Code for A Volumetric Transformer for Accurate 3D Tumor Segmentation

Himashi Amanda Peiris

Last update: Dec 20, 2022

Related tags

Deep Learning deep-learning transformer tumor-segmentation pytorch-implementation 3d-medical-imaging-segmentation volumetric-transformer pure-transformer

Overview

VT-UNet

This repo contains the supported pytorch code and configuration files to reproduce 3D medical image segmentaion results of VT-UNet.

Environment

Prepare an environment with python=3.8, and then run the command "pip install -r requirements.txt" for the dependencies.

Data Preparation

For experiments we used four datasets:
- BRATS 2021 : http://braintumorsegmentation.org/
- MSD BRATS, LIVER, PANCREAS : http://medicaldecathlon.com/

File structure

 BRATS2021
  |---Data
  |   |--- RSNA_ASNR_MICCAI_BraTS2021_TrainingData
  |   |   |--- BraTS2021_00000
  |   |   |   |--- BraTS2021_00000_flair...
  |   
  |              
  |   
  |
 VT-UNet
  |---train.py
  |---test.py
  |---pretrained_ckpt
  |---saved_model
  ...

Pre-Trained Weights

Swin-T: https://github.com/SwinTransformer/storage/releases/download/v1.0.0/swin_tiny_patch4_window7_224.pth
Download Swin-T pre-trained weights and add it under pretrained_ckpt folder

Pre-Trained Base Model For BraTS 2021

VT-UNet-B: https://drive.google.com/file/d/1tLpEfyKgQ8xgvM3D1Aqi8aD3ILVB3du7/view?usp=sharing
Download VT-UNet-B pre-trained model and add it under saved_model folder before running test.py

Train/Test

Train : Run the train script on BraTS 2021 Training Dataset with Base model Configurations.

python train.py --cfg configs/vt_unet_base.yaml --num_classes 3 --epochs 350

Test : Run the test script on BraTS 2021 Training Dataset.

python test.py --cfg configs/vt_unet_base.yaml --num_classes 3

Acknowledgements

This repository makes liberal use of code from open_brats2020, Swin Transformer, Video Swin Transformer and Swin-Unet

References

Citing VT-UNet

    @misc{peiris2021volumetric,
      title={A Volumetric Transformer for Accurate 3D Tumor Segmentation}, 
      author={Himashi Peiris and Munawar Hayat and Zhaolin Chen and Gary Egan and Mehrtash Harandi},
      year={2021},
      eprint={2111.13300},
      archivePrefix={arXiv},
      primaryClass={eess.IV}
    }

Comments

Data preprocess

Hi @himashi92

Thanks for this awesome work and repo. I am trying to replicate this on the Liver data in the decathlon. When I run the the train command for the base training CUDA_VISIBLE_DEVICES=0 nohup vtunet_train 3d_fullres vtunetTrainerV2_vtunet_tumor_base 3 0 &> base.out &

I get the following error below KeyError: 'BRATS_001'(): `stage: 0 {'batch_size': 2, 'num_pool_per_axis': [5, 5, 5], 'patch_size': array([128, 128, 128]), 'median_patient_size_in_voxels': array([195, 207, 207]), 'current_spacing': array([2.473119 , 1.89831205, 1.89831205]), 'original_spacing': array([1. , 0.76757812, 0.76757812]), 'do_dummy_2D_data_aug': False, 'pool_op_kernel_sizes': [[2, 2, 2], [2, 2, 2], [2, 2, 2], [2, 2, 2], [2, 2, 2]], 'conv_kernel_sizes': [[3, 3, 3], [3, 3, 3], [3, 3, 3], [3, 3, 3], [3, 3, 3], [3, 3, 3]]}

stage: 1 {'batch_size': 2, 'num_pool_per_axis': [5, 5, 5], 'patch_size': array([128, 128, 128]), 'median_patient_size_in_voxels': array([482, 512, 512]), 'current_spacing': array([1. , 0.76757812, 0.76757812]), 'original_spacing': array([1. , 0.76757812, 0.76757812]), 'do_dummy_2D_data_aug': False, 'pool_op_kernel_sizes': [[2, 2, 2], [2, 2, 2], [2, 2, 2], [2, 2, 2], [2, 2, 2]], 'conv_kernel_sizes': [[3, 3, 3], [3, 3, 3], [3, 3, 3], [3, 3, 3], [3, 3, 3], [3, 3, 3]]}

