SAM Adapter
5. LoRA for SAM

Citation

Please cite our paper if you find our codes or paper helpful, we really appreciate it [🥹 citation, please, cry cry]:

@misc{gu2024build,
      title={How to build the best medical image segmentation algorithm using foundation models: a comprehensive empirical study with Segment Anything Model}, 
      author={Hanxue Gu and Haoyu Dong and Jichen Yang and Maciej A. Mazurowski},
      year={2024},
      eprint={2404.09957},
      archivePrefix={arXiv},
      primaryClass={cs.CV}
}