{
    "$schema": "http://json-schema.org/draft-04/schema#",
    "required": [
        "config",
        "inputs"
    ],
    "type": "object",
    "properties": {
        "inputs": {
            "required": [
                "BVAL_1",
                "BVEC_1",
                "NIFTI_1"
            ],
            "type": "object",
            "properties": {
                "anatomical": {
                    "type": "object",
                    "properties": {
                        "type": {
                            "enum": [
                                "nifti"
                            ]
                        }
                    }
                },
                "BVAL_1": {
                    "type": "object",
                    "properties": {
                        "type": {
                            "enum": [
                                "bval"
                            ]
                        }
                    }
                },
                "BVAL_2": {
                    "type": "object",
                    "properties": {
                        "type": {
                            "enum": [
                                "bval"
                            ]
                        }
                    }
                },
                "BVEC_2": {
                    "type": "object",
                    "properties": {
                        "type": {
                            "enum": [
                                "bvec"
                            ]
                        }
                    }
                },
                "BVEC_1": {
                    "type": "object",
                    "properties": {
                        "type": {
                            "enum": [
                                "bvec"
                            ]
                        }
                    }
                },
                "NIFTI_1": {
                    "type": "object",
                    "properties": {
                        "type": {
                            "enum": [
                                "nifti"
                            ]
                        }
                    }
                },
                "NIFTI_2": {
                    "type": "object",
                    "properties": {
                        "type": {
                            "enum": [
                                "nifti"
                            ]
                        }
                    }
                }
            }
        },
        "config": {
            "required": [
                "cleanIter",
                "imresample",
                "track_algorithm",
                "computeCSD",
                "fiberWeighting",
                "track_stepSizeMm",
                "catTime",
                "track_minLengthThreshMm",
                "qmr_metadata_ndirs",
                "qmr_metadata_sex",
                "savefigs",
                "rotateBvecsWithRx",
                "catX",
                "catY",
                "catZ",
                "bsplineInterpFlag",
                "track_faThresh",
                "maxDist",
                "track_whichAlgorithm",
                "clip2rois",
                "phaseEncodeDir",
                "track_offsetJitter",
                "track_nfibers",
                "cutoffUpper",
                "cleanClippedFibers",
                "numberOfNodes",
                "track_maxLengthThreshMm",
                "numBootStrapSamples",
                "qmr_runcontrolcomp",
                "flipLrApFlag",
                "track_faMaskThresh",
                "auto",
                "eddyCorrect",
                "track_wPuncture",
                "base_outname",
                "maxLen",
                "computenorms",
                "track_angleThresh",
                "track_seedVoxelOffset_1",
                "normalization",
                "cutoffLower",
                "qmr_metadata_bvalue",
                "noiseCalcMethod",
                "catTR",
                "rotateBvecsWithCanXform",
                "nStep",
                "track_whichInterp",
                "cleanFibers",
                "qmr_metadata_age_comp",
                "qmr_meatadata_age",
                "track_seedVoxelOffset_2",
                "fitMethod",
                "dwOutMm_3",
                "dwOutMm_2",
                "dwOutMm_1"
            ],
            "type": "object",
            "properties": {
                "cleanIter": {
                    "default": 5,
                    "type": "integer"
                },
                "imresample": {
                    "default": 0,
                    "type": "integer"
                },
                "track_algorithm": {
                    "default": "mrdiffusion",
                    "type": "string"
                },
                "computeCSD": {
                    "default": 0,
                    "type": "integer"
                },
                "fiberWeighting": {
                    "default": 1,
                    "type": "integer"
                },
                "qmr_meatadata_age": {
                    "default": 0,
                    "type": "integer"
                },
                "catTime": {
                    "default": false,
                    "type": "boolean",
                    "id": "-t"
                },
                "track_minLengthThreshMm": {
                    "default": 50,
                    "type": "integer"
                },
                "track_angleThresh": {
                    "default": 30,
                    "type": "integer"
                },
                "qmr_metadata_sex": {
                    "default": "unknown",
                    "type": "string"
                },
                "savefigs": {
                    "default": 0,
                    "type": "integer"