I am using stage 1 from these plans I am using batch dice + CE loss

I am using data from this folder: /home/VT-UNet/VTUNet/DATASET/vtunet_preprocessed/Task003_Liver/vtunetData_plans_v2.1 ############################################### loading dataset loading all case properties 2022-08-16 04:36:37.549490: Creating new 5-fold cross-validation split... 2022-08-16 04:36:37.550782: Desired fold for training: 0 2022-08-16 04:36:37.550879: This split has 387 training and 73 validation cases. Traceback (most recent call last): File "/home/VT-UNet/transegvenv/bin/vtunet_train", line 33, in sys.exit(load_entry_point('vtunet', 'console_scripts', 'vtunet_train')()) File "/home/VT-UNet/VTUNet/vtunet/run/run_training.py", line 134, in main trainer.initialize(not validation_only) File "/home/VT-UNet/VTUNet/vtunet/training/network_training/vtunetTrainerV2_vtunet_liver_base.py", line 90, in initialize self.dl_tr, self.dl_val = self.get_basic_generators() File "/home/VT-UNet/VTUNet/vtunet/training/network_training/vtunetTrainer.py", line 401, in get_basic_generators self.do_split() File "/home/VT-UNet/VTUNet/vtunet/training/network_training/vtunetTrainerV2_vtunet_liver_base.py", line 410, in do_split self.dataset_tr[i] = self.dataset[i] KeyError: 'BRATS_001'`

Any idea how to fix this, also but separately I get an error when I try to do the vtunet_train_3d?

opened by b3r-prog 7
dataset

Hello, author, through your paper, I found that you divided 1251 pieces of data into training, verification and testing for experiments, rather than taking part in the 21 challenge to obtain 251 verification sets for experiments. Is this a convincing division?

opened by H-CODE6 7
Ask for data help

Hello, I'd like to ask if you can provide the treatment of liver or pancreatic tumors. The code shows the treatment of brats2021 data. I need to deal with the segmentation of gastric cancer data. The data type is DCM. Thank you for sharing.

opened by huying12 7
Training & Testing On MSD Data

First of all, thanks @himashi92 for this amazing work. Since we do not have access to BraTS data and want to run your model on the MSD data set given here, it would be very helpful if you could help me with that. What will be the tree structure of the code before running & what changes in the code need to be done? It would be further more helpful if could add your code of running it on MSD data here in this repo.

opened by abdur75648 7
Still overflowing GPU VRAM with reduced batch size

Hi! I'm still having issues with overflowing my VRAM (RTX 3090 24GB) whenever attempting to train. Even after I've redued my batch size to 1. Any ideas on what I can do?

opened by Chadkowski 5

RuntimeError: CUDA out of memory

Traceback (most recent call last):
  File "train.py", line 314, in <module>
    main(arguments)
  File "train.py", line 166, in main
    segs_S1 = model_1(inputs_S1)
  File "/home/yusongli/.bin/anaconda3/lib/python3.8/site-packages/torch/nn/modules/module.py", line 1102, in _call_impl
    return forward_call(*input, **kwargs)
  File "/home/yusongli/_project/shidaoai/task/01_seg/VT-Unet/vtunet/vision_transformer.py", line 49, in forward
    return self.swin_unet(x)
  File "/home/yusongli/.bin/anaconda3/lib/python3.8/site-packages/torch/nn/modules/module.py", line 1102, in _call_impl
    return forward_call(*input, **kwargs)
  File "/home/yusongli/_project/shidaoai/task/01_seg/VT-Unet/vtunet/vt_unet.py", line 1118, in forward
    x, x_downsample, v_values_1, k_values_1, q_values_1, v_values_2, k_values_2, q_values_2 = self.forward_features(
  File "/home/yusongli/_project/shidaoai/task/01_seg/VT-Unet/vtunet/vt_unet.py", line 960, in forward_features
    x, v1, k1, q1, v2, k2, q2 = layer(x, i)
  File "/home/yusongli/.bin/anaconda3/lib/python3.8/site-packages/torch/nn/modules/module.py", line 1102, in _call_impl
    return forward_call(*input, **kwargs)
  File "/home/yusongli/_project/shidaoai/task/01_seg/VT-Unet/vtunet/vt_unet.py", line 726, in forward
    x, v1, k1, q1 = blk(x, attn_mask, None, None, None)
  File "/home/yusongli/.bin/anaconda3/lib/python3.8/site-packages/torch/nn/modules/module.py", line 1102, in _call_impl
    return forward_call(*input, **kwargs)
  File "/home/yusongli/_project/shidaoai/task/01_seg/VT-Unet/vtunet/vt_unet.py", line 392, in forward
    x, x2, v, k, q = self.forward_part1(x, mask_matrix, prev_v, prev_k, prev_q, is_decoder)
  File "/home/yusongli/_project/shidaoai/task/01_seg/VT-Unet/vtunet/vt_unet.py", line 340, in forward_part1
    attn_windows, cross_attn_windows, v, k, q = self.attn(x_windows, mask=attn_mask, prev_v=prev_v, prev_k=prev_k,
  File "/home/yusongli/.bin/anaconda3/lib/python3.8/site-packages/torch/nn/modules/module.py", line 1102, in _call_impl
    return forward_call(*input, **kwargs)
  File "/home/yusongli/_project/shidaoai/task/01_seg/VT-Unet/vtunet/vt_unet.py", line 191, in forward
    attn = q @ k.transpose(-2, -1)
RuntimeError: CUDA out of memory. Tried to allocate 9.02 GiB (GPU 0; 23.70 GiB total capacity; 11.37 GiB already allocated; 8.42 GiB free; 13.10 GiB reserved in total by PyTorch) If reserved memor
y is >> allocated memory try setting max_split_size_mb to avoid fragmentation.  See documentation for Memory Management and PYTORCH_CUDA_ALLOC_CONF

