manifest.json

{
  "name": "cni-dcm-convert",
  "label": "CNI-DCM-CONVERT - DICOM conversion utility",
  "description": "CNI-DCM-CONVERT uses SciTran's data library (https://github.com/vistalab/scitran-data) to convert raw DICOM data (within a zip archive) to NIfTI, Montage, and PNG (screenshot acquisitions) formats. DCM-CONVERT supports Siemens and GE DICOM data. This gear will also use dcm2niix to generate bids-sidecar metadata. Those metadata will be added to the output NIfTI file's info object in Flywheel.",
  "maintainer": "Michael Perry <lmperry@stanford.edu>",
  "author": "Scientific Transparency (RF Dougherty, K Hahn, R Bowen, G Schaefer, LM Perry, H Wu)",
  "url": "https://github.com/vistalab/scitran-data",
  "source": "https://github.com/cni/cni-dcm-convert",
  "license": "Apache-2.0",
  "flywheel": "0",
  "version": "2.6.0",
  "custom": {
    "flywheel": {
      "suite": "Stanford CNI"
    },
    "gear-builder": {
      "category": "converter",
      "image": "stanfordcni/cni-dcm-convert:2.6.0"
    }
  },
  "config": {
    "convert_montage": {
      "description": "Convert DICOM archive to MONTAGE format. (Default=false)",
      "default": false,
      "type": "boolean"
    },
    "convert_nifti": {
      "description": "Convert DICOM archive to NIfTI format. (Default=true)",
      "default": true,
      "type": "boolean"
    },
    "convert_png": {
      "description": "Convert screenshot acquisitions to PNG. (Default=false)",
      "default": false,
      "type": "boolean"
    },
    "convert_mux": {
      "description": "By default we do not convert DICOMs which are acquired with a muxarcepi* psd or have 'mux' in the series description. This flag forces the reconstruction of those data as well. *CAUTION* If the NIfTI file created here will have the same name as the reconstructed MUX file the existing will be overwritten! (Default=false)",
      "default": false,
      "type": "boolean"
    },
    "output_name": {
      "description": "Name to be used for the output NIfTI file. OPTIONAL: By default the gear will use <Study_ID>_<Series_Num>_<Acq_Num>.nii.gz.",
      "type": "string",
      "optional": true
    }
  },
  "inputs": {
    "dicom": {
      "description": "DICOM archive (.zip file)",
      "base": "file",
      "type": {
        "enum": [
          "dicom"
        ]
      }
    }
  }
}