| Re: Medical Imaging Question [message #16578] |
Fri, 06 August 1999 00:00 |
davidf
Messages: 2866
Registered: September 1996
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Senior Member |
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Larry Busse (ljb@ljbdev.com) writes:
> In MR and CT, images are usually displayed with a gray map that is
> appropriate for the particular area being imaged or diagnostic
> procedure. The look-up tables are sometimes referred to as
> "lung-window", or "bone-window", or "soft-tissue-window". These
> correspond to different window/level settings where
> window = (WhiteValue - BlackValue) and
> level = (WhiteValue + BlackValue)/2.
Let me see if I understand this correctly. Are you saying
that I might have sliders that would select a "window" of
data. Say between the values of 1000 and 3500, and that
what I would see on my display would be something like
this:
TV, BytScl(image, Max=3500, Min=100, Top=!D.Table_Size-1)
In other words, the gray scale values could be a portion
or window onto the entire data universe. If this is so,
how do you usually implement such a sliding window into
your data?
Many thanks to all (including bashful e-mail senders)
for their comments. :-)
Cheers,
David
--
David Fanning, Ph.D.
Fanning Software Consulting
Phone: 970-221-0438 E-Mail: davidf@dfanning.com
Coyote's Guide to IDL Programming: http://www.dfanning.com/
Toll-Free IDL Book Orders: 1-888-461-0155
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| Re: Medical Imaging Question [message #16579 is a reply to message #16578] |
Fri, 06 August 1999 00:00  |
Larry Busse
Messages: 7
Registered: February 1999
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Junior Member |
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David,
I'm no expert on DICOM but I've worked in enough Radiology departments
to shed a little light on your question.
As you probably know, the DICOM standard was developed to allow the many
different kinds of medical imaging equipment (CT, MRI, Ultrasound,
Nuclear Medicine, etc.) to provide data in a format that could be
handled by workstations and computer networks throughout hospitals. I
think the notion of digitizing images to 12-bits (or 4096 gray levels)
was done to preserve the full dynamic range of older recording media
such as x-ray film. The doctors basically didn't want to loose any
information (contrast resolution or spatial resolution) just because the
data was going to be digitized and sent over a computer network.
In MR and CT, images are usually displayed with a gray map that is
appropriate for the particular area being imaged or diagnostic
procedure. The look-up tables are sometimes referred to as
"lung-window", or "bone-window", or "soft-tissue-window". These
correspond to different window/level settings where
window = (WhiteValue - BlackValue) and
level = (WhiteValue + BlackValue)/2.
and the curve from black to white can be linear of some other curve. If
the window is greater than 256 and the display only capable of 256
levels, then you won't see every level.
All this meant to say that I don't think it's necessary (or possible) to
see 4096 shades of gray on the screen but it is important to preserve
all the info in the data because looking for a tumor in the lung will
require much different display settings that looking for a tumor in a
bone.
I hope this helps. For more general info on DICOM try
http://www.rsna.org/REG/practiceres/dicom/
Good Luck,
David Fanning wrote:
>
> Mirko (mirko_vukovic@notes.mrc.sony.com) writes:
>
>> davidf@dfanning.com (David Fanning) wrote:
>>>
>>> I've got a 12-bit Dicom image. I want to display this in
>>> such a way that there is a direct correlation between
>>> the pixel value (0 to 4094) and the representation of
>>> that pixel value on the display. How do I do that?
>>>
>>
>> Can you please expand on that? What do you mean by direct correlation?
>> For a 4-bit image would color be a good correlation
>> (16 values <=> 16 colors/intensities)?
>
> I mean by this that I want to "see" 4094 shades of gray.
> Now I know there are only 256 "pure" shades of gray, so
> I presume that I have to fudge a gray somehow. For example,
> the pure gray (128, 128, 128) could be fudged by something
> like (128, 128, 135). The latter is not really a gray, but
> it's almost gray and presumably it "looks" different than
> the pure gray. My question really boils down to this: Is there
> some standard way to "fudge" gray values between the pure
> gray values, so that it appears as though I have 4094
> shades of gray? And if so, what is the algorithm to
> go from the pixel representation on the display to the
> real pixel value?
>
> Cheers,
>
> David
>
> --
> David Fanning, Ph.D.
> Fanning Software Consulting
> Phone: 970-221-0438 E-Mail: davidf@dfanning.com
> Coyote's Guide to IDL Programming: http://www.dfanning.com/
> Toll-Free IDL Book Orders: 1-888-461-0155
--
Larry Busse Phone: (606)344-9433
L.J.B. Development Fax: (606)341-8486
3384 Madison Pike mailto:larry@ljbdev.com
Fort Wright, KY 41017 http://www.ljbdev.com
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~
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| Re: Medical Imaging Question [message #16582 is a reply to message #16578] |
Fri, 06 August 1999 00:00 |
davidf
Messages: 2866
Registered: September 1996
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Senior Member |
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Struan Gray (struan.gray@sljus.lu.se) writes a lengthy
verson of "it ain't gonna happen":
Thanks for this information, Struan. This is basically
what I thought, but didn't have the background to
support my beliefs. I'm going to write it up as an
article, if you don't mind, so that I don't have to keep
answering this question over and over. :-)
Cheers,
David
--
David Fanning, Ph.D.
