README.md

MTMAUNet

MTMAUNet: Multi-Task Multi-axis Attention UNet

Environment

pytorch>=1.6
monai>=1.0.0
accelerate>=0.5.0

Inference

Configure configs/Config.yaml

dataset:
    test: ./test.csv   # your infer csv path
val_model: ./checkpoint.pth.tar  # weight file

test.csv file example, It is better to use absolute position

/dataset/img/img_001.nii.gz
/dataset/img/img_002.nii.gz

Run command

python infer.py

Training or verification

Configure configs/Config.yaml

dataset:
    root: ./dataset_dir # your dataset path 
    cv:
        dir_name: cv  # your fold csv dir
        fold: 0 # your fold k
    split: 
        train: train.csv  # your train csv name
        val: val.csv # your val csv name

train.csv or val.csv file example, use a relative location to dataset.root

img_001.nii.gz, seg_001.nii.gz, 0
img_002.nii.gz, seg_002.nii.gz, 1

Run command

python train.py   # train
python val.py     # val

Acknowledgement

Code based on DynUNet in monai.

Code based on 3D-MaxViT-pytorch in 3D-MaxViT-pytorch.