manifest.json

{
  "name": "extract-cmrr-physio",
  "label": "CMRR: Extract CMRR Physio",
  "description": "Extract physiological log files from encoded '_PHYSIO' DICOM file generated by CMRR MB sequences (>=R015, >=VD13A), Generate BIDs compliant files if desired",
  "maintainer": "Flywheel <support@flywheel.io>",
  "author": "E. Auerbach, CMRR, 2016",
  "url": "https://github.com/flywheel-apps/extract-cmrr-physio",
  "source": "https://github.com/CMRR-C2P/MB",
  "license": "MIT",
  "flywheel": "0",
  "version": "1.2.7",
  "custom": {
    "docker-image": "flywheel/extract-cmrr-physio:1.2.7",
    "gear-builder": {
      "category": "converter",
      "image": "flywheel/extract-cmrr-physio:1.2.7"
    },
    "flywheel": {
      "classification": {
        "species": [
          "Human",
          "Animal"
        ],
        "organ": [
          "Any"
        ],
        "therapeutic_area": [
          "Any"
        ],
        "modality": [
          "MR"
        ],
        "function": [
          "Utility"
        ]
      },
      "suite": "Utility"
    }
  },
  "inputs": {
    "DICOM_ARCHIVE": {
      "description": "Zipped archive containing CMRR Physio data",
      "base": "file",
      "type": {
        "enum": [
          "dicom",
          "archive"
        ]
      }
    }
  },
  "config": {
    "Generate_Bids": {
      "description": "Generate BIDS compatible physio files",
      "type": "boolean",
      "default": true
    },
    "Generate_json": {
      "description": "Generate the BIDS '.json' file for viewing",
      "type": "boolean",
      "default": false
    },
    "Generate_Raw": {
      "description": "Keep the raw '.log' files created by the matlab dicom to physio program",
      "type": "boolean",
      "default": true
    },
    "Generate_QA": {
      "description": "Generate QA plots of the physio measures for visual inspection",
      "type": "boolean",
      "default": true
    },
    "Process_Data": {
      "description": "Check to perform processing on the physio data, or leave unchecked to push raw data to BIDS format",
      "type": "boolean",
      "default": true
    },
    "Missing_Data": {
      "description": "How to handle missing data in the physio recordings",
      "type": "string",
      "enum": [
        "gap_fill",
        "uniform",
        "upsample",
        "none"
      ],
      "default": "gap_fill"
    },
    "Interpolation_Method": {
      "description": "Method to use for signal interpolation",
      "type": "string",
      "enum": [
        "fill",
        "linear",
        "nearest",
        "zero",
        "slinear",
        "quadratic",
        "cubic",
        "nan"
      ],
      "default": "nan"
    },
    "Fill_Value": {
      "description": "The value to fill missing data with if Interpolation_Methods is 'Fill'",
      "type": "number",
      "default": 0
    },
    "gear-log-level": {
      "default": "INFO",
      "description": "Gear Log verbosity level (ERROR|WARNING|INFO|DEBUG)",
      "type": "string",
      "enum": [
        "ERROR",
        "WARNING",
        "INFO",
        "DEBUG"
      ]
    },
    "Dry-Run": {
      "type": "boolean",
      "default": false,
      "description": "Log all commands, but do not execute."
    }
  },
  "command": "python /flywheel/v0/run.py"
}