DICOM
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General description
DICOM (Digital Imaging and Communications in Medicine) is far and away the most widely-used (and probably the oldest) electronic file format in medical imaging. Nearly every device that acquires medical images -- ultrasound, CT, PET, and MRI -- acquire DICOM images in normal operation. There's a 20-part specification detailing the file format and its ecosystem. The IANA has assigned TCP and UDP port 104 to DICOM-related traffic.
It's kind of a big deal.
However, as with any sufficiently-adopted standard, there are splinter factions. The most common format is 2-dimensional images or "slices" that can be formed into a 3-dimensional image; however, some manufacturers have extended the standard to save 3 or even 4-dimensional images in a "mosaic" format.
File format
While there are many complications involved in decoding a DICOM file, fundamentally it is simply a sequence of data blocks called attributes or elements. Each attribute contains a 16-bit group number and a 16-bit element number, conventionally written in hexadecimal and separated with a comma, e.g. (0028,0011).
Standard attributes
If an attribute's group number is even, then it is a standard attribute defined in the DICOM specification, and the group and element number together uniquely identify the meaning of the attribute.
Private attributes
If the group number is odd, then it is a private attribute, and it will have been preceded by a special attribute supplying a "private creator" identification string. A private attribute is uniquely identified by the combination of its creator identifier, group number, and the low byte of its element number.
Some examples of creator identifiers are GEMS_IMAG_01 and Philips Imaging DD 001. An identifier is usually specific to a manufacturer of medical equipment, not to a particular medical device. Unfortunately, instead of having one specification per manufacturer, private attributes are usually only documented in device-specific "DICOM Conformance Statements", which list only the attributes used by that one device.
Examples of DICOM Conformance Statements (search the documents for "private creator"):
Compilations:
Image data
If a DICOM file contains image data, it contains either a single image, or a video clip (usually composed of multiple still images all having the same size and color format). There is an extension called Papyrus that can store multiple different images in a single file.
The image format is determined by attribute (0002,0010): Transfer Syntax UID. Defined formats include
- Run-length encoding: UID 1.2.840.10008.1.2.5
- DEFLATE: UID 1.2.840.10008.1.2.1.99
- JPEG (lossy): UID 1.2.840.10008.1.2.4.50, etc.
- Lossless JPEG: UID 1.2.840.10008.1.2.4.57, etc.
- JPEG-LS: UID 1.2.840.10008.1.2.4.80 and .81
- JPEG2000: UID 1.2.840.10008.1.2.4.90, etc.
- MPEG2, MPEG4: UID 1.2.840.10008.1.2.4.100, etc.
Software
Software that reads DICOM files is pretty much everywhere. Most neuroimaging analysis packages have some way of importing DICOMs and turning them in to a higher-dimensional file; open-source stand-alone libraries abound, as well.
- PyDICOM
- dcm2nii
- Grassroots DICOM
- Philips DICOM Viewer For Microsoft Windows. Linked to in the sidebar of pages such as this one.
