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S. Daniel Kwak
09-17-1997, 11:12 PM
Dear Biomch-L members:

Requesting information through Biomch-L was very helpful. I would like to thank all those who replied to my request and provided insight into medical image analysis.

S. Daniel Kwak

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Original posting:

>Dear Biomech-l members:
>I am searching for a commercially available image analysis/processing
>software to process MR and CT images. I am looking for a programmable
>software that has many standard routines built into it and that allows
>a user to add custom modules to the program.
>I browsed through the Biomech-l archive but did not find many other such
>programs. I am aware of NIH/image, Photoshop, AVS, and PV-wave. Would
>any of you know other image analysis software that is easily programmable?
>I would appreciate the product name, company name, contact telephone number,
>and a brief opinion on the product. Of course, I will compile all the
>replies and post it on Biomech-l.

>S. Daniel Kwak
>sdk@obl.bidmc.harvard.edu
>Orthopedic Biomechanics Lab
>Beth Israel Deaconess Medical Center
>330 Brookline Ave, RN115
>Boston, MA 02135

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Summary of replies:

It seems like MATLAB is a popular image processing program. One needs to purchase additional image processing toolbox for more options. Few respondents have noted slow computing of the program. PV-wave is also a versatile programmable image processing software. It has many advantages over point-and-click programs, but it costs a little more. For 3D medical image analysis, ANALYZE from Mayo Clinic and 3dviewnix from U Penn are available. Some free programs include NIH/image, UTHSCSA ImageTool, and Khoros. Please see below for more detailed description of the program and contact information.

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FYI:

NIH image (many references found in Biomch-l archive)
Adobe Photoshop (http://www.adobe.com/)
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AVS (http://www.avs.com/)

>From Dave Giurintano, MSME
Chief
Paul Brand Biomechaincs Lab
Gillis W. Long Hansen's Disease Center

One of my former co-workers, Loyd Myers, is up in Seattle now working for a
company that writes image analysis code to pin point beams for radiation
therapy based on analysis of mri images. When Loyd was still at Carville,
he wrote code for image analysis of ct and mri scans using AVS. Maybe he
can get you his modules or help you with advice on using AVS. I've used it
for visualization of my mechanics simulations and I really like it. His
e-mail address is myers@eskimo.com.

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PV-Wave (http://www.vni.com/)

>From Timothy A Niiler
University of Delaware Sports Science Lab

Check out PV-Wave. It is both a programming language and an environment.
Wave started out as IDL - interactive data language which was used for
image processing for many years by the astronomy community. Then several
years ago, for reasons which are not totally clear to me, PV-Wave became a
separate product from IDL. Wave features a C-like programming syntax for
its command language with several distinct advantages.

In addition Wave variables are polymorphic so that it makes for easy
conversion between types without all the normal headaches. Wave supports
a large set of intrinsic functions, the IMSL libraries and user libraries
which allow one to cut on developing time. Most of these routines are
even named what you would expect (so for fitting a surface, you would look
for SURFACE_FIT). Included in these routines are plenty which can be used
for image processing. Also included are basic functions which allow
loading and displaying of images, vectors and arrays.

Another important feature of Wave is that it can be run via compiled
procedures or interactively. This allows for rapid debugging in the case
of a crash.

Wave allows the developer to rapidly create front end graphics user
interfaces with the usual stuff (radio buttons, menues, display windows,
etc..)

Lastly, if you get PV-Wave Extreme Advantage, I believe that it allows you
to circumvent the programming in favor of a GUI "point and click"
environment (which can incidentally save your worksessions in the form of
the command language I described above).

Sounds great, huh? It is except for the price. Expect to drop a couple
of grand for the use of the stuff.

To get more info check out:
http://www.vni.com/products/wave/extreme.html#advantage

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Evergreen Technologies (207-326-8300)

>From Mirena Paravic

One of the problems you will have is getting the CT and MRI images into a
format that the rest of the imaging world can read. Therefore, I suggest
starting with a company called Evergreen Technologies 207-326-8300. They
write and sell both drivers for various CT machines as well as some image
analysis softwares of their own.
If you are using a GE CT helical scanner I have some more info for you...

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MATLAB (http://www.mathworks.com)

>From James C. Iatridis, Ph.D.
Department of Orthopaedics and Rehabilitation
University of Vermont

I have some experience using MATLAB software (The Mathworks,
http://www.mathworks.com, info@mathworks.com, 508-647-7000) for image
analysis. I used the software for digitizing scanned images. My needs
were relatively rudimentary and I did not need the additional image
processing toolbox. I was particularly impressed with the programmability
of the software and the ease of debugging. However, the software's image
reading and scaling routines were often time consuming (this may be
enhanced with some of the routines found in the toolbox).

------------------------------------------------------------------------------

>From Ted Morris
Center For Advanced Manufacturing Design And Control
Institute of Technology, U of Minnesota

Have you looked at Matlab's Image Processing toolbox? Not sure which image
formats are directly supported. Their DSP toolbox may also be helpful for
this purposee.

------------------------------------------------------------------------------
>From Yu-Hua Jiang
Dept. of Mechanical Engineering
School of Engineering
University of Maryland, Baltimore County(UMBC)
|websit:http://www.gl.umbc.edu/~yjiang/

It seems to me both MATLAB and IDL have very good image processing
capabilities. I would suggest you having a quick look at both of them via
their websites if you have never used them and are not looking for some
very specialized packages. The URLs of them are

IDL: http://www.rsinc.com/
MATLAB: http://www.mathworks.com/

Both of them are high level interpreting language environments therefore
they are easily programmable as you desired as well as command line
operatible. Furthermore they are general numerical analysis packages with
great capabilities of multi-dimensional data analysis and visualization.
They also have very good GUI toolkits for developing you own scripts.

The main drawbacks of these packages are the computing efficiencies. They
are generally slower than C or Fortan for computing intensive jobs.
Sometimes it may become intolerably slow when you would like to do
something like multi-dimensional convolution such as those in
three-dimensional image processing. As I was told MATLAB does not have
paralell processing capabilities so that you would not be able to take
advantages of any multiprocessor machines you may access. Fortunately,
however, MATLAB has very good interface capability for C subroutines and
library. The best way to do such computing intensive jobs may be to
combine a more efficient C subroutine developed on the indepth
knowledge of the image processing you are doing with the good
visualization capacities of MATLAB or IDL.

It is hard for me to compare the two packages in detail. It seems to me
MATLAB is good in general data processing but IDL is somehow more user
friendly and has better capacities of multi-dimensional array handling.

It is better to use newest versions of either package, MATLAB5 or
IDL5.0. The capability of 3 or higher dimension data processing were not
available in MATLAB before version 5.

You can find all the contact informations on the websites. You can also
request free demos.

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ANALYZE (www.mayo.edu/bir)

>From Richard A. Robb, Ph.D.
Professor of Biophysics
Professor of Computer Science
Mayo Medical and Graduate School
Director Biomedical Imaging Resource
Mayo Foundation\Clinic
WebSite: www.mayo.edu/bir

You may wish to look at our web pages (in my signature below) and review
Analyze. Especially read "What's New With Analyze?" This comprehensive
software has many standard and advanced image proocessing and display
capabilities, plus it can have custom modules added to it.

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>From Jarrod Meerkin
School of Human Movement Studies
Queensland University of Technology

I am using the Analyse software from the Mayo Clinic to determine
cross-sectional area and volumes from MRI scans. The software is now
available for windows NT which should be a little easier than the unix
based software I am using. Would be interested in your other replies.
Hope this is of help. Not to sure of Analyse's programming capabilities.

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rapid prototyping techniques

>From Ariel Sverdlik

Try:
www.visiblep.com
www.materialise.be
www.cyberf.com
www.primenet.com/~dcr_inc

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UTHSCSA ImageTool program (FTP from ftp://maxrad6.uthscsa.edu)

>From Lynne E. Bilston, PhD
Department of Mechanical and Mechatronic Engineering
University of Sydney
http://www.mech.eng.usyd.edu.au/staff/bilston.html

Check out Image tool, from Univ of Texas Health Centre San Antonia.
It's a PC NIH-Image like program. It supports plugins etc, and is free.

UTHSCSA ImageTool program (developed at the University of Texas
Health Science Center at San Antonio, Texas and available from the
Internet by anonymous FTP from ftp://maxrad6.uthscsa.edu)

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Optimas (http://www.optimas.com)

>From Alex Kerin
Department of Anatomy
School of Veterinary Science

I use an image analysis program called Optimas. They have several
versions available, for 32 bit systems, 16 bit, and a demo version. The
program has a built-in macro language that may or may not do what you
want. I have found it useful, but only use it for relatively simple
work. The interfacing (via OLE) to other programs (Excel for example)
seems to work very well as well, so this may be another way to acheive
what you want.

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Explorer (No relevant result found when searched through Yahoo web serach engine with key words "Explorer" and "image")

>From Dr. Sam Evans
Medical Systems Engineering Research Unit,
UWC School of Engineering

There is a program called Explorer that might also be very good for
your purposes, but I can't remember who makes it.

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STRIM (http://www.matra-datavision.com)

>From Dr Rami J Abboud, BEng, MSc, PhD
Lecturer in Orthopaedics & Trauma Surgery
Consultant Clinical BioEngineer
Foot Pressure Analysis Lab
Orthopaedic & Trauma Surgery Dept
Dundee Royal Infirmary

STRIM by matra vision or Matlab.

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Khoros from Khoral Research (http://www.khoros.unm.edu)

>From William A. Hoff
Assistant Professor
Engineering Division
Colorado School of Mines
whoff@mines.edu (email)
http://silurian.mines.edu/~whoff (home page)

You should look at Khoros, from Khoral Research, for your image processing
software needs. Their web site is http://www.khoral.com. It is available
at no cost via ftp. For a free package, it is extremely polished, well
documented, and has many (400+) routines built into it. I have been using
it for more than 5 years for algorithm prototyping and also teaching computer
vision courses. There is also a very large user community that regularly
contributes new routines and a mail list/newsgroup where you can get
answers to questions. As far as disadvantages go, it only runs on Unix
and X-windows workstations, is fairly large (200 or more MB), and is not
that easy to develop new routines for (although the procedure is well
documented).

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Sigma-Scan from Jandel Scientific (http://www.jandel.com)

>From Bill Noffsinger
Chief Technologist
Department of Pulmonary Physiology
& Respiratory Sleep Disorders Clinic
Sir Charles Gairdner Hospital

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IDL (http://www.rsinc.com/)

>From Yu-Hua Jiang
Dept. of Mechanical Engineering
School of Engineering
University of Maryland, Baltimore County(UMBC)
|websit:http://www.gl.umbc.edu/~yjiang/

Check comments by Yu-Hua Jiang in MATLAB section.

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3dviewnix (http://www.mipg.upenn.edu)

>From Thomas S. Buchanan, Ph.D.
Associate Professor of Mechanical Engineering
Orthopaedic Biomechanics Center
University of Delaware
WWW: http://www.me.udel.edu/buchanan

You might try looking at 3dviewnix. It is a very robust image analysis
software package and the source code (in C) is available. It is available
from the Medical Image Processing Group of the Dept of Radiology at U Penn.
(http://www.mipg.upenn.edu).