DICOM (Digital Imaging and Communications in Medicine) refers to a broad and complex set of standards for medical images and related information. We gratefully acknowledge support from the NIAID for ChimeraX development related to medical image analysis.
ChimeraX can read many but not all DICOM files. Errors may arise from trying to read types of data that are not yet handled properly, such as screen captures, non-axial series, and series encoded with 16-bit lossless jpeg. ChimeraX can also read the NIfTI (.nii) and NRRD (.nrrd) formats often used for medical images.
See also: ChimeraX DICOM Reference, Download DICOM, DICOM Browser, DICOM Metadata, DICOM in VR tutorial, ChimeraX for Medical Image Analysis
In ChimeraX, DICOM format is indicated by the filename suffix .dcm or the format dicom option in the open command.
Menu: File... Open DICOM Folder – in the resulting dialog, browse to location, choose directory, click Choose
– or –
click in the Medical Image tab of the Toolbar – in the resulting dialog, browse to location, choose directory, click Choose
– or –
Command: open directory-pathname format dicom
...where directory-pathname may contain * as wildcard and should be enclosed in quotation marks if it includes spaces. Each image stack found will be opened as a separate model.
Menu: File... Open, browse to location, click first file, Shift-click last file to select the entire set, click Open...where pathname-glob specifies the name and location of multiple files, typically using * as wildcard and enclosed in quotation marks if it contains spaces.
– or –
Command: open pathname-glob
The open command verbose option shows detailed debugging information for DICOM input.
In general, 3D maps described as image series are read (DICOM modalities CT, MR, RTDOSE, etc.).
Some DICOM files contain 4D data or time series that can be played with the time slider shown automatically by ChimeraX or with the vseries command.
Some DICOM files contain SEG objects (segmentations as binary maps), and these are automatically associated with the corresponding image series to synchronize plane display. They can also be displayed as isosurfaces, for example: volume #22.214.171.124.5 show style surf level 1 region all
Radiotherapy structure set (RTSTRUCT) contours are also read and displayed.
DICOM files also contain associated information (metadata). This information is not shown automatically when the files are opened, but can be displayed with the DICOM Browser and DICOM Metadata tools.
Models read from DICOM are arranged in a hierarchy, as shown in the Model Panel:
The DICOM Browser also shows the hierarchy.
Each volume data model read from DICOM is initially displayed as a single Z plane in the “image” style. DICOM-specific defaults for image-style rendering correspond to the volume command options: