Download docker image
$ docker pull piotrekwoznicki/adpkd-net:v0.1
More instructions on the inference can be found at Docker Hub.
Run
1. Launch the container:
$ bash launch_container.sh [path_to_dataset - will be mounted at /workspace/data]
2. Run inference:
$ cd /workspace/source
$ bash fit.sh \
-i / --InputVol [abs_path_to_nifti_image]
-o / --OutputDir [where_to_save_segmentation_and_JSON]
--small [whether to use single model - OPTIONAL (requires shorter calculation time)]
3. Run inference for test:
$ cd /workspace/source
$ bash fit.sh \
-i /workspace/test_data/T2_ax.nii.gz
-o /workspace/data/test_results_ax
$ bash fit.sh \
-i /workspace/test_data/T2_cor.nii.gz
-o /workspace/data/test_results_cor