ABLTempSeg.json

{
    "json_version": "1.3",
    "id": "temporal_bone_segmentation",
    "type": "docker",

    "name": "ABL Temporal Bone Segmentation",
    "organ": "Ear",
    "task": "Segmentation",
    "status": "In Development",
    "modality": "CT",
    "version": "1.4",
    "description": "Automatically segment the temporal bone using a deep-learning model. Please ensure that the input image has been properly aligned.",
    "maintainers": ["Soodeh Nikan (ABL at UWO)", "Ben Connors (ABL at UWO)"],
    "citation": "",
    "website": "https://abl.uwo.ca",

    "docker": {
        "image_name": "uwoabl/temporal-bone-segmentation",
        "image_tag": "latest",
        "data_path": "/tmp"
    },

    "inputs": {
        "input_vol": {
            "name": "Input Volume",
            "description": "Volume to pass to the segmenter.",
            "status": "required",
            "flag": "-i",
            "extension": ".nii.gz",
            "type": "volume",
            "labelmap": false,
            "pre": []
        }
    },

    "params": {
        "gpus": {
            "name": "GPU Count",
            "description": "Number of GPUs to use in inference.",
            "flag": "--gpus=",
            "type": "int",
            "default": 1,
            "min": 1,
            "max": 16
        },
        "cuda": {
            "name": "CUDA Devices",
            "description": "Comma-separated list of CUDA devices to use (leave empty for all)",
            "flag": "--cuda=",
            "type": "string",
            "default": ""
        },
        "threads": {
            "name": "Thread Count",
            "description": "Number of pre-processing threads to use (may only affect training)",
            "flag": "--threads=",
            "type": "int",
            "default": 4,
            "min": 1,
            "max": 256
        },
        "disable_growth": {
            "name": "Disable TensorFlow GPU Memory Growth",
            "description": "Can lead to worse performance, but may help on low VRAM systems (<8GB)",
            "flag": "--no-allow-growth",
            "type": "bool",
            "default": false
        },
        "cpu_resampling": {
            "name": "Use CPU Resampling",
            "description": "Use CPU resampling instead of CUDA; quality should be the same, but it's a lot slower",
            "flag": "--cpu-resampling",
            "type": "bool",
            "default": false
        },
        "no_island_removal": {
            "name": "Disable Island Removal",
            "description": "Disable the island removal done by the model (does not affect the Slicer island removal)",
            "flag": "--no-island-removal",
            "type": "bool",
            "default": false
        }
    },

    "outputs": {
        "output_seg": {
            "name": "Output Segmentation",
            "description": "Segmentation to put output into.",
            "status": "required",
            "flag": "-o",
            "extension": ".nii.gz",
            "type": "segmentation",
            "colours": {
                "1": [0.3764, 0.4470, 0.5176],
                "2": [0.9568, 0.9176, 0.6235],
                "3": [0.5019, 0.6431, 0.6352],
                "4": [0.9647, 0.8901, 0.7607],
                "5": [0.9647, 0.8901, 0.7607],
                "6": [0.9647, 0.8901, 0.7607],
                "7": [0.6941, 0.0666, 0.0549],
                "8": [0.8627, 0.6980, 0.6705],
                "9": [0.9411, 0.9411, 0.9137, 0.3]
            },
            "names": {
                "1": "Sigmoid Sinus",
                "2": "Facial Nerve",
                "3": "Bony Inner Ear",
                "4": "Malleus",
                "5": "Incus",
                "6": "Stapes",
                "7": "Carotid Artery",
                "8": "Internal Auditory Canal and Dura",
                "9": "External Auditory Canal"
            },
            "master": "input_vol",
            "labelmap": true,
            "post": [
                {
                    "name": "Island Removal",
                    "description": "Remove all islands",
                    "status": "suggested",
                    "locked": true,
                    "operation": "seged",
                    "action": "Islands",
                    "targets": [],
                    "params": {
                        "Operation": "KEEP_LARGEST_ISLAND",
                        "MinimumSize": "1"
                    }
                },
                {
                    "name": "Show in 3D",
                    "description": "Show the result in 3D",
                    "status": "suggested",
                    "locked": false,
                    "operation": "render_3d",
                    "params": {}
                }
            ]
        },
        "input_vol_resampled": {
            "name": "Resampled Input Volume",
            "description": "Resampled volume from the model.",
            "status": "optional",
            "flag": "-r",
            "extension": ".nii.gz",
            "type": "volume",
            "labelmap": false,
            "post": []
        }
    }
}