itkimage2paramap can be used to convert a parametric map provided in any of the formats supported by ITK, such as NRRD or NIFTI, as a DICOM Parametric Map image object.

Usage

   --inputDICOM <std::string>
     File name of the DICOM image file that should be used to populate the
     composite context (attributes related to the patient and imaging
     study).

   --outputDICOM <std::string>
     File name of the DICOM Parametric map object with the result of the
     conversion.

   --inputMetadata <std::string>
     File name of the JSON files containing metadata attributes.

   --inputImage <std::string>
     File name of the parametric map image in a format readable by ITK
     (NRRD, NIfTI, MHD, etc.).

Detailed usage

Most of the effort will be required to populate the content of the meta-information JSON file. Its structure is defined by this JSON-Schema file. Interpretation of JSON-Schema may require some effort, especially considering that this particular file uses externally defined items. It may be easier to start with an example JSON file that "instantiates" this schema, such as this one.

In the following, we will guide you through the contents of this file - line by line.

{
  "@schema": "https://raw.githubusercontent.com/qiicr/dcmqi/master/doc/schemas/pm-schema.json#",

  "SeriesDescription": "Apparent Diffusion Coefficient",
  "SeriesNumber": "701",
  "InstanceNumber": "1",
  "BodyPartExamined": "PROSTATE",

These lines correspond to the metadata attributes that will be populated in the resulting DICOM Parametric Map image object. It is your choice how you want to populate those. There are certain constraints on the values of these attributes. If those constraints are not met, converter will fail. In the future, we will provide instructions for validating your meta-information file.

  "QuantityValueCode": {
    "CodeValue": "113041",
    "CodingSchemeDesignator": "DCM",
    "CodeMeaning": "Apparent Diffusion Coefficient"
  },
  "MeasurementUnitsCode": {
    "CodeValue": "um2/s",
    "CodingSchemeDesignator": "UCUM",
    "CodeMeaning": "um2/s"
  },
  "MeasurementMethodCode": {
    "CodeValue": "DWMPxxxx10",
    "CodingSchemeDesignator": "99QIICR",
    "CodeMeaning": "Mono-exponential diffusion model"
  },
  "SourceImageDiffusionBValues": [
    "0",
    "1400"
  ],
  "AnatomicRegionSequence": {
    "CodeValue": "T-9200B",
    "CodingSchemeDesignator": "SRT",
    "CodeMeaning": "Prostate"
  },
  "FrameLaterality": "U",
  "RealWorldValueSlope": 1,
  "DerivedPixelContrast": "ADC"
}

QuantityValueCode, MeasurementUnitsCode, MeasurementMethodCode, AnatomicRegionSequence are attributes (code tuples) to describe the meaning the pixels stored in this parametric map. AnatomicRegionSequence, DerivedPixelContrast, FrameLaterality are the only attributes that are required. All others are optional.

Each code tuple consists of the three components: CodeValue, CodingSchemeDesignator and CodeMeaning. CodingSchemeDesignator defines the "authority", or source of the code. Each CodeValue should be unique for a given CodingSchemeDesignator. CodeMeaning is a human-readable meaning of the code. DICOM defines several coding schemes recognized by the standard listed in PS3.16 Section 8.

This tool can be used to convert a DICOM Parametric Map Image object into ITK image format, and generate a JSON file holding meta information.

Usage

   -t <nrrd|mhd|mha|nii|nifti|hdr|img>,  --outputType <nrrd|mhd|mha|nii
      |nifti|hdr|img>
     Output ITK format for the output image. (default: nrrd)

   --outputDirectory <std::string>
     Directory to store parametric map in an ITK format, and the JSON
     metadata file.

   --inputDICOM <std::string>
     File name of the DICOM Parametric map image.

Examples of DICOM Parametric map objects

You can experiment with the converter using the following objects:

• ADC map image of the prostate (zip archive)

dcmqi provides command line tools to convert results of post-processing of the image data, such as by applying certain model to the data, into DICOM format. As an example, Apparent Diffusion Coefficient (ADC) maps derived by fitting various models to the Diffusion-Weighted Magnetic Resonance Imaging (DW-MRI) data have been shown promising in characterizing aggressiveness of prostate cancer. The result of conversion is DICOM Parametric map object.

Mandatory metadata that needs to be specified to enable conversion include:

• Quantity being measured

• Units of the quantity being measured

• Measurement method

Each of these items, in addition to some other attributes, must be specified using coded values. An example of the metadata file is available here.