Dear, Image J. [Volume measurement of pixels in exact range of CT numbers[= gray number or gray scale]

[Woo Hyoung Kim]

Dear developer group of Image J.

Hi, I'm on a study about measuring some volume in Computed tomography.
I've been searching some plug-ins. but I couldn't find the exact plugin with
the function that I expected.

the function that i was looking for was this

1. To draw ROIs of the exact HU unit(gray scale number used in CT, -1000 is
air, 0 is water, +1000 or more is metal)
    such as ......... for water, -10 ~ +10 would be my HU unit of interest.
    so by typing in -10 and +10 , the every pixel would be selected.

    * and the selection should be done on every consecutive slides that i've
opened.( abominal CT ...has about 50-60 cuts of tomography...)


2. And after selecting every pixels that had HU(CT number) of -10~+10,
volume measurement should be done to calculate ... muscle....volume.


Actually, since I know the thickness of each slice, the measuring part can
be done by manually calculating.... If i can finally get the total area of
muscle on every slides.


But the selecting every pixels with specific range of HU in every
slides...... It would be quite consuming if it is done just by drawing
polygonal ROIs on every single tomographs with mouse.
and also, every pixels that represents muscle should be selected. even it is
really little in even such as gastric wall.
That's why It is technically impossible include every pixels that fits in
the HU range.

So, If any of you know how to select every pixels containing specific range
of HU, please help me find my way :)
Thank you in advance.



Woo Hyoung Kim
Nuclear medicine
Wonkwang university Iksan Korea.

[Michael Doube]

> So, If any of you know how to select every pixels containing specific range
> of HU, please help me find my way :)
> Thank you in advance.
Dear Woo Hyoung Kim

You might like to try Volume Fraction in BoneJ, http://bonej.org/volfrac

You set the threshold using ImageJ's threshold dialog (Image > Adjust >
Threshold) and it calculates the volume of all pixels within the
thresholded range and inside an ROI, if an ROI is drawn, and reports
this as BV (bone volume; it could be anything though).  If you would
rather specify the threshold in a dialog (i.e. enter the numbers 0 , 100
) rather than use the threshold dialog, contact me off-list.

Michael

[Michael Doube]

>> So, If any of you know how to select every pixels containing specific range
>> of HU, please help me find my way :)
>> Thank you in advance.

> You might like to try Volume Fraction in BoneJ, http://bonej.org/volfrac

The correct URL is http://bonej.org/volumefraction :-|

[Matthijs E.]

Hi Woo Hyoung Kim,

I was wondering how you managed to calculate all this in the end?
Currently I am doing my own research and I am struggling with same problem as you. I need to know what amount of visceral fat can be found on a CT, based upon 3 slices of CT of the abdomen.

My range of interest would be between -90 and -130 HU but I am not sure how to do that with ImageJ.
This is my first research project I am doing alone so I am at a loss of where to find the correct information.

Hopefully you can help me out!

Thanks in advance,

Matthijs Engbrenghof
4th year medical student
Netherlands

[Herbie-3]

Matthijs Engbrenghof,

you may have a look at:
<http://rsb.info.nih.gov/ij/plugins/ct-window-level/index.html>

With respect to the DICOM-format see the ImageJ-UserGuide:
<http://rsb.info.nih.gov/ij/docs/index.html>

HTH

Herbie

:::::::::::::::::::::::::::::::::::::
On 08.02.14 22:34, Matthijs E. wrote:

