xnat-nif-qc-analysis/command.json at master · MonashBI/xnat-nif-qc-analysis · GitHub

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{
  "name": "QC Analysis",
  "label": null,
  "description": "Analyses QC sessions acquired as per the NIF TDRS SOP",
  "version": "1.0",
  "schema-version": "1.0",
  "info-url": null,
  "image": "monashbiomedicalimaging/xnat-nif-qc-analysis",
  "type": "docker",
  "index": null,
  "working-directory": null,
  "command-line": "/repo/xnat_pipeline.sh #SESSIONID# #T1# #T2# #DMRI#",
  "environment-variables": {},
  "ports": {},
  "mounts": [
    {
      "name": "workdir",
      "writable": true,
      "path": "/workdir"
    }
  ],
  "inputs": [
    {
      "name": "Session ID",
      "description": "XNAT ID of the session",
      "type": "string",
      "required": true,
      "replacement-key": "#SESSIONID#"
    },
    {
      "name": "T1 32Ch Scan Name",
      "description": "Name of the T1-weighted saline phantom with 32 Channel Head Coil",
      "type": "string",
      "matcher": null,
      "default-value": "",
      "required": true,
      "replacement-key": "#T1#",
      "command-line-flag": null,
      "command-line-separator": null,
      "true-value": null,
      "false-value": null
    },
    {
      "name": "T2 32Ch Scan Name",
      "description": "Name of the T2-weighted saline phantom with 32 Channel Head Coil",
      "type": "string",
      "matcher": null,
      "default-value": "",
      "required": true,
      "replacement-key": "#T2#",
      "command-line-flag": null,
      "command-line-separator": null,
      "true-value": null,
      "false-value": null
    },
    {
      "name": "dMRI 32Ch Scan Name",
      "description": "Name of the Diffusion MRI saline phantom with 32 Channel Head Coil",
      "type": "string",
      "matcher": null,
      "default-value": "",
      "required": true,
      "replacement-key": "#DMRI#",
      "command-line-flag": null,
      "command-line-separator": null,
      "true-value": null,
      "false-value": null
    }
  ],
  "outputs": [],
  "xnat": [
    {
      "name": "QC Analysis",
      "description": "Analyses QC sessions acquired as per the NIF TDRS SOP",
      "contexts": ["xnat:imageSessionData"],
      "external-inputs": [
	    {
          "name": "session",
          "description": "Input session",
          "type": "Session",
          "required": true
        }
	  ],
      "derived-inputs": [
        {
          "name": "session-id",
          "description": "The session's id",
          "type": "string",
          "derived-from-wrapper-input": "session",
          "derived-from-xnat-object-property": "label",
          "provides-value-for-command-input": "Session ID"
        }
      ],
      "output-handlers": []
    }
  ]
}