{
    "paths": {
        "topdir": "..",
        "agecsv": "config/ages.csv",
        "imgcsv": "config/subjects.csv",
        "tmpdir": "cache",
        "outdir": "output"
    },
    "images": {
        "default": "t2w",
        "ref": "config/domain.nii.gz",
        "t1w": {
            "prefix": "images/t1w/",
            "suffix": ".nii.gz",
            "interp": "linear",
            "datatype": "float",
            "normalization": "z-score",
            "rescaling": [1, 100],
            "sharpen": true,
            "bkgrnd": 0,
            "bins": 0
        },
        "t2w": {
            "prefix": "images/t2w/",
            "suffix": ".nii.gz",
            "interp": "linear",
            "datatype": "float",
            "normalization": "z-score",
            "rescaling": [1, 100],
            "sharpen": true,
            "bkgrnd": 0,
            "bins": 0
        },
        "tissues": {
            "prefix": "labels/tissues/",
            "suffix": ".nii.gz",
            "labels": "1..9",
            "interp": "nn"
        },
        "structures": {
            "prefix": "labels/structures/",
            "suffix": ".nii.gz",
            "labels": "1..87",
            "interp": "nn"
        }
    },
    "iterations": 8,
    "registration": {
        "affine": {
            "prefix": "global/",
            "suffix": ".dof"
        },
        "config": [
            {
                "energy": "Symmetric",
                "model": "SVFFD",
                "ffdim": "SS",
                "intsteps": 64,
                "liederiv": false,
                "bchterms": 2,
                "channels": ["t2w"],
                "measures": {"t2w": "NMI"},
                "padding": true,
                "interpolation": "Linear with padding",
                "foreground": "Union",
                "levels": 3,
                "resolution": 1.0,
                "spacing": [8.0, 16.0, 32.0],
                "bending": 1e-3,
                "jacobian": 0e-0,
                "blurring": {"tissues": 2, "structures": 2}
            },
            {
                "levels": 4,
                "resolution": 0.5,
                "spacing": [8.0, 8.0, 16.0, 32.0]
            },
            {
                "spacing": 4.0
            },
            {
                "spacing": 4.0
            },
            {
                "spacing": 4.0
            },
            {
                "bending": 5e-3,
                "jacobian": 1e-5,
                "spacing": 2.0
            },
            {
                "spacing": 2.0
            },
            {
                "spacing": 2.0
            }
        ],
        "growth": {
            "enabled": true,
            "exclavg": false,
            "bchterms": 3
        }
    },
    "regression": {
        "means": [36, 37, 38, 39, 40, 41, 42, 43, 44],
        "sigma": [1.64, 1.31, 1.0, 0.77, 0.64, 0.73, 0.86, 1.18, 1.5],
        "epsilon": 0.01,
        "precision": 2
    },
    "evaluation": {
        "measures": {
            "t2w": ["sdev", "gini", "entropy", "grad"],
            "tissues": ["entropy", "label-consistency", "grad(2)"],
            "structures": ["entropy", "label-consistency"]
        },
        "rois": {
            "structure={l:02d}": ["structures", "all"],
            "tissue={l:d}": ["tissues", "all"]
        }
    },
    "environment": {
        "queue": {
            "short": "local",
            "long": "local"
        },
        "threads": 8
    }
}