Install DCMTK (the DICOM Toolkit).

The recommended way to prepare DICOM files for 3D modeling and surface reconstructions in PS is to create for each patient a folder named DCMTK which contains an HFS AXIAL study series with slice spacing < 1 mm and consisting of 16-bit MONOCHROME DICOM files with little endian Transfer Syntax UID (tag 0002,0010 = 1.2.840.10008.1.2) that have been converted to .xml file format. XML (Extensible Markup Language) is a modern, cross platform, native file format of MacOS that supports both text and embedded binary data (e.g. using base64 encoding) and hence is used extensively by both MacOS and all PS file operations. XML is a markup language similar to HTML, but without predefined tags. Instead, a user defines their own tags designed specifically for their needs. This is a powerful way to store data in a format that can be stored, searched, and easily shared over networks.

The DICOM toolkit DCMTK is a collection of cross platform libraries and applications implementing large parts the DICOM standard for Unix operating systems including MacOS. To install DCMTK you must first install a package manager for MacOS such as Homebrew. Follow the instructions on the Homebrew web site. Once you have installed Homebrew, you can then install DCMTK from a MacOS terminal window using the command brew install dcmtk. Be sure to make note of the Unix file path at which DCMTK was installed, it may differ slightly depending upon your version of MacOS. The file path is typically something like usr/local/bin. If you have successfully installed DCMTK and PS can find it, the indicator button on the right of the Multiplanar Reconstruction (MPR) window status line will be green. If the button is red you will need to customize the file path to DCMTK in PS Folders Preferences. Click the red button to take you to the folder preferences window.

Create a DCMTK Folder for Default Pixel Data.

With the DCMTK toolkit installed and located:

  1. Launch PS6 and select the MPR window. Thw window will likely be empty as illustrated below. The DCMTK indicator icon on the right of the window toolbar should be green indicating that the DICOM toolkit is installed and reachable. PS version 6.8.6 and later supports the dragging & dropping of folders containing DICOM images onto the MPR window which in turn will launch appropriate Unix shell scripts that interact with dcmtk functions. PS version 6.8.7 adds optional dcmtk drop zones, supports additional dcmtk functions such as dcmconv which converts old DICOM files that are missing a preamble and/or group 2 meta header, and displays transfer syntax in the window status line during the drag along with a suggestion regarding which drop zone to use to prepare the images. By default, the drop zones are hidden but will appear in response to dragging a folder onto the window. Click the DCMTK drop zones button to toggle display of the drop zones and regain screen space once the dcmtk functions are no longer needed.
  2. EmptyWindow
  3. For each patient, create a study series folder named DICOM (note: folder names CT, MRI and DJPEG are also allowed) somewhere other than at the 1st level of your patient folder and place within it an HFS AXIAL series of DICOM files (e.g. xxx.dcm). The DICOM folder should contain only the images that comprise a single study series. In this example we have a patient folder Tutorial2022, Posterior and within it we have created a sub-folder named originals in which to store materials of interest to this patient, but which are to be ignored when dragging the patient folder onto the PS Image window. The PS Image window ignores sub-folders other than those with special names such as DCMTK or RAW when searching a dragged folder for images. Within the sub-folder originals we have created a study series folder named DICOM, and within the DICOM folder are a series of DICOM (.dcm) files. All of the .dcm files should belong to the same series and use the default little endian DICOM Transfer Syntax UID (tag 0002,0010 = 1.2.840.10008.1.2).
  4. DICOM1
  5. Drag the DICOM folder onto the MPR window of PS6. PS6 will create a new folder (in the same location as the original folder) named DCMTK that contains .xml versions of all the DICOM files that were found in the DICOM folder. This is done using the dcm2xml function that is part of the DCMTK toolkit.
  6. DCMTK1
  7. Drag the DCMTK folder to the 1st level within your patient folder along with any other ophthalmology imaging files such as b-scans US1, US2, and fundus images optomap, misc# and so on... With a DCMTK folder at the 1st level with a patient folder, there is no longer any need to manually export planar reconstructions such as Axial, Sagittal, Equator, t-Coronal and t-Meridan from OsiriX or Horus although you may still do so.
  8. DCMTK2
  9. You can either manually drag a DCMTK folder onto the MPR window to load its images, or you may simply drag the patient folder itself onto the Image window as is usually done when intializing a new patient plan. Once a DCMTK folder has been parsed and its images loaded you will be presented with the MPR Calibration Sheet. You can review the metadata tags of the image series in this sheet.
  10. Step5
  11. Close the MPR Calibration Sheet and you can begin 3D eye modeling.
  12. Step6