Program Summary Walk Through of the Overview

 

Installation

You must correctly locate R. You can also locate the file model.ikl and any OSEM style files you may wish to use. If you do not wish to alter model.ikl you can allow the internal version to be used. If you do not wish to use OSEM style files or only only wish to use standard layouts of them, you do not need to create and store them. See -OS option later.

R program must be present somewhere on your path. model.ikl (if used) should be in the directory named in IMAGEDIRECTORY environment variable. OSEM style files (if used) must be in a subdirectory named OSProj of the directory named in IMAGEDIRECTORY environment variable. OSEM style files have the following naming requirements. The extension of the file is the number of projections with leading zero (if required) to make three characters. e.g. for 64 projections the file is named ARBITRARY.064. When you specify -OS:stylefile to use this style file, you would use -OS:ARBITRARY. The number of projections, taken from the other options, will be automatically appended.

Certain environment variables should be set or their defaults known.

IMAGEDIRECTORY

This points to the location of the model.ikl file and the OSProj subdirectory. Default value is current directory. The model.ikl file contains a list of all the Interfile keys. If the file does not exist an internal version will be used. The OSProj directory contains all the OSEM style files. These are only used by the -OS option for non-standard OSEM layouts.

 

PROCESSORS

Number of processors available on your system. R will make use of multiple parallel threads, where appropriate, when there is more than a single processor available. Default value is 1.