Fanning Software Consulting
Phone: 970-221-0438 E-Mail: davidf@dfanning.com
Coyote's Guide to IDL Programming: http://www.dfanning.com/
Toll-Free IDL Book Orders: 1-888-461-0155
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| Re: Medical Imaging Question [message #16583 is a reply to message #16578] |
Fri, 06 August 1999 00:00 |
Struan Gray
Messages: 178
Registered: December 1995
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Senior Member |
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David Fanning, davidf@dfanning.com writes:
> I want to "see" 4094 shades of gray.
This is hard. A really good monitor designed for photogrammetry
might get you to 8-9 bits of true greyscale, especially if you use
duo- or tri-toning as you suggested, but 12 bits is hopeless. The
only way to display 12 linear bits is by writing onto sheet film with
a well-calibrated laser-based film recorder, and hanging it on a
lightbox - and even there you're pushing the envelope.
Then you have to deal with the human eye. Visual perception (as
opposed to the physics of the retina) is logarithmic: a rough figure
is that the eye-brain system can distinguish intensity variations of
the order of 1%. With linear encoding of intensity you are wasting
bits in the bright areas of your image (where the bit transitions are
packed more densely than 1%) and losing detail in the shadows (where,
at worst case the bits represent 50% variations in intensity). This,
along with technical issues to do with the response of TV tubes, is
why a gamma function helps, ie I = I^gamma looks more detailed and
even than I alone, with gamma = 0.45 being so-called optimal for the
human eye.
People say that 12-bit linear encoding is about the maximum the
human eye can resolve, unless the scene subtends a very large angle
and the viewer can dark-adapt their eyes to individual sub-scenes.
8-bit gamma encoding of this looks pretty good, but some infomation is
lost and the best strategy for monitor-based viewing is to keep the
12-bit information and allow the user to scan and zoom around the
image, creating locally-valid 8-bit gamma versions of the information
as appropriate. In IDL this would be simple.
Your final option is to do some image processing. There are
several well-established ways of enhancing detail in images with a
large dynamic range. Photoshop users (and darkroom enthusiasts) are
familiar with the unsharp mask. I use a technique called Statistical
Differencing, which is essentially an unsharp mask weighted by the
local statisitics: it applies a more agressive mask in areas which
lots of small detail. Plotting in light-shaded form in 3D can be
surprisingly effective, which is mathematically the same as the common
trick of adding the local derivative to the original image. All these
tricks help the viewer see detail at the expense of the local average
intensity.
I culled these references from a discussion of the human eye and
perception in rec.photo.digital, they might be worth a look if you're
really interested:
The Reproduction of Colour (in Photograpy, Printing, and
Television) by R.W.G. Hunt.
Illumination and Color in Computer Generated Imagery, by Roy Hall
Digital Color Management, by Edward Giorgianni and Thomas Madden
Color Appearance Models, by Mark Fairchild
Struan
(Apologies if you see more than one copy of this - my newsserver
promised me it hadn't accepted the first one(s))
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| Re: Medical Imaging Question [message #16599 is a reply to message #16578] |
Thu, 05 August 1999 00:00 |
Axel vom Endt
Messages: 9
Registered: March 1999
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Junior Member |
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David Fanning wrote:
>
> I mean by this that I want to "see" 4094 shades of gray.
I'm not sure about the reference for this, but I read somewhere that the
human eye cannot even distinguish between 256 levels of gray. Isn't that
the reason to use the fancy color tables in IDL?
From what I understand about medical imaging the 4096 levels are meant
to have some headroom, so that you can zoom into some parts of the
intensity range to enhance certain features of the image without losing
resolution.
I think that these fudged gray scales have only been used in the old
days of the PC, when you had to use 256 colors out of 262144 on your VGA
card, i.e. 2^6 different shades each of r,g,b and therefore only 64
levels of pure gray. I've done that once, but the results haven't been
impressive.
Hope that helps
Axel
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| Re: Medical Imaging Question [message #16603 is a reply to message #16599] |
Thu, 05 August 1999 00:00 |
davidf
Messages: 2866
Registered: September 1996
|
Senior Member |
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Mirko (mirko_vukovic@notes.mrc.sony.com) writes:
> davidf@dfanning.com (David Fanning) wrote:
>>
>> I've got a 12-bit Dicom image. I want to display this in
>> such a way that there is a direct correlation between
>> the pixel value (0 to 4094) and the representation of
>> that pixel value on the display. How do I do that?
>>
>
> Can you please expand on that? What do you mean by direct correlation?
> For a 4-bit image would color be a good correlation
> (16 values <=> 16 colors/intensities)?
I mean by this that I want to "see" 4094 shades of gray.
Now I know there are only 256 "pure" shades of gray, so
I presume that I have to fudge a gray somehow. For example,
the pure gray (128, 128, 128) could be fudged by something
like (128, 128, 135). The latter is not really a gray, but
it's almost gray and presumably it "looks" different than
the pure gray. My question really boils down to this: Is there
some standard way to "fudge" gray values between the pure
gray values, so that it appears as though I have 4094
shades of gray? And if so, what is the algorithm to
go from the pixel representation on the display to the
real pixel value?
Cheers,
David
--
David Fanning, Ph.D.
Fanning Software Consulting
Phone: 970-221-0438 E-Mail: davidf@dfanning.com
Coyote's Guide to IDL Programming: http://www.dfanning.com/
Toll-Free IDL Book Orders: 1-888-461-0155
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