3dviewnix 1.1 update (long)

Vision List Digest: Article 17, Volume 14, Issue 31
From: "Dr. Jie Tian"
Post-Followup: submission@VISLIST.com

The binaries in the FTP site constitute the official 1.1 version of 3DVIEWNIX
as it is sent out in the source code form to the receipients of 3DVIEWNIX.
Happy and useful 3D Imaging !



---------
3DVIEWNIX : A DATA-, MACHINE-, AND APPLICATION-
--------- INDEPENDENT SOFTWARE SYSTEM FOR THE VISUALIZATION
AND ANALYSIS OF MULTIDIMENSIONAL IMAGES


Below you will find extensive information on :

- 3DVIEWNIX Distribution Modes
- 3DVIEWNIX FTP demo version
- 3DVIEWNIX Datafiles
- 3DVIEWNIX User Manual
- 3DVIEWNIX Tutorials
- 3DVIEWNIX Features
- 3DVIEWNIX via World Wide Web (WWW).

If you have any questions, please contact us via e-mail at :

Vhelp@mipg.upenn.edu


Thank you for your interest in 3DVIEWNIX.


FROM THE MEDICAL IMAGE PROCESSING GROUP (MIPG), UPenn







============================
3DVIEWNIX DISTRIBUTION MODES
============================
We have created an FTP version for
the new 3DVIEWNIX 1.1 Version that can be anonymously FTPed from our
server --- mipgsun.mipg.upenn.edu. (130.91.180.111). You should go
to the directory : /pub/3dviewnix1.1/BINARIES. The new FTP version has
full functionality as the source code version that is distributed.

You may already know that 3DVIEWNIX has been picked
up as one of the TOP 10 GRAPHICS SOFTWARE PRODUCTS OF THE YEAR for 1993
by IEEE Computer Graphics and Applications (January 1993, pp. 87). In
order for more people to access the power of 3DVIEWNIX, we have
extensively changed our policy of distributing 3DVIEWNIX. We now have
the following modes of distribution.

---------------------------------------------------------------
| | Mode of Distribution |Copyright Restrictions |
---------------------------------------------------------------
| | | |
| 1. | 3dviewnix 1.1 (with source | Some restrictions |
| | code). $1000.00 | (see Confidentiality |
| | | Agreement #1) |
| | Full functionality | |
| | | |
---------------------------------------------------------------
| | | |
| 2. | 3dviewnix 1.1 (in binary | Very few restrictions |
| | form). $1000.00 | (see Confidentiality |
| | | Agreement #2) |
| | Full functionality | |
| | | |
---------------------------------------------------------------
| | | |
| 3. | 3dviewnix 1.1 (in binary | No restrictions |
| | form - via anonymous FTP). | |
| | FREE | |
| | | |
| | Full functionality | |
| | | |
---------------------------------------------------------------
| | | |
| 4. | A video tape demonstrating | No restrictions |
| | the functionality of 3DVIEWNIX| |
| | with numerous medical examples| |
| | (length 25 mins). $25.00 | |
| | | |
---------------------------------------------------------------


The two types of Confidentiality Agreement forms can be anonymously
FTPed from our server (mentioned above). They are in the directory :
/pub/3DVIEWNIX 1.1/3DVIEWNIX_ORDER_KIT.

You can access lots of goodies via anonymous FTP like MPEG movies
(/pub/3DVIEWNIX1.1/MPEG_MOVIES), 3DVIEWNIX data files
(/pub/3DVIEWNIX1.1/DATA), a list of 3DVIEWNIX papers and technical
reports (/pub/3DVIEWNIX1.1/PAPERS), 3DVIEWNIX Library Reference Manual
(/pub/3DVIEWNIX1.1/MANUALS), lots of filters for converting 3DVIEWNIX
files into other standard formats and vice versa
(/pub/3DVIEWNIX1.1/SRC).

