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SegmentationFileFormat.md

File metadata and controls

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File formats for image segmentations

Commonly used file formats

DICOM

DICOM allows saving image segmentations along with rich, structured metadata in a standard, very well documented way in DICOM Segmentation.

Pro:

  • Compatibility with clinical software: DICOM is universally supported by all clinical imaging softare, DICOM Segmentation is not very widely supported but its adoption is increasing.
  • Long-term stability: DICOM format is changed very slowly and carefully
  • Rich, structured metadata storage, all defined carefully in the DICOM standard

Con:

  • Standard is very large, complex
  • Low performance: size of segmentation metadata may be huge (magnitudes larger than the segmentation data itself), encoding and decoding can be magnitudes slower compared to simple 3D image formats

NRRD

Very simple and efficient file format for storing multi-dimensional images. 3D Slicer and related software established convention for storing segmentation metadata (commonly referred to as .seg.nrrd files).

Pro:

  • Very simple
  • Compatibility with research software and toolkits: most libraries and research application support this file format
  • Common convention exists for storing essential metadata
  • File header is human-readable: easily readable, modifiable with any text editor

Con:

  • Not compatible with clinical software
  • Common conventions for metadata storage only include essential metadata (not as rich or structured as DICOM)

NIFTI

Very limited, yet complex and ambiguous file format. Unfortunately, for historical reasons, it is commonly used in medical image computing.

Pro:

  • Compatibility with research software and toolkits: most libraries and research application support this file format
  • Somewhat simple: simpler than DICOM, but much more complex than NRRD
  • It can store some neuroimaging-specific metadata in a standard way: this makes the file format beneficial for neuroimaging

Con:

  • Orientation definition in NIFTI files can be ambiguous: there are multiple ways to define orientation, they can be both present, and contain contradicting information. Various softare will interpret these ambiguous files differently. See for example these discussions: 1, 2, 3
  • Not compatible with clinical software
  • Common convention for storing essential metadata does not exist
  • File header is not human-readable: you cannot use a text editor/viewer to see the actual file header but you always have to rely on a parser to give you an interpretation of the file header

Recommended file formats

  • DICOM format is recommended for long-term archival due to compatibility and stability of the file format and the ability to encode rich, structured metadata in a well-defined manner.
  • NRRD file format is recommended for local storage and data exchange, due to its simplicity, efficiency, and non-ambiguity.
  • NIFTI format usage may be justified for neuroimaging, as many neuroimaging pipelines only support this format.