Workshop day 3

From I Do Imaging
Jump to: navigation, search

PACS Server

We will be installing a PACS server to send and receive DICOM images. An excellent resource on DICOM communications is Understanding DICOM with Orthanc

Install Orthanc and then optionally configure it with a known AE Title and port number. Send a series of DICOM files to your PACS server.

Command Line

Some operations on medical images can be performed quickly and efficiently using the command line. Running programs from the command line requires more knowledge about the program, since options are not provided visually or through menus. At first, it takes a while to perform even simple tasks on the command line. With practice, however, the command line becomes a fast and powerful way to run programs.

Command-line programs are particularly common on Linux/Unix systems, since they are commonly used for servers and commercial applications. Most of these programs can also be run on the Mac, since MacOS has a fully Posix-compliant shell available through the Terminal. Knowledge of the command line is essential for professional users.

Excellent examples of powerful command-line applications are the dcmtk and dcm4che2/dcm4che3 toolkits for DICOM, and the Turku PET Utilities for ECAT.

Exercises

dcm4che3

Use the storescu program from dcm4che3 to test connectivity to an Orthanc server running on your workstation. dcm4che3 has been installed on your remote workstation, and is in your path.

  1. Start an Orthanc server with its default configuration. You can start it either from Windows Explorer, or from the command line.
  2. The text window that opens with Orthanc will display the AE Title and port number that Orthanc is using. If you are using the default configuration, the AE Title will be ORTHANC and the port will be 4242.
  3. As port 4242 is a non-standard port, it must be allowed through the Windows firewall. Check the firewall settings to ensure that Orthanc is allowed to communicate, either as an application or as a designated port (4242).
  4. Open a PowerShell or Cygwin command-line window.
  5. Check that the dcm4che3 directory is in your path by issuing the command storescu --help. If this program is in your path, you will get a long help response. The example at the end of the help text is a useful starting point.
  6. Query your Orthanc server: storescu -c ORTHANC@localhost:4242

Turku PET Utilities

Try the following programs:

lmhdr
Display the main header of an ECAT PET image, including patient and scanner information.
eframe
Display the frame and timing information of an ECAT PET image.
ecat2nii
Convert an ECAT PET image to NIFTI.