There is a WWW home page on 3DVIEWNIX which can be accessed via Mosaic.
The URL is
http: //mipgsun.mipg.upenn.edu.

If you have any questions or concerns regarding 3DVIEWNIX, feel free to
contact us via e-mail : Vhelp@mipgsun.mipgsun.upenn.edu. You can reach
us by surface mail also:

Dr. Jayaram K. Udupa
Medical Image Processing Group
Department of Radiology
University of Pennsylvania
418 Service Drive - 4th Floor Blockley Hall
Philadelphia, PA 19104-6021

Phone : (215) 662-6780
FAX : (215) 898-9145


=========================
3DVIEWNIX 1.1 FTP Version
=========================


1. The FTP account can be accessed as follows:

Hostname: ftp.mipg.upenn.edu (IP address: 130.91.180.111 or 130.91.180.114)
Username: anonymous
Password: your e-mail address


2. Once you are logged in, type the following command:

% cd /pub/3DVIEWNIX1.1/BINARIES



3. Set the transfer mode to 'binary' by typing the command:

% binary


4. Files for SUN, SGI, PC and HP platforms are available in this directory.
Depending on the architecture of your platform you should 'get'
the appropriate one by typing the following command:

% get 3dviewnix_1_1_sgi_4_0_5C.tar.Z
(for Silicon Graphics machines running IRIX 4.x)
or
% get 3dviewnix_1_1_sgi_5_2.tar.Z
(for Silicon Graphics machines running IRIX 5.x)
or
% get 3dviewnix_1_1_sun_sunos4_1_3U1.tar.Z
(for Sun SPARC machines running SunOS 4.1.x)
or
% get 3dviewnix_1_1_sun_solaris2_3.tar.Z
(for Sun SPARC machines running Solaris 2.x (SunOS 5.x))
or
% get 3dviewnix_1_1_pc_linux_0_99_11.tar.Z
(for PCs running Linux 0.99.11 or higher)
or
% get 3dviewnix_1_1_hp_hpux_9_05.tar.Z
(for HP 9000/700 series machines running HP-UX 9.x)



5. Once the file is transferred type the command:

% quit


6. Now that you are back in your own machine you have to uncompress
the transferred file by issuing the command:

% uncompress 3dviewnix_1_1_sgi_4_0_5C.tar.Z
(for Silicon Graphics machines running IRIX 4.x)
or
% uncompress 3dviewnix_1_1_sgi_5_2.tar.Z
(for Silicon Graphics machines running IRIX 5.x)
or
% uncompress 3dviewnix_1_1_sun_sunos4_1_3U1.tar.Z
(for Sun SPARC machines running SunOS 4.1.x)
or
% uncompress 3dviewnix_1_1_sun_solaris2_3.tar.Z
(for Sun SPARC machines running Solaris 2.x (SunOS 5.x))
or
% uncompress 3dviewnix_1_1_pc_linux_0_99_11.tar.Z
(for PCs running Linux 0.99.11 or higher)
or
% uncompress 3dviewnix_1_1_hp_hpux_9_05.tar.Z
(for HP 9000/700 series machines running HP-UX 9.x)



7. The next step is to 'untar' the file:

% tar xvf 3dviewnix_1_1_sgi_4_0_5C.tar
(for Silicon Graphics machines running IRIX 4.x)
or
% tar xvf 3dviewnix_1_1_sgi_5_2.tar
(for Silicon Graphics machines running IRIX 5.x)
or
% tar xvf 3dviewnix_1_1_sun_sunos4_1_3U1.tar
(for Sun SPARC machines running SunOS 4.1.x)
or
% tar xvf 3dviewnix_1_1_sun_solaris2_3.tar
(for Sun SPARC machines running Solaris 2.x (SunOS 5.x))
or
% tar xvf 3dviewnix_1_1_pc_linux_0_99_11.tar
(for PCs running Linux 0.99.11 or higher)
or
% tar xvf 3dviewnix_1_1_dec_osf1_V3_0.tar
(for DEC Alpha machines running OSF1 V3.0)
or
% tar xvf 3dviewnix_1_1_hp_hpux_9_05.tar
(for HP 9000/700 series machines running HP-UX 9.x)



Follow further instructions given in the README file.
We hope you find the demo version of 3DVIEWNIX 1.1 both interesting
and useful. If you have any comments/suggestions on how we can improve
this demo version of 3DVIEWNIX 1.1, please send us an e-mail at :

Vhelp@mipg.upenn.edu



===================
3DVIEWNIX Datafiles
===================

The data sets for this demo version of 3DVIEWNIX 1.1 are in separate
compressed tar files. There are three data sets available via anonymous
FTP : DATA SET X (3dviewnix_1_1_data_x.tar.Z), DATA SET Y
(3dviewnix_1_1_data_y.tar.Z) and DATA SET Z (3dviewnix_1_1_data_z.tar.Z).
For most people DATA SET X should be sufficient to test all the modules
in 3DVIEWNIX 1.1. These files can be accessed via WWW also. Please note
that when you start 3dviewnix, you should be in the directory where the
data files are or should soft link these files by using the command :

ln -s ~3dviewnix/DATA/* .

To access these data sets :

WWW : http://www.mipg.upenn.edu

FTP : machine : ftp.mipg.upenn.edu (130.91.180.111 or 130.91.180.114)
login : anonymous
passwd : your e-mail address
directory : cd /pub/3DVIEWNIX1.1/DATAFILES/DATA_Y or DATA_Z

The index of all the data files available on the net is :

DATA SET X :
NAME SIZE DESCRIPTION
============ ================ =================================
EXPER_00.IM0 4,457,664 bytes CT: Dry Skull 8 bit IMAGE0 data
EXPER_00.BS0 1,669,330 bytes CT: Dry Skull binary SHELL0 data
EXPER_00.BSI 72,192 bytes CT: Dry Skull binary SHELL0 icon
EXPER_00.BS1 2,602,818 bytes CT: Dry Skull binary SHELL1 data
EXPER_00.MV0 762,646 bytes CT: Dry Skull 8 bit MOVIE0 data
EXPER_00.SH0 4,484,454 bytes CT: Dry Skull 8 bit SHELL0 data
EXPER_00.SHI 110,226 bytes CT: Dry Skull 8 bit SHELL0 icon
============ ================ =================================
Total size 14,159,778 bytes
============ ================ =================================


DATA SET Y :
NAME SIZE DESCRIPTION
============ ================ =================================
SKULL2.IM0 4,327,040 bytes CT: head 8 bit IMAGE0 data
SKULL2.SH0 15,380,270 bytes CT: head non-binary SHELL0 data
SKULL2.SHI 306,516 bytes CT: head non-binary SHELL0 icon
SKULL2.MV0 2,765,584 bytes CT: head 24 bit (True Color) MOVIE0 data
106680_01.IM0 8,390,690 bytes MR: head 4D, 16 bit IMAGE0 data
mri10010a_1.IM0 2,032,536 bytes MR: brain T1 8 bit IMAGE0 data
mri10010a_2.IM0 2,032,536 bytes MR: brain T2 8 bit IMAGE0 data
============ ================ =================================
Total size 35,235,172 bytes
============ ================ =================================


