mjpyeon / pytorch-dicom-classification

Code for analyzing medical images saved as .dicom files

pytorch-dicom-classification

PyTorch framework to classify dicom (.dcm) files

Dependencies

python 3.6.4
pytorch 0.4.0
torchvision 0.2.1
numpy 1.14.1
pydicom 1.0.2
scikit-image 0.13.1

Usage

CAUTION: You must define your own labeling function in model.py

preprocess dataset

python preprocessing.py /path/to/src/dir/ /path/to/dest/dir/

split dataset for k-fold validation

python split.py /path/to/src/dir/ k

train dataset

python main.py --architecture resnet152 --output_dim 8192 --num_labels 17 --k 5 --src /path/to/src/dir/

evaluation

python eval.py --ckpt /path/to/checkpoint/ --data_dir /path/to/src/dir/ --multilabel True --batch_size 64 --labels labels.csv