fw-gear-nifti-to-dicom 0.5.0

Convert NIfTI1 to DICOM

NIfTI to DICOM (nifti-to-dicom)

Overview

Usage

Summary

The NIfTI to DICOM gear is a Flywheel gear for the conversion of NIfTI images into DICOM format. This gear takes as required input a NIfTI file and includes an optional input for a template DICOM. If a DICOM is not input and find_dicom_in_container is enabled, the gear will search for a template DICOM at runtime. If a template DICOM is not provided, the gear will look for a JSON sidecar corresponding with the input NIfTI.

Cite

None

License

License: MIT

Classification

Category: Converter

Gear Level:

• Project
• Subject
• Session
• Acquisition
• Analysis

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[[TOC]]

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Inputs

• nifti-file
  • Name: nifti-file
  • Type: NIfTI File
  • Optional: False
  • Description: A NIfTI file to be converted to DICOM
• dicom
  • Name: dicom
  • Type: DICOM File
  • Optional: True
  • Description: A template DICOM to be used to populate DICOM tags.
  • Notes: All public DICOM tags from the file are used to populate the output DICOM tags, except SeriesInstanceUID is replaced - by default with a deterministic UID generated from subject/session/acquisition labels and the NIfTI filename (not the original), or with the reference DICOM's own SeriesInstanceUID if match_series_instance_uid is enabled - Value1 of ImageType is set to DERIVED, and Value2 of ImageType is set to SECONDARY

Config

• allow_no_sidecar
  • Name: allow_no_sidecar
  • Type: bool
  • Description: Allow for conversion to continue even if neither a DICOM nor a JSON sidecar is found, or if the found JSON sidecar does not have ImageOrientationPatientDICOM. WARNING: Unexpected orientation output may occur.
  • Default: False
• copy_metadata_from_dicom
  • Name: copy_metadata_from_dicom
  • Type: bool
  • Description: Copy Flywheel File metadata (modality, classification, info, tags) from template DICOM to output DICOM
  • Default: False
• debug
  • Name: debug
  • Type: bool
  • Description: Log debug statements
  • Default: False
• find_dicom_in_container
  • Name: find_dicom_in_container
  • Type: bool
  • Description: Search NIfTI parent acquisition container for a DICOM file. If a DICOM is already provided as input, this option is ignored. Otherwise, if a DICOM is not found, gear fails. If more than one DICOM is found, gear will use the DICOM with shortest filename.
  • Default: False
• force_16_bit
  • Name: force_16_bit
  • Type: bool
  • Description: Force output to be 16-bit (either UInt16 or Int16, depending on input).
  • Default: False
• overwrite_dicom
  • Name: overwrite_dicom
  • Type: bool
  • Description: Overwrite input template DICOM file. If template DICOM is not present in the same acquisition container as the NIfTI input, the output DICOM will be named to match the template DICOM file but will be saved in the NIfTI acquisition container. If no DICOM file is input/found, this option is ignored.
  • Default: False
• tag
  • Name: tag
  • Type: str
  • Description: Tag to be added to output DICOM file.
  • Default: "nifti-to-dicom"

Outputs

Files

• Converted DICOM
  • Name: Converted DICOM
  • Type: DICOM File
  • Optional: False
  • Description: The result of converting the input NIfTI to DICOM

Metadata

If copy_metadata_from_dicom is enabled and a DICOM file is provided to the gear, either as as input or by enabling find_dicom_in_container, the Flywheel file metadata from the template DICOM will be copied to the output file. This includes modality, classification, info, and tags.

Pre-requisites

Prerequisite Gear Runs

No prerequisite gear runs are required for running nifti-to-dicom.

Prerequisite Files

To run this gear with a template DICOM, the DICOM must either exist within the same acquisition container as the input NIfTI or be provided to the gear as input.

To run this gear with a JSON sidecar, either a JSON sidecar must exist within the same acquisition container as the input NIfTI and have a matching filename (i.e example.nii.gz matches example.json), or a JSON file named nifti_to_dicom_config.json must exist at the project level.

Prerequisite Metadata

If using the sidecar method and no "modality" exists in the JSON, the gear looks at first the input NIfTI file modality and then the sidecar's file modality. To ensure that the approriate SOPClassUID is set on the output file, check the JSON sidecar for "modality" and, if it does not exist, update the NIfTI file's modality to the correct modality. As a fallback, output DICOM files are set to "MR" (SOPClassUID: "1.2.840.10008.5.1.4.1.1.4").

The copy_metadata_from_dicom configuration option allows for copying Flywheel File metadata from the template DICOM to the output DICOM. If this option is selected, the template DICOM file metadata should exist in the state in which the user wants it copied. The modality, classification, info, and tags are copied from the template DICOM.