DATA SET Z :
NAME SIZE DESCRIPTION
============ ================ =================================
naren.BS1 5,306,004 bytes MR: foot binary SHELL0 structure system (4D)
naren_abs.PLN 28,869 bytes MR: foot PLAN file of the absolue motion
naren_rel.PLN 28,822 bytes MR: foot PLAN file of the relative motion
naren_003.IM0 3,933,706 bytes MR: foot 8 bit IMAGE0 data (time inst 1)
naren_005.IM0 3,933,702 bytes MR: foot 8 bit IMAGE0 data (time inst 2)
naren_009.IM0 3,933,700 bytes MR: foot 8 bit IMAGE0 data (time inst 3)
naren_007.IM0 3,933,702 bytes MR: foot 8 bit IMAGE0 data (time inst 4)
naren_011.IM0 3,933,702 bytes MR: foot 8 bit IMAGE0 data (time inst 5)
naren_013.IM0 3,933,700 bytes MR: foot 8 bit IMAGE0 data (time inst 6)
naren_015.IM0 3,933,700 bytes MR: foot 8 bit IMAGE0 data (time inst 7)
naren_017.IM0 3,933,702 bytes MR: foot 8 bit IMAGE0 data (time inst 8)
============ ================ =================================
Total Size 36,833,309 bytes
============ ================ =================================

***********************************************************************



=======================================================================
3DVIEWNIX User Manual
=======================================================================

The demo version comes with the complete 3DVIEWNIX User Manual in postscript
form. Feel free to print it and circulate amongst the users. If you are
interested in learning how to program with the 3DVIEWNIX libraries, you can
access the 3DVIEWNIX Library Reference Manual via WWW
(http://mipgsun.mipg.upenn.edu). You will need the 3DVIEWNIX source code
and the library for you to do programming in 3DVIEWNIX. You can get the
source code from us for a fee ($1000). If you need more information on how
to acquire 3DVIEWNIX source code, please contact :

Prof. J. K. Udupa
Medical Image Processing Group
Department of Radiology
University of Pennsylvania
418 Service Drive - 4th Floor Blockley Hall
Philadelphia, PA 19104-6021
U.S.A.

Phone: +1-215-662-6780
FAX: +1-215-898-9145
email: Vhelp@mipg.upenn.edu
WWW: http://www.mipg.upenn.edu


***********************************************************************



=======================================================================
3DVIEWNIX Tutorials
=======================================================================

There are three tutorials that come with this demo version of 3DVIEWNIX.
They are in postscipt as well as in plain ascii format. You can access
these tutorials via WWW (http://www.mipg.upenn.edu) also. The tutorials
are :

Tutorial 1 : How to import data into 3dviewnix

Tutorial 2 : How to create 3D objects

Tutorial 3 : How to manipulate 3D objects


***********************************************************************



=======================================================================
3DVIEWNIX Features
=======================================================================


ENHANCEMENTS IN V1.1

Bug fixes: Most known bugs have been fixed.

3DVIEWNIX now runs under the control of the window manager. So it can be
inconified, moved and created in windows of desired size.

PORT-DATA: Several standard data formats are now supported for both
Input and Output including Sun Raster, PPM, and PGM.

MANIPULATE: Commands to manipulate shells have been extensively
enhanced. Most Manipulate operations that were previously meant for only
binary shells now operate on fuzzy shells also.

An extensive Library Reference Manual is provided. This describes all
library functions of 3DVIEWNIX. The manual helps you to develop programs
within the 3DVIEWNIX framework. Man pages are provided for all library
functions.

A collection of stand-alone useful image processing programs with
description is provided.

"How To" tutorials to help get started are included.

Miscellaneous: Help files are available in both HTML and ASCII format.
Within 3DVIEWNIX either format can be used to view help instructions
depending on the viewer available on the workstation and on how
3DVIEWNIX is configured. Several other improvements have been made to
the user interface. Functions are now available for the effective
display of true-color images on pseudo-color devices.

3DVIEWNIX FUNCTIONALITIES

3DVIEWNIX is a transportable, inexpensive software system developed by
the Medical Image Processing Group, Department of Radiology, University
of Pennsylvania, Philadelphia. It has state-of-the-art capabilities for
visualizing, manipulating, and analyzing multidimensional, multimodality
image information. It is designed to run on UNIX machines under
X-windows. It uses a data protocol that is a multidimensional
generalization of the ACR-NEMA standards. It has been installed on a
variety of platforms including SGI, SUN, PCs, IBM RS 6000s, HP700s, and
Stardent, all from a single source code version.

