{
    "title": "Invocation manifest for FreeSurfer (v6.0.1): Recon-All",
    "$schema": "http://json-schema.org/draft-04/schema#",
    "type": "object",
    "properties": {
        "config": {
            "type": "object",
            "properties": {
                "subject_id": {
                    "type": "string"
                },
                "parallel": {
                    "type": "boolean",
                    "default": true
                },
                "n_cpus": {
                    "type": "integer",
                    "minimum": 1
                },
                "reconall_options": {
                    "default": "-all -qcache",
                    "type": "string"
                },
                "hippocampal_subfields": {
                    "default": true,
                    "type": "boolean"
                },
                "brainstem_structures": {
                    "default": true,
                    "type": "boolean"
                },
                "register_surfaces": {
                    "default": true,
                    "type": "boolean"
                },
                "convert_surfaces": {
                    "default": true,
                    "type": "boolean"
                },
                "convert_volumes": {
                    "default": true,
                    "type": "boolean"
                },
                "convert_stats": {
                    "default": true,
                    "type": "boolean"
                },
                "freesurfer_license": {
                    "type": "string"
                }
            },
            "required": [
                "parallel",
                "reconall_options",
                "hippocampal_subfields",
                "brainstem_structures",
                "register_surfaces",
                "convert_surfaces",
                "convert_volumes",
                "convert_stats"
            ]
        },
        "inputs": {
            "type": "object",
            "properties": {
                "api-key": {
                    "type": "object"
                },
                "freesurfer_license_file": {
                    "type": "object",
                    "properties": {}
                },
                "anatomical": {
                    "type": "object",
                    "properties": {
                        "type": {
                            "enum": [
                                "nifti",
                                "dicom",
                                "archive"
                            ]
                        }
                    }
                },
                "t1w_anatomical_2": {
                    "type": "object",
                    "properties": {
                        "type": {
                            "enum": [
                                "nifti"
                            ]
                        }
                    }
                },
                "t1w_anatomical_3": {
                    "type": "object",
                    "properties": {
                        "type": {
                            "enum": [
                                "nifti"
                            ]
                        }
                    }
                },
                "t1w_anatomical_4": {
                    "type": "object",
                    "properties": {
                        "type": {
                            "enum": [
                                "nifti"
                            ]
                        }
                    }
                },
                "t1w_anatomical_5": {
                    "type": "object",
                    "properties": {
                        "type": {
                            "enum": [
                                "nifti"
                            ]
                        }
                    }
                },
                "t2w_anatomical": {
                    "type": "object",
                    "properties": {
                        "type": {
                            "enum": [
                                "nifti"
                            ]
                        }
                    }
                }
            },
            "required": [
                "api-key",
                "anatomical"
            ]
        }
    },
    "required": [
        "config",
        "inputs"
    ]
}