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- {
- "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
- }
- }
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