PURPOSE OF 3DVIEWNIX

To promote widespread clinical use of 3D imaging

To promote cooperative research -- technical and clinical -- in 3D
imaging

To enable end users and researchers to set up a very inexpensive,
state-of-the-art, 3D imaging system

UNIQUE FEATURES OF 3DVIEWNIX

Transportable - based on UNIX, X-windows and C

Based on a multidimensional generalization of ACR-NEMA standards

Application-independent

Image dimensionality independent

Can handle rigid, non-rigid, static, and dynamic objects and object
assemblies

Can handle object information from multiple modalities and longitudinal
acquisitions

Multitudes of visualization, manipulation, and analysis methods
incorporated

Open software system distributed with source code

3DVIEWNIX OPERATIONS

Preprocessing

Visualization

Manipulation

Analysis

PREPROCESSING

Volume-of-Interest:

To specify a subset of the n-dimensional (nD) volume image

To specify an itensity-interval-of-interest for reducing the number of
bits

Interpolation:

To create isotropically sampled data of lower or higher resolution than
input

Many interpolating functions

Interpolation in n dimensions

Both grey-level and shape-based methods

Filtering:

A variety of forms of enhancing and smoothing filters

Used for filtering surfaces, for normal estimation, for interpolation,
and volume rendering

Masking:

For assisting segmentation

Quick operation using "paint brushes"

Thresholding:

Multiple intervals can be specified

Iso-surface generation at any resolution

Segmentation:

2-feature cluster partitioning

Quick gesture-controlled (user-guided) boundary segmentation (live-wire
method)

Classification:

1-feature multiple material classification for opacity assignment

2-feature material classification for opacity assignment

Boundary Formation:

Connected, oriented, closed 3D surfaces are formed

Surfaces may have any resolution

Image Algebra:

Image addition, subtraction, logical operations

VISUALIZATION

Slice:

Sophisticated form of slice display in montage and cycle modes

Multiple input volumes of any dimensionality can be handled
simultaneously

Multiple color maps

Static montage viewing and dynamic cine viewing of slices

Arbitrary magnification

Reslice:

Guided by 3D display

Reslicing through multidimensional volumes

Surface Rendering:

Multitudes of methods

Multiple objects with translucency and color

Based on the notion of a structure system:
A structure system may be a collection of static objects, dynamic rigid
objects, dynamic non-rigid objects or any of these coming from multiple
modalities

Structure systems are visualized in their natural form, e.g., a beating
heart is displayed in that manner

Viewing properties of objects can be changed independently

Volume Rendering:

A new very fast method called shell rendering

Interactive rendering

Interactive opacity and color modification

Interactive measurement of fuzzy surfaces

MANIPULATION

One of the most sophisticated set of operations in 3DVIEWNIX

A variety of complex operations including cut away, reflect, separate,
move, surface marking, measure, animation

Complex surgical procedures can be simulated

These operations for both hard and fuzzily defined structures

ANALYSIS

Measurement:

A variety of inter- and intra-structure morphometry

A variety of image intensity-based measurements such as density profile,
time density curves, region-of-interest statistics and their variation
with time

Region-of-interest statistics for objects that are carved out
interactively

Registration:

Based on matching homologous features -- points, curves, entire surfaces

For merging information from multiple modalities

For motion description and analysis of rigid objects

Motion Analysis:

Rigid object assemblies

Animation of motion and its quantification

Comparison of motion of two assemblies of objects such as two joints

Relationship between moving surfaces

ON-GOING WORK

Fuzzy connected component object segmentation

A variety of user-steered quick segmentation strategies: live-wire,
live-band, live-region methods

