Chapter 1 : Introduction

3DVIEWNIX is a data-, machine-, and application-independent software system developed by the Medical Image Processing Group, Department of Radiology, University of Pennsylvania, Philadelphia. It provides a variety of sophisticated methods for visualizing (being able to see), manipulating (being able to alter), and analyzing (being able to quantify) structure information captured in multidimensional, multimodality image data . This document describes in detail how these methods can be used in various applications to fulfill the objective of imaging. It does not describe the methods, the algorithms and their implementational details. These will be covered in another document. The number of possible processing paths through 3DVIEWNIX for visualizing, manipulating and analyzing multidimensional data is very large. The document will not describe them all. However, we describe each basic processing operation in sufficient detail so that the users will be able to explore them on their own. We will also make some specific recommendations as to the processing paths that we found that are best suited for several application situations.

The examples drawn for illustration are all from medical imaging . We hope the users will give their own application-specific interpretations and thereby be able to use 3DVIEWNIX operations in their own field.

3DVIEWNIX is based on the Unix operating system, X-Windows, and the C programming language. Data handled by 3DVIEWNIX are all represented in a protocol that is a multidimensional generalization of the ACR-NEMA (2.0) standards.

1.1 How To Use This Document

Section 2 describes the 3DVIEWNIX installation procedure. Systems managers or those who are responsible to install 3DVIEWNIX at your site should read that section. We recommend that all those who are interested in 3DVIEWNIX including end-users, developers, and imaging researchers, read Sections 1 and 3-7. In addition, if you are an end-user, you may study only those sections that describe the particular operations in which you are interested. For example, if your main concern is visualization, you may study Sections 1 and 3 to 7 and 10. However, this sort of partitioning cannot be done for several reasons. For example, the data have to be somehow brought into the 3DVIEWNIX system, and often, some form of preprocessing is required to visualize data. This implies that you will have to use some PORT-DATA and PREPROCESS commands, although you may not care about other commands under these headings. Another reason is that the main operations of visualization, manipulation and analysis cannot be compartmentalized independently of each other. Some form of visualization is always needed whatever is the 3D imaging operation. Therefore, a given operation is often available under more than one of these main headings. In addition to visualization, some simple forms of analysis are available under each of the three categories. Hence, to be able to decide which command is the best to realize a given operation, we advise the user to eventually become familiar with all major commands available in 3DVIEWNIX.

In each of the main chapters in this manual devoted to the description of a particular group of commands, we first describe how the commands and options that are common to the commands in the group work. This will be followed by a description of the remaining commands. Although straightforward description of commands in this manner is essential, that by itself may not reveal the powerful operations that are possible when the commands and options are combined in certain ways . Therefore, at the end of the description of certain complex commands, we give examples to illustrate how the command fits in in our overall scheme of operations. Additionally, in Chapter 14, we present "3D Imaging Recipes" that exemplify complex operations expressed as combinations of commands and options. They not only exemplify specific visualization, manipulation, and analysis procedures, but hopefully also serve to introduce the users to the nuances of 3DVIEWNIX so that they may on their own explore other operations in analogous ways.

User Manual Library Ref. Manual Tutorial