The DICOM Reader provides FME with access to data in the DICOM format.
Overview
DICOM (Digital Imaging and Communications in Medicine) is a standard for the storage and transmission of medical imagery, along with associated metadata. DICOM files can contain a wide variety of medical image types, such as MRI, CT Scan, Ultrasound, and many more modalities. These images are registered in a local coordinate system, but there is currently no support for georeferencing information.
DICOM files are organized in a hierarchical structure:
|
Patient |
A person or animal |
|
Study |
A group of related imaging procedures |
|
Series |
A single series of images, captured sequentially |
A DICOM dataset often contains multiple series, each of which belongs to a study. The dataset may also contain multiple studies, each belonging to a particular patient.
Each DICOM file has metadata in the form of tags. Tags store data about the patient, the procedure, the device that captured the image, and variety of other details. FME treats these metadata tags as feature attributes. Tags can be identified by a keyword, or by a pair of hexadecimal numbers. For example, the tag (0008|0060) is known by the keyword Modality, and it contains a code corresponding to type of image in the file (such as MR for Magnetic Resonance Imaging or CT for Computed Tomography).
In addition to the set of tags defined by the DICOM specification there are also “Private” tags, which are defined by the manufacturer of the imaging device that produced the DICOM files.
FME has two DICOM readers. Each reader has a different strategy for associating DICOM files:
- DICOM_FILE Reader – Reads a single DICOM image or DICOMDIR index file for one or more folders of DICOM images.
- DICOM_DIR Reader – Reads all DICOM files in a single specified folder, and is primarily useful when a DICOMDIR file does not exist for reading.
DICOM_FILE Reader Overview
The DICOM_FILE Reader considers a single DICOM image file or a DICOMDIR file to be a dataset.
If the file is a DICOM image file, then it contains pixel data for one or more image frames. Each image frame in the file will be treated as an FME raster feature.
Otherwise, if the file is a DICOMDIR index file, then it contains information about a set of DICOM image files in the same folder or in subfolders next to the DICOMDIR file. In this case, the DICOM_FILE Reader will read one or more FME raster features from each image file described in the DICOMDIR file.
DICOM_DIR Reader Overview
The DICOM_DIR Reader considers all of the DICOM image files in a single folder to be a dataset. The DICOM_DIR Reader will read one or more FME raster features from each DICOM image file in the folder.
FME Raster Features
FME raster features represent raster data and use several concepts that are unlike those used in the handling of vector data.
For comprehensive information about how FME processes raster data, see Rasters.
DICOM files can contain rasters with a variety of interpretations. Commonly, they will contain a single numeric band of signed/unsigned integers (8-, 16-, 32- or 64-bit), or floating-point values (32- or 64-bit). Other times, they may contain RGB or RGBA multi-band rasters (8 or 16 bits per band).