Main_Page

• Pet-Ct Viewer, Introduction
  • 2 ways to operate the program
• Read CD and other locations, Introduction
• Read BI database, Introduction
• Choose Fiji Startup program
• Read Clear Canvas Studies, Introduction
• Nuclear Medicine analysis

Pet-Ct Viewer, Introduction

See the general overview.

A common study in Nuclear Medicine is a PET-CT or a SPECT-CT study. The PET (Positron Emission Tomography) or SPECT (Single Photon Emission Computed Tomography) maps the area of radioactive absorption, and the CT (Computed Tomography) shows the anatomy of the body. These 2 images are overlaid as a fusion image showing the radioactive uptake on the background of the anatomy.

Sometimes MRI (Magnetic Resonance Imaging) is used in addition to the CT as another way to look at the anatomical structure. The MRI can also be fused with the radioactive uptake.

This program uses DICOM data already loaded into the Fiji viewer. The Opening dialog allows you to choose which series you wish to use.

2 ways to operate the program

1) Most commonly you will have both PET (or SPECT) together with CT (and maybe MRI) where the two datasets are to be fused. You choose at least 2 datasets and fusion will be available.

2) Sometimes there are cases where there is only PET or SPECT or CT. With only one dataset, fusion is impossible but you can still see the data in 3 orthogonal views.

Read CD and other locations, Introduction

One accepted method to import studies is drag and drop of folders containing the series of interest. The physicians found this trying and preferred to see the patient with his studies displayed allowing either the entire study or individual studies to be imported. This is generally from CDs from external hospitals but it also works for general locations, like camera folders on the server. A more detailed explanation is here

Read BI database, Introduction

At Beth Israel there is a miniPACS used to read, write and delete studies and reports. Outside BI the Orthanc server is more common. The presentation of studies is similar to Read CD and it will automatically bring up the Pet-Ct Viewer if the data read corresponds to a Pet-Ct study. A more detailed explanation is here or at Orthanc server.

Choose Fiji Startup program

You can choose which program will start whenever you restart Fiji.

Usually Read from CD is chosen, but another common choice is Read BI Studies which is used when reading from the Orthanc server. If you are using Fiji primarily for microscopy or something else, you may prefer the choice of None.

To setup the choice go to Fiji -> Plugins -> Nuclear Medicine -> Choose Startup Program...

Read Clear Canvas Studies, Introduction

The hospital considered using Clear Canvas to store studies. While Clear Canvas has some ability to activate Fiji, it is fairly limited. This plugin allows the parsing of the Clear Canvas xml files to allow a direct read of their stored DICOM files, without the necessity of first reading in the files into their software. In particular, this plugin will read the Clear Canvas data into Fiji and will automatically launch Pet-Ct Viewer if the data is suitable for it. A more detailed explanation is here

Nuclear Medicine analysis

Two programs have been ported over from the hospital programs. For more detailed explanations see Gastric Emptying and Renal Clearance.