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unknown user
02-17-1999, 01:21 AM
In a message dated 2/16/99 10:30:41 AM Eastern Standard Time,
julie.matthews@integrum.se writes:

Dear Biomechs'

Thank you for the amazingly fast responses to my questions about converting CT
SCAN data

The summary.

I had 16 responses

>You might want to try our Mimics software, which can be downloaded from
www.materialise.com.
It allows you to create STL-files (triangultated surfaces), VRML files
and IGES output (points, lines, splines and Nurbs surfaces). Furthermore
Mimics allows the import of CAD data into the image dataset and as such
you can see if a CAD Design fits a patient.

The scan data itself should stay formatted in the way the scanner
manufacturer archives the data, and can be recognized by Mimics
automatically. Before you ask for the data you might want to check if
the scanner format is compatible with our software.

Regards,


Mark Bliek
Materialise
6111 Jackson Road
Ann Arbor, MI 48103
Phone (734) 662-5057
Fax (734) 662-7891
http://www.materialise.com

>First, images acquired at the CT scanner (if it is a recent one) may be
available in a semi-standard format called DICOM. If it is not available in
DICOM, then you may have some problems because the data will likely be stored
in a proprietary format. See if the scanner can can send DICOM data to you
somehow.

Second, how will you get the data? Most hospitals are not set up to send their
data outside and the optical disks they store the data on usually use the
proprietary format of the scanner manufacturer.

Third, what kind of viewing software do you have? (I take it that you do not
want to view the data right at the CT scanner or a 3-D workstation that may be
connected to it). Your viewing software may have a utility to handle DICOM
data directly. If not, then you may have to go through some conversion from
DICOM to .stl or some other format that your viewing software can handle. SO,
see what formats your viewing software can handle.

I know this is just raising questions, but if you can answer these, then you
should be able to view your data successfully.

If you have any questions, you can contact me at the email below. Good luck.
(P.S. where are you phyiscally located? there may be a data savvy
institution near you)

Michael McNitt-Gray, Ph.D.
Assistant Professor
UCLA Radiological Sciences
mmcnittgray@mednet.ucla.edu
ph: (310) 206-3285
fax: (310) 206-2967

>The answers to your questions depend very much on what kind of scanner the
hospital is using, and what format they will be giving you the data in.

We use GE MR and CT scanners at my hospital. GE has their own proprietary
format for the images. But they can also be output as DICOM format images.
DICOM (Digital Imaging and Communication in Medicine) is a new, cross
platform format that is becoming more popular.

Find out how the data will be coming to you, and what scanner it will be
done on.

DPT

>look up past discussions in the biomch archives...I have attached one from
a while ago that I saved since I myself have made bone models from Ct
data.

good luck,

Dean Inglis

Department of Civil Engineering \ Email: dean@numog.eng.mcmaster.ca
BSB B101A \ Voice: (905) 525-9140 x23167
McMaster University \ Fax: (905) 524-2121
Hamilton, Ontario, Canada L8S 4M1 \

>IBM Data Explorer is a very useful tool for handling
these types of data.

There are more specialized packages as your application
develops.

It doesn't surprise me the hospital radiology
technicians and staff know nothing about handling these
data outside the console where they are collected.
Consider yourself lucky that you can save the data take
them off the console!

Good luck.

Best,
David

+---------------------------------------------------------------------+
| David Dean, Ph.D., Assistant Professor |
| Director, Imaging Laboratory |
| Dept. Neurological Surgery, Bolton DO3080 |
| Case Western Reserve University Voice: (216) 368-1975 |
| 10900 Euclid Avenue FAX: (216) 368-3204 |
| Cleveland, OH 44106 USA E-mail: dxd35@po.cwru.edu |

>Check at: http://www.arielweb.com

>I've done some work with this. There are many programs to do the
conversions. Try checking

http://biocomp.stanford.edu/3dreconstruction/index.html a site that gives an
overview of many of the products out there
http://idt.net/~dclunie/ for some real techie data conversion stuff
http://rsb.info.nih.gov/nih-image/ for some freeware that is in widespread
use - I don't know how 3-D it is though


And the one we're using (it doesn't show up on the first site though?) which
is fantastic for conversion of CT to CAD:
http://www.materialise.com/ - the mimics/medcad products

The format you get them in is more dependant on what you have to read the
data, i.e. Optical Disk, 4mm DAT, 8mm tape, etc.