Usage

The NIfTI to DICOM gear converts NIfTI images to DICOM format using either an associated JSON sidecar or a template DICOM.

The optional template DICOM can be input explicitly as the dicom gear input, or the config option find_dicom_in_container can be enabled to tell the gear to search the parent acquisition container of the NIfTI image for a DICOM file. When searching for the DICOM file, the gear currently selects the DICOM with the shortest filename in the acquisition container.

If a template DICOM is used, all public DICOM tags from the DICOM are used to create the converted DICOM, except a new SeriesInstanceUID is generated, Value1 of ImageType is set to DERIVED and Value 2 is set to SECONDARY, see DICOM standard.

If a DICOM is not input or found, the gear will look for a JSON sidecar to populate metadata. The gear first searches the acquisition container of the nifti file input for a JSON file with a filename that matches the NIfTI file (example.nii.gz matches example.json). If a match is not found, the gear then searches the parent project for a file named nifti_to_dicom_config.json.

If neither a DICOM nor a JSON file is available to the gear at runtime, or if the found JSON file does not include ImageOrientationPatientDICOM, by default the gear fails. To override this safety measure, allow_no_sidecar can be enabled. When allow_no_sidecar is True and ImageOrientationPatientDICOM is not available to the gear, the conversion will continue and the output orientation will be set to the input NIfTI orientation. This may result in unexpected orientation outcomes.

Limitations

• Pixel Data type: Currently this gear does not handle NIfTI pixel data with complex values, or RGB values.
• Dimensions: Supports both 3D and 4D NIfTI input.
  • 4D conversion with a reference DICOM requires a genuine round-trip: the reference DICOM series must be the same acquisition the NIfTI was itself derived from (matching instance count and volume/slice structure), not an arbitrary or unrelated DICOM series - the gear pixel-matches NIfTI volumes back to reference DICOM instances and will fail validation otherwise.
  • 4D conversion without a reference DICOM requires a JSON sidecar with enough information to determine the 4th dimension's meaning (RepetitionTime for time-series, PET frame-timing fields, or an accompanying .bval/.bvec pair for diffusion) - see the nifti_4d_dimension config option. If neither a reference DICOM nor a sufficient JSON sidecar is available, the gear fails with a clear error rather than guessing.
  • Some 4D MR acquisition types aren't yet validated for sidecar-only conversion: ASL/perfusion is rejected outright with a clear error, and cardiac-gated cine isn't distinguished from an ordinary time-series and may be misclassified.
• Orientation:
  • When only a sidecar is provided, the gear uses ImageOrientationPatientDICOM in the JSON to re-orient the NIfTI. This field must be present for correct orientation.
  • Additionally, the ImageOrientationPatientDICOM field only carries in-plane information, not plane to plane. So the z-axis is calculated using a cross-product of the first two columns of this matrix. There may be some cases where the z-direction needs to be further flipped, but it is not clear when.
• Multiframe reference DICOM: When a DICOM is input, all of the tags that are consistent throughout the DICOM header are copied into the output DICOM. This method was developed for use with DICOM archives (zip files of multiple individual DICOM slices) and using a multiframe DICOM may result in unintended tags being copied over to the output DICOM.
• Modality: Currently, the gear supports MR, CT, OPT, and PET modalities when using the sidecar conversion method. To use a modality outside of this list with the sidecar conversion method, manually add "SOPClassUID" and "MediaStorageSOPClassUID" to the JSON Sidecar according to the DICOM standard value.

Workflow

graph LR;
    A[NIfTI]:::input --> D;
    B[DICOM] -->|optional| D;
    C[JSON sidecar] -->|optional| D
    A -->|Input as `nifti-input`| E

    D[Acquisition Container]:::container --> E((Gear));
    E:::gear -->|Output saved back to parent acquisition| D;

    classDef container fill:#57d,color:#fff
    classDef input fill:#7a9,color:#fff
    classDef gear fill:#659,color:#fff

1. Upload NIfTI file to Acquisition container
2. Optionally, upload corresponding JSON sidecar to Acquisition container
3. Optionally, upload template DICOM to Acquisition container
4. Select NIfTI file within Acquisition container as input to gear
5. Confirm configuration options
6. Gear places converted DICOM file within same Acquisition container

Logging

The nifti-to-dicom gear logs various messages throughout the gear run to help the user know what the gear is doing and if any errors are encountered.

Testing

The nifti-to-dicom gear is tested both with pytest unit tests as well as an end-to-end Jupyter Notebook testing suite within the Scientific Solutions gear-testing repository to ensure consistent, reliable outcomes.

Contributing

For more information about how to get started contributing to this gear, check out CONTRIBUTING.md.