hucanpei / mrbrains18

This code is written to participate in the MRBrainS18 competition.

MRBrainS18

This code is written to participate in the MRBrainS18 competition.

The method we use comes from this paper: From neonatal to adult brain mr image segmentation in a few seconds using 3d-like fully convolutional network and transfer learning

Preprocess:

1)histogram equalization(only for T1);

2)stack 3 continue slices as a RGB image;

3)flip and rotate for [$0,\pm 5,\pm 10,\pm 15$] for data augmentation;

4)crop to reduce background in image and ensure width and height can be devided by 16;

Network

Simply pass image in 3 modalities through 3 streams of VGG, and concat them in every stage.

Run

python ./train.py --gpu_id=0 --data_path='path' --val_num=1 

The meaning of this line of code is running this code with GPU 0 and validating with sample 1.

Code explanation

Main file is 'train.py', includes train and validation process.

folder 'data_loader' includes preprocess code and dataloader.

folder 'models' includes some networks.

'loss.py' defines sone loss functions.

'metrics.py' computes dice coefficients.

'validate.py' generates '.nii.gz' file for validation set.

'test.py' is an independent file to generate '.nii.gz' file for test sample.

folder 'fig_out' storages visualized results and train curve, in png foramt.

'evaluation.py' is modified from official code to compute metrics.

folder 'evaluation' storages output '.nii.gz' and label '.nii.gz' for computing metrics.

folder 'docker' is used to containerize test code.

folder 'documents' contains poster,slides,description and results for extension of icip paper.

Visualization

mrbrains18's Issues

DATA

Hello, can you share the MRBrain dataset? Or can you explain how to download it? I've been unable to sign in. My email is [email protected] Thank you

Dataset download

Hi. I'm trying to download the MRBrainS18 dataset recently and I've sent my confidentiality agreement to [email protected].
However, no reply is received and the website seems to be unavailable now. Could you send me a copy of the dataset? My email is [email protected]. Please help me. Thank you very much.

thanks

canpi666

batch size

Can the batch size in your program be adjusted? I always make an error when I try to adjust. The following is an error message：
RuntimeError: invalid argument 0: Sizes of tensors must match except in dimension 0. Got 160 and 224 in dimension 2 at ..\aten\src\TH/generic/THTensor.cpp:711

Questions about selecting data

How to select six data sets for training and one for testing

Steps after training

How to test ，Do you need to change anything