PET-CT plugins to fiji Files

For a general overview see http://petctviewer.org/

The recommended method is to download BI quick user guide.pdf. This contains detailed instructions, including youtube demos, showing exactly how to set up everything. Another possibility is to go to http://fiji.sc/User:Ilan and follow the instructions there. Finally there is the now outdated method which is more cumbersome and is described below.

(Old proceedure) As a convenience for new users there is a newUser.zip file. It is simpler for new users just to download this file and unzip its contents. Inside it there are simplified instructions. (For ImageJ users, please read ImageJ_Installation.txt.) Alternatively you may continue to read the instructions below.

There are 5 separate plugins:
1) Pet_Ct_Viewer.jar for display of PET/SPECT - CT/MRI studies, including fusion of the modalities.
2) Read_CD.jar is for reading studies from a CD/DVD as well as from a general location.
3) Gastric_Emptying is a standard Nuclear Medicine program for gastric emptying, renal clearance, Save As Dicom and "postage stamps".
4) Read_ClearCanvas_Studies.jar is for reading DICOM studies from the Clear Canvas database.
5) Read_BI_Studies is for reading and writing DICOM studies to our database.

Contact ilan.tal@gmail.com for questions.
Copy the jar file (Pet_Ct_Viewer.jar) , or files (Pet_Ct_Viewer.jar + Read_CD.jar + Gastric_Emptying.jar + Read_ClearCanvas_Studies.jar + Read_BI_Studies.jar) into the Fiji, plugins directory.

On my machine there is a Fiji.app directory, under which is the plugins directory.
The lib directory is somewhat out of date. On Fiji the automatic download described in BI quick user guide will automatically update the lib files to more recent versions. Only if you are installing to an ImageJ and not to Fiji will you need this directory. In the case of ImageJ, copy the lib directory into the plugins directory.
(If you prefer, you may copy the contents of the lib directory directly into the jars directory. The jar files in the lib directory MUST be present, but they need not be in the subdirectory "lib". The files in the lib directory include infovis.jar, vecmath-1.5.2.jar and japng.jar. These must be available to Pet_Ct_Viewer.jar.)

When you operate Fiji additional menu items will appear, to allow use of the plugins. Read_CD and Read_ClearCanvas will appear under File->Import.

Automatic update of all jar files is available by using http://fiji.sc/Update_Sites.  This replaces PluginsUpdater.jar and StartupMacros.txt.

There is a very useful set of plugins written by Tony Parker. It is recommended to install these in your copy of Fiji. They are not copied to this site but can be found at: http://www.med.harvard.edu/JPNM/ij/plugins/TPcollection.html.

Note: there is no need to copy this readme file to the target system.