DICOM Files

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, ui view, DICOM in VR tutorial, DICOM segmentation 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.

• All of the DICOM files in a directory and its subdirectories can be opened in a single operation if the format is specified:

  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.

• Alternatively, multiple DICOM files comprising a single 3D image stack can be opened as follows:

  Menu: File... Open, browse to location, click first file, Shift-click last file to select the entire set, click Open
  – or –
  Command: open  pathname-glob

  ...where pathname-glob specifies the name and location of multiple files, typically using * as wildcard and enclosed in quotation marks if it contains spaces.

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 #1.1.1.1.5 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.

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DICOM Model Hierarchy

Models read from DICOM are arranged in a hierarchy, as shown in the Model Panel:

1. DICOM folder (if multiple patients)
2. patient (ID)
3. study (date)
4. series (description), each corresponding to a volume model, typically 3D imaging (e.g. CT, MRI) and derivations thereof (e.g., segmentations)

The DICOM Browser also shows the hierarchy.

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DICOM Initial Display Settings

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:

• projectionMode 3d
• colormapOnGpu true
• fullRegionOnGpu true
• appearance initial