If I can help you in any other way, please don't hesitate to call / e-mail /
FAX, etc.

Mark
Mark Manasas / mmanasas@jpius.jnj.com / 508-880-8213 /
508-880-8122 FAX

>These are the suggetions which hopefully to be helpful to you...

1 via CT scan, output format is (.ct)
2 transfer to Mimics, (a 3D software), output format is (.3dd)
3 import to FEM(finite element) software, then you will have created
the interface with CTM, to generate a
stereolithography (.stl) file
4 Use surfacer software to rebuild the surface.

That is all I know.
Good luck

Kam

>There are a lot of 3D reconstruction programs. Most recent CT systems are
provided with a 3D reconstruction routine. But there are also stand-alone
systems. Here are 2 references:

Silhouette - ISG Technologies - http://www.isgtec.com,
3DViewnix - MIPG, University of Pennsylvania -
http://www.mipg.upenn.edu/~Vnews/

Moreover, there are some people who have developped their own 3D recon
program. One of my colleagues is among them (Serge Van Sint Jan,
sinjans@ulb.ac.be or sintjans@dmu.ac.uk). He will probably answer you himself.

Best regards,

Veronique

************************************************
Veronique Feipel, PhD
Laboratory for Functional Anatomy
University of Brussels (CP 619)
808, route de Lennik
B-1070 Brussels, Belgium
Phone: ++ 32-2-555 6329
Fax: ++ 32-2-555 6378
Email: vfeipel@ulb.ac.be
Homepage: http://homepages.ulb.ac.be/~vfeipel/

>What we use at our lab to view and manipulate CT data is a programme called
Mimics. It's from a company called Materialise and you can download an
evaluation version of their software from their website at
http://www.materialise.com. I don't know how powerful this evaluation
version is, but with the full Mimics version you can read in and view
almost all CT data formats (you can always contact them for a specific
format). Moreover, Mimics has some tools that enables the user to build
CAD models (in the neutral IGES format) from the CT data or to create 3D
models for visualisation purposes only.
I hope this information helps you a bit.
Good luck,


Hans

************************************************** *************
Hans Van Oosterwyck
Ph.D. student
Katholieke Universiteit Leuven
Division of Biomechanics and Engineering Design
Celestijnenlaan 200a
B-3001 Heverlee
Belgium
tel +32 16 32 75 71
fax +32 16 32 79 94
e-mail: hans.vanoosterwyck@mech.kuleuven.ac.be

>I received the message below from a colleague in the University of Limerick
where I used to work. I did some work on constructing 3-dimensional models
of bones from CT scans and I might be able to give you some information.
Firstly I not so sure how familiar you are with displaying CT images in 3d,
what program you intend using etc. and also I'm not sure what you are trying
to do exactly. Anyway, if you only need to display a 3 dimensional view of a
bone from CT scans for visual purposes, then there is a crude rendering
facility available in the software on CT machines (Siemens machines at any
rate). However if you want to reconstruct the geometry of the bone for say
Finite Element Modeling, then this feature is useless. You will need to scan
the bone, save the scans and reconstruct in 3D using a program. If you do
not need a specific bone, then there are scans available on the internet
through The Visible Human Project. There are also pointers to sites with
info on 3d construction from CT scans. Maybe this info. is useless to you -
I'm not sure. I don't have the web site details here but I can get them for
you if you can't find them using a search engine. However if you have to
scan a bone then CT file formats all conform to a standard. There are
shareware programs available to open these, such as SCIONIMAGE (available on
the internet)

If you think any of this info. is of use, email me more details of what you
need and I will get it for you.

