{
    "title": "Invocation manifest for BIDS fMRIPrep: A Robust Preprocessing Pipeline for fMRI Data",
    "$schema": "http://json-schema.org/draft-04/schema#",
    "type": "object",
    "properties": {
        "config": {
            "type": "object",
            "properties": {
                "skip-bids-validation": {
                    "default": false,
                    "type": "boolean"
                },
                "task-id": {
                    "default": "",
                    "type": "string"
                },
                "echo-idx": {
                    "default": "",
                    "type": "string"
                },
                "n_cpus": {
                    "default": 0,
                    "type": "integer"
                },
                "mem_mb": {
                    "default": 0,
                    "type": "integer"
                },
                "anat-only": {
                    "default": false,
                    "type": "boolean"
                },
                "boilerplate": {
                    "default": false,
                    "type": "boolean"
                },
                "md-only-boilerplate": {
                    "default": false,
                    "type": "boolean"
                },
                "error-on-aroma-warnings": {
                    "default": false,
                    "type": "boolean"
                },
                "verbose": {
                    "default": "",
                    "enum": [
                        "",
                        "v",
                        "vv",
                        "vvv"
                    ],
                    "type": "string"
                },
                "ignore": {
                    "default": "",
                    "type": "string"
                },
                "longitudinal": {
                    "default": false,
                    "type": "boolean"
                },
                "t2s-coreg": {
                    "default": false,
                    "type": "boolean"
                },
                "output-spaces": {
                    "default": "MNI152NLin2009cAsym",
                    "type": "string"
                },
                "bold2t1w-dof": {
                    "enum": [
                        6,
                        9,
                        12
                    ],
                    "default": 6,
                    "type": "integer"
                },
                "force-bbr": {
                    "default": false,
                    "type": "boolean"
                },
                "force-no-bbr": {
                    "default": false,
                    "type": "boolean"
                },
                "medial-surface-nan": {
                    "default": false,
                    "type": "boolean"
                },
                "dummy-scans": {
                    "default": 0,
                    "type": "integer"
                },
                "use-aroma": {
                    "type": "boolean",
                    "default": false
                },
                "aroma-melodic-dimensionality": {
                    "default": -200,
                    "type": "integer"
                },
                "return-all-components": {
                    "default": false,
                    "type": "boolean"
                },
                "fd-spike-threshold": {
                    "default": 0.5,
                    "type": "number"
                },
                "dvars-spike-threshold": {
                    "default": 1.5,
                    "type": "number"
                },
                "skull-strip-template": {
                    "enum": [
                        "OASIS30ANTs",
                        "NKI"
                    ],
                    "default": "OASIS30ANTs",
                    "type": "string"
                },
                "skull-strip-fixed-seed": {
                    "default": false,
                    "type": "boolean"
                },
                "fmap-bspline": {
                    "default": false,
                    "type": "boolean"
                },
                "fmap-no-demean": {
                    "default": false,
                    "type": "boolean"
                },
                "use-syn-sdc": {
                    "default": false,
                    "type": "boolean"
                },
                "force-syn": {
                    "default": false,
                    "type": "boolean"
                },
                "no-submm-recon": {
                    "default": false,
                    "type": "boolean"
                },
                "cifti-output": {
                    "default": false,
                    "type": "boolean"
                },
                "fs-no-reconall": {
                    "default": false,
                    "type": "boolean"
                },
                "resource-monitor": {
                    "default": false,
                    "type": "boolean"
                },
                "reports-only": {
                    "default": false,
                    "type": "boolean"
                },
                "run-uuid": {
                    "default": "",
                    "type": "string"
                },
                "write-graph": {
                    "default": false,
                    "type": "boolean"
                },
                "stop-on-first-crash": {
                    "default": false,
                    "type": "boolean"
                },
                "notrack": {
                    "default": false,
                    "type": "boolean"
                },
                "gear-abort-on-bids-error": {
                    "default": false,
                    "type": "boolean"
                },
                "gear-log-level": {
                    "default": "INFO",
                    "type": "string",
                    "enum": [
                        "ERROR",
                        "WARNING",
                        "INFO",
                        "DEBUG"
                    ]
                },
                "gear-run-bids-validation": {
                    "default": true,
                    "type": "boolean"
                },
                "gear-save-intermediate-output": {
                    "default": false,
                    "type": "boolean"
                },
                "gear-intermediate-files": {
                    "default": "",
                    "type": "string"
                },
                "gear-intermediate-folders": {
                    "default": "",
                    "type": "string"
                },
                "gear-dry-run": {
                    "default": false,
                    "type": "boolean"
                },
                "gear-keep-output": {
                    "default": false,
                    "type": "boolean"
                },
                "gear-keep-fsaverage": {
                    "default": false,
                    "type": "boolean"
                },
                "gear-FREESURFER_LICENSE": {
                    "type": "string",
                    "default": ""
                }
            },
            "required": [
                "skip-bids-validation",
                "task-id",
                "echo-idx",
                "n_cpus",
                "mem_mb",
                "anat-only",
                "boilerplate",
                "md-only-boilerplate",
                "error-on-aroma-warnings",
                "verbose",
                "ignore",
                "longitudinal",
                "t2s-coreg",
                "output-spaces",
                "bold2t1w-dof",
                "force-bbr",
                "force-no-bbr",
                "medial-surface-nan",
                "dummy-scans",
                "use-aroma",
                "aroma-melodic-dimensionality",
                "return-all-components",
                "fd-spike-threshold",
                "dvars-spike-threshold",
                "skull-strip-template",
                "skull-strip-fixed-seed",
                "fmap-bspline",
                "fmap-no-demean",
                "use-syn-sdc",
                "force-syn",
                "no-submm-recon",
                "cifti-output",
                "fs-no-reconall",
                "resource-monitor",
                "reports-only",
                "run-uuid",
                "write-graph",
                "stop-on-first-crash",
                "notrack",
                "gear-abort-on-bids-error",
                "gear-log-level",
                "gear-run-bids-validation",
                "gear-save-intermediate-output",
                "gear-intermediate-files",
                "gear-intermediate-folders",
                "gear-dry-run",
                "gear-keep-output",
                "gear-keep-fsaverage",
                "gear-FREESURFER_LICENSE"
            ]
        },
        "inputs": {
            "type": "object",
            "properties": {
                "key": {
                    "type": "object"
                },
                "freesurfer_license": {
                    "type": "object",
                    "properties": {}
                }
            },
            "required": [
                "key"
            ]
        }
    },
    "required": [
        "config",
        "inputs"
    ]
}