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mcmrsr's Introduction

Data Description

Two in-house private datasets: pelvic and brain and one public dataset: fastMRI are utilized in our experiments. For the private data, all studies have been approved by the local Institutional Review Board (IRB). The IRB asked us to protect the privacy of participants and to maintain the confidentiality of data. Since we cannot make the two datasets publicly available, we won't claim them as our contribution.

Environment and Dependencies

Requirements:

  • Python 3.6
  • Pytorch 1.4.0
  • scipy
  • scikit-image
  • opencv-python
  • tqdm

Our code has been tested with Python 3.6, Pytorch 1.4.0, torchvision 0.5.0, CUDA 10.0 on Ubuntu 18.04.

To Run Our Code

  • Train the model
python train_demo.py
  • Test the model
python test_demo.py --resume ' '

where --resume trained model.

mcmrsr's People

Contributors

xaimi-lab avatar

Stargazers

 avatar Meronym avatar  avatar Calvin Pang avatar  avatar  avatar  avatar Zhang Jiulou avatar GIT avatar yuez_ustc avatar  avatar SHI Xuan avatar nothing  avatar lbjcelsius avatar Gail Yip avatar XiaoMeng avatar  avatar Jac Sun avatar  avatar goddesshs avatar  avatar  avatar Shoujin Huang avatar Yubo Huang avatar ThanhLamNguyen avatar  avatar  avatar Yunheng WU avatar  avatar Yanyu Xu avatar Dimitris Karkalousos avatar  avatar Linyer avatar  avatar  avatar wind222 avatar Bin Chen avatar David Yang avatar Jingbo Lin avatar lin-hui-jun avatar  avatar

Watchers

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mcmrsr's Issues

训练问题

您好,我想问下用自己的数据集训练,要进行那几个数据集预处理!

Training problems

Hello, I used the public dataset fastmri for training. The following error occurred. The dataset is:
knee_singlecoil_val.tar
knee_singlecoil_test_v2.tar
knee_singlecoil_train.tar
What does the keyword T2 stand for

Traceback (most recent call last):
File "train_demo.py", line 136, in
for it, data in enumerate(train_bar):
File "/data2/qfl/YES/envs/McMRSR/lib/python3.6/site-packages/tqdm/std.py", line 1195, in iter
for obj in iterable:
File "/data2/qfl/YES/envs/McMRSR/lib/python3.6/site-packages/torch/utils/data/dataloader.py", line 521, in next
data = self._next_data()
File "/data2/qfl/YES/envs/McMRSR/lib/python3.6/site-packages/torch/utils/data/dataloader.py", line 1203, in _next_data
return self._process_data(data)
File "/data2/qfl/YES/envs/McMRSR/lib/python3.6/site-packages/torch/utils/data/dataloader.py", line 1229, in _process_data
data.reraise()
File "/data2/qfl/YES/envs/McMRSR/lib/python3.6/site-packages/torch/_utils.py", line 434, in reraise
raise exception
KeyError: Caught KeyError in DataLoader worker process 0.
Original Traceback (most recent call last):
File "/data2/qfl/YES/envs/McMRSR/lib/python3.6/site-packages/torch/utils/data/_utils/worker.py", line 287, in _worker_loop
data = fetcher.fetch(index)
File "/data2/qfl/YES/envs/McMRSR/lib/python3.6/site-packages/torch/utils/data/_utils/fetch.py", line 49, in fetch
data = [self.dataset[idx] for idx in possibly_batched_index]
File "/data2/qfl/YES/envs/McMRSR/lib/python3.6/site-packages/torch/utils/data/_utils/fetch.py", line 49, in
data = [self.dataset[idx] for idx in possibly_batched_index]
File "/data2/qfl/McMRSR/datasets/cartesian_dataset.py", line 37, in getitem
T2_256_img_real = T2_img['T2'].real
KeyError: 'T2'

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