Regards,

Kieran

> _____________________________________ ___ _
> Kieran Pearse Tel :
> +353-1-671-8177
> MV Technology Ltd. Fax : +353-1-671-8470
> Unit 24, IDA Enterprise Centre E-mail : k.pearse@mvt.ie
> Pearse Street, Web : http://www.mvt.ie
> Dublin 2, Ireland

>You could save it as xls files if I am not wrong. Then, you could use
a software called Surface to import the files to Finite element
(Ansys). Please check it out. I think I do have a little more detail
about this. But, I don't have it with me now. I will email again to
you tomorrow.

Best regards,
Horng, Kam

>Yes, there is a program call surfdriver that does what you need. check
www.surfdriver.com. There is another program called mimics (look for it in
altavista)

best regards,
Carmen

>The original format will depend on the platform connected to the Ct-Scan.
Most probably it will be in standard format for medical imaging: DICOM(DCM)
or ACR-NEMA.

Note Dicom stores grey image as 12 bits, which allows much more pixel depth
than "classical" bitmap formats usually
used on PC (like BMP or TIFF which are 8 bits).

Here is an URL where you can find a (free!) program, DICOM2, to convert Dicom
files to various formats:
http://www.hds.utc.fr/~barre/medical/dicom2/index.html

With some luck, the CT you will use will have some built-in conversion
functions, but I doubt it will do the job on
a list of files, rather you will have to select the file one by one (which is
not the case of DICOM2).

An advice, try to keep the 12 bits/depth. It will allow you easier better
threshold/segmentation of the data. Now, I
have no experience with 12 bits grey data on PC-based system. I think most
(all?) PC hardware show trouble to
display more than 256 (8 bits) grey values, but I may be wrong ... on Unix
system it works fine anyway.

With some courage you can write your own data reader directly from DCM files
(if it is the format you will get of
course). If you need some information on DCM format, please, tell me and I'll
send you a description.

> Unfortunately the local hospital is of very little help in this respect.

Welcome in the world of "sorry, no time!".

Hope this helps a bit,

Serge

--------------------------------------------------------------------------
Serge VAN SINT JAN, Ph.D. | In sabbatical from:
School of Computing Sciences | Department of Human Anatomy and Embryology
De Montfort University | University of Brussels, Belgium
Hammerwood Gate |
Milton Keynes MK7 6HP - UK
phone: + 44 1908 695511 (ext. 4146)
+ 44 1908 834933
fax: + 44 1908 834948
email: sintjans@dmu.ac.uk
WWW: http://homepages.ulb.ac.be/~sintjans

>The easiest format for CT data is DICOM, although there are many
variations on what is supposed to be a standard format. I have hundreds
CT examinations of a wide range of normal and pathologic of fractured bones,
And I have converted most to DICOM format. There are a few commercial
vendors of software that will allow direct transfer of CT data from the
scanner
to your computer. We use Digital Jacket. There are also numerous software
packages for visualizing the data. The cheapest (free) is VTK. We use AVS
from Advanced Visualization Systems, since we can make 2D and 3D
measurements and develop surgical planning applications using this platform.

You can get lots of information on medical image formats from
the medical image format FAQ. You can get that
on the archive site ftp://rtfm.mit.edu in the directory
pub/usenet/news.answers.

There are also several newsgroups devoted to this problem, such as
alt.image.medical.

There is also a FAQ on volume visualization that you can get from


I hope this helps.
John Hipp, Ph.D.
Baylor College of Medicine
(713) 986-5772

>We have been through this process and found that a program
called "VELOCITY" will do the job you want. To find out more, please
contact a company called DCR @ 909 305 1055. They will show you how to do
it and recommend the hardware you need to perform the task.

Regards, Dan Antonelli




Thank you
George J Iwanski
Pioneer Surgical Technology

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