docs/getting-started.md

Getting Started

Installation

For installation and downloading the saved weights of the models, please check the github repository.

Data Format

Input bpMRI scans should have all three sequnces, T2W, ADC and DWI as separate files in NRRD format. The prostate mask and heatmap are generated by the sample for each sample. To train the models or run testing with reference labels, the data pipeline uses MONAI's decathlon-format JSON:

{
    "train": [
        {
            "image": "path/to/t2.nrrd",
            "dwi": "path/to/dwi.nrrd",
            "adc": "path/to/adc.nrrd",
            "mask": "path/to/prostate_mask.nrrd",
            "heatmap": "path/to/heatmap.nrrd",
            "label": 0
        }
    ],
    "test": [...]
}

Sample JSON files are available in the github repository. Paths are relative to data_root. PI-RADS labels are 0-indexed (0 = PI-RADS 2, 3 = PI-RADS 5). csPCa labels are binary (0 or 1).