Notice: I modified the dataloader to fit my own dataset. I've serched lots of solution but failed to solve this. Very sad :-( Could you please help me? Maybe the model is too large to train? I don't know. Thanks!

opened by ysl2 5

Error when run train.py

Hi, I am trying to regenerate the result, I got the following error. Any help with this? Thanks

AssertionError Traceback (most recent call last) ~/Desktop/projects/VT-UNet-main/train.py in 300 arguments = parser.parse_args() 301 os.environ['CUDA_VISIBLE_DEVICES'] = arguments.devices --> 302 main(arguments)

~/Desktop/projects/VT-UNet-main/train.py in main(args) 109 optimizer = torch.optim.Adam(params, lr=args.lr, weight_decay=args.weight_decay) 110 --> 111 full_train_dataset, l_val_dataset, bench_dataset = get_datasets(args.seed, fold_number=args.fold) 112 train_loader = torch.utils.data.DataLoader(full_train_dataset, batch_size=args.batch_size, shuffle=True, 113 num_workers=args.workers, pin_memory=True, drop_last=True)

~/Desktop/projects/VT-UNet-main/dataset/brats.py in get_datasets(seed, on, fold_number, normalisation) 90 base_folder = pathlib.Path(get_brats_folder(on)).resolve() 91 print(base_folder) ---> 92 assert base_folder.exists() 93 patients_dir = sorted([x for x in base_folder.iterdir() if x.is_dir()]) 94

AssertionError:

opened by shathaa1983 3
About Results on BraTS

The paper <A Volumetric Transformer for Accurate 3D Tumor Segmentation> evaluates the VT-UNet's performance on BraTS 2021 dataset, but the MICCAI paper <A Robust Volumetric Transformer for Accurate 3D Tumor Segmentation> evaluates the VT-UNet on MSD BraTS task. Why not evaluate and report the performance of VT-UNet on BraTS 2021 any more in the MICCAI paper?

opened by auroua 2
how to predict on Brats Validation case?

First of all, thank you for your excellent work,i want to ask you a question,how to use this cood to predict a case.Brats Validation dataset only have four files,it don't have seg file, i want to use this code to predict on every validation case,looking forward to your reply.

opened by wangnanv5 2
Data processing questions about Brats21

Thank you very much for your excellent work, I noticed that in your Brats.py code, the fusion of different tags into ET, TC, WT also occurs in many data processing examples, such as Monai. But I see that your paper is still classified and evaluated according to the label of the competition, right? Looking forward to your reply.

opened by Breeze-Zero 2
Inference failed due to missing posporcessing.json file

Dear author, I find your paper very interesting and I'm new in the medical imaging field. I am trying to reproduce your model results for version 1 and version 2.

In version 1, I couldn't find the HD95 code, therefore I copied it from here. It gives the wrong HD95 during evaluation, can you please provide this version 1.

In version 2, when I run the inference code it gives the error shown in the figure. To resolve this issue I run consolidate_postprocessing_simple.py to compute the postprocessing.json file. But this says fold_0, fold_1, fold_2, etc are missing. I trained the model for fold=0 as described in the instructions. Could you please see this?

opened by mustansarfiaz 1

Code for A Volumetric Transformer for Accurate 3D Tumor Segmentation

Related tags

Overview

VT-UNet

Environment

Data Preparation

Pre-Trained Weights

Pre-Trained Base Model For BraTS 2021

Train/Test

Acknowledgements

References

Citing VT-UNet

Comments

Owner

Himashi Amanda Peiris

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