                },
                "rotateBvecsWithRx": {
                    "default": 0,
                    "type": "integer"
                },
                "catX": {
                    "default": false,
                    "type": "boolean",
                    "id": "-x"
                },
                "catY": {
                    "default": false,
                    "type": "boolean",
                    "id": "-y"
                },
                "catZ": {
                    "default": false,
                    "type": "boolean",
                    "id": "-z"
                },
                "bsplineInterpFlag": {
                    "default": 0,
                    "type": "integer"
                },
                "track_faThresh": {
                    "default": 0.2,
                    "type": "number"
                },
                "maxDist": {
                    "default": 5,
                    "type": "integer"
                },
                "cleanFibers": {
                    "default": 1,
                    "type": "integer"
                },
                "clip2rois": {
                    "default": 1,
                    "type": "integer"
                },
                "phaseEncodeDir": {
                    "default": 2,
                    "type": "integer"
                },
                "track_offsetJitter": {
                    "default": 0,
                    "type": "number"
                },
                "track_nfibers": {
                    "default": 500000,
                    "type": "integer"
                },
                "cutoffUpper": {
                    "default": 90,
                    "type": "integer"
                },
                "qmr_metadata_ndirs": {
                    "default": 30,
                    "type": "integer"
                },
                "numberOfNodes": {
                    "default": 100,
                    "type": "integer"
                },
                "qmr_metadata_bvalue": {
                    "default": 1000,
                    "type": "integer"
                },
                "eddyCorrect": {
                    "default": 1,
                    "type": "integer"
                },
                "numBootStrapSamples": {
                    "default": 500,
                    "type": "integer"
                },
                "flipLrApFlag": {
                    "default": 0,
                    "type": "integer"
                },
                "track_faMaskThresh": {
                    "default": 0.3,
                    "type": "number"
                },
                "auto": {
                    "default": true,
                    "type": "boolean",
                    "id": "-a"
                },
                "cleanClippedFibers": {
                    "default": 0,
                    "type": "integer"
                },
                "track_wPuncture": {
                    "default": 0.2,
                    "type": "number"
                },
                "base_outname": {
                    "default": "none",
                    "type": "string"
                },
                "maxLen": {
                    "default": 4,
                    "type": "integer"
                },
                "computenorms": {
                    "default": 1,
                    "type": "integer"
                },
                "track_whichAlgorithm": {
                    "default": 1,
                    "type": "integer"
                },
                "track_seedVoxelOffset_1": {
                    "default": 0.25,
                    "type": "number"
                },
                "noiseCalcMethod": {
                    "default": "b0",
                    "type": "string"
                },
                "normalization": {
                    "default": "spm",
                    "type": "string"
                },
                "cutoffLower": {
                    "default": 10,
                    "type": "integer"
                },
                "qmr_runcontrolcomp": {
                    "default": 1,
                    "type": "integer"
                },
                "track_stepSizeMm": {
                    "default": 1,
                    "type": "integer"
                },
                "catTR": {
                    "default": 0,
                    "type": "number",
                    "id": "-tr"
                },
                "dwOutMm_2": {
                    "default": 2,
                    "type": "integer"
                },
                "track_whichInterp": {
                    "default": 1,
                    "type": "integer"
                },
                "track_maxLengthThreshMm": {
                    "default": 250,
                    "type": "integer"
                },
                "qmr_metadata_age_comp": {
                    "default": 0,
                    "type": "integer"
                },
                "track_seedVoxelOffset_2": {
                    "default": 0.75,
                    "type": "number"
                },
                "fitMethod": {
                    "default": "ls",
                    "type": "string"
                },
                "dwOutMm_3": {
                    "default": 2,
                    "type": "integer"
                },
                "nStep": {
                    "default": 50,
                    "type": "integer"
                },
                "dwOutMm_1": {
                    "default": 2,
                    "type": "integer"
                },
                "rotateBvecsWithCanXform": {
                    "default": 1,
                    "type": "integer"
                }
            }
        }
    },
    "title": "Invocation manifest for AFQ Pipeline: Automated Fiber Quantification Pipeline"
}