diff --git a/README.md b/README.md index f8ec9f4..98f5bc8 100644 --- a/README.md +++ b/README.md @@ -16,6 +16,9 @@ pip install dlicv ```bash git clone https://github.com/georgeaidinis/DLICV +cd DLICV +conda create -n DLICV -y python=3.8 && conda activate DLICV +pip install . ``` ## Usage @@ -26,16 +29,44 @@ git clone https://github.com/georgeaidinis/DLICV from dlicv.compute_icv import compute_volume # Assuming your nifti file is named 'input.nii.gz' -volume_image = compute_volume("input.nii.gz") +volume_image = compute_volume("input.nii.gz", "output.nii.gz", "path/to/model/") ``` ### From the terminal ```bash -dlicv compute --input input.nii.gz --output output.nii.gz +DLICV --input input.nii.gz --output output.nii.gz --model path/to/model ``` -Replace the `input.nii.gz` with the path to your input infit file. +Replace the `input.nii.gz` with the path to your input nifti file, as well as the model path. + +Example: + +Assuming a file structure like so: + +```bash +. +├── in +│   ├── input1.nii.gz +│   ├── input2.nii.gz +│   └── input3.nii.gz +├── model +│   ├── fold_0 +│   ├── fold_1 +│   │   ├── debug.json +│   │   ├── model_final_checkpoint.model +│   │   ├── model_final_checkpoint.model.pkl +│   │   ├── model_latest.model +│   │   ├── model_latest.model.pkl +│   └── plans.pkl +└── out +``` + +An example command might be: + +```bash +DLICV --input path/to/input/ --output path/to/output/ --model path/to/model/ +``` ## Contact