demo.mp4
- miniconda (download here)
- 3D Slicer version 5.0 or later.
- 3D Slicer MONAI Label Plugin. (install step here)
- python 3.9
conda create --name CardiacLab python=3.9 -y
pip install torch==1.12.1+cu113 torchvision==0.13.1+cu113 torchaudio==0.12.1 --extra-index-url https://download.pytorch.org/whl/cu113
pip install -r requirements.txt
monailabel start_server \
--app radiology \
--studies "D:\tmp\data" \
--conf models segmentation_cardiac \
--conf network unetcnx_a1 \
--conf --download_ckp_id <ID> \
--conf --target_spacing "0.7, 0.7, 1.0" \
--conf --spatial_size "128, 128, 128"\
--conf --intensity "-42, 423"
--app
: type of app.--studies
: input data dir.--conf models
: type of service.--conf network
: type of network.--conf --download_ckp_id
: download model checkpoint file from google drive.--conf --target_spacing
: target spacing.--conf --spatial_size
: spatial size (ROI).--conf --intensity
: intensity.
- set config to
run/config.toml
.
model = 'unetcnx_a1'
[segmentation_cardiac.unetcnx_a1]
app = "radiology"
studies = "D:\\tmp\\data"
models = "segmentation_cardiac"
network = "unetcnx_a1"
download_ckp_id = "<ID>"
target_spacing = "0.7, 0.7, 1.0"
spatial_size = "128, 128, 128"
intensity = "-42, 423"
- run
run/segmentation.py
.
python run/segmentation.py
- connect server
- upload data
- run
- done