Fast volume rendering of fuzzy structure assemblies with digital
perspective

Manipulation of shells (fuzzy objects) and shell algebra

Manipulation of soft-tissue objects

Registration of shells (fuzzy objects) and their motion analysis

Portable system integration


=======================================================================
3DVIEWNIX via World Wide Web (WWW)
=======================================================================

Hello 3DVIEWNIX Users:

We are pleased to announce the creation of a WWW (World Wide Web) server,
here at the Medical Image Processing Group, Department of Radiology,
University of Pennsylvania. This server has tons of information on 3DVIEWNIX.
In order to access this information you should be running NCSA Mosaic,
which is freely FTPable from University of Illinois at Urbana Champaign
(UIUC). The document that can be viewed via Mosaic has fancy text, graphics
and sound (true multimedia). If you think, you would be interested in
knowing more about Mosaic, and 3DVIEWNIX information via Mosaic, read on ...


What is NCSA Mosaic?

- Mosaic is an Internet-based global hypermedia browser that
allows you to discover, retrieve, and display documents and data
from all over the Internet.
- Mosaic is part of the World Wide Web project, a distributed
hypermedia environment originated at CERN and collaborated upon
by a large, informal, and international design and development
team.
- Mosaic helps you explore a huge and rapidly expanding universe of
information and gives you powerful new capabilities for
interacting with information.


What is global hypermedia?

- Global hypermedia means that information located around the world
is interconnected in an environment that allows you to travel
through the information by clicking on hyperlinks --
terms, icons, or images in documents that point to other, related
documents. Any hyperlink can point to any document anywhere on
the Internet.

The best -- and most enjoyable -- way to learn what Mosaic can do is to view
some of the exemplary global hypermedia applications on the Internet. These
applications were developed by people all over the world and
demonstrate the power and flexibility of advanced multimedia-capable
desktop computers linked to high-speed reliable global networking.


NCSA Mosaic Flavors:


NCSA Mosaic comes in three flavors.

- NCSA Mosaic for the X Window System
- Mosaic for the Apple Macintosh
- Mosaic for Microsoft Windows


About NCSA Mosaic for the X Window System:


NCSA Mosaic for the X Window System is a networked information
discovery, retrieval, and collaboration tool and World Wide
Web browser developed at the National Center for Supercomputing
Applications.


Availability:


You can retrieve copies of NCSA Mosaic in both source and executable
binary form from NCSA's anonymous FTP server :
ftp.ncsa.uiuc.edu.


3DVIEWNIX 1.1 Information Is Now Available Via World Wide Web :


Currently we have information on 3DVIEWNIX on our WWW server
(www.mipg.upenn.edu), which is in a form that can be interpreted
by WWW clients (HTML format). If you have not tried Mosaic, we would
encourage you all to try it. It's very user friendly!!


3DVIEWNIX Via WWW :

Start Mosaic as :
% Mosaic http://www.mipg.upenn.edu (color)

%Mosaic -mono http://www.mipg.upenn.edu (mono)


If you think this is too much, then let Mosaic come up the usual way,
and then select "Open URL" option under "File" in Mosaic. This will
pop up a window where you should type : http://www.mipg.upenn.edu
This will take you to our WWW server. From this point it is easy. Just
click whatever selection you want and you should be able to access
a lot of information on 3dviewnix.

Note:

We are constantly upgrading the information available from our WWW
server, so don't be surprised if some information is temporarily not
available. The 3DVIEWNIX LIBRARY REFERENCE MANUAL is now available
on line. There are several tutorials on how to use 3DVIEWNIX 1.1 to
import data, create 3D objects and manipulate 3D objects. If you have
any questions about Mosaic or 3dviewnix via Mosaic, please contact us
at Vhelp@mipg.upenn.edu.

So start webbing right away and explore the new information (super)
highway!!


/**********************************************************************/
From

Medical Image Processing Group
Department of Radiology
University of Pennsylvania

Vhelp@mipg.upenn.edu
/**********************************************************************/

http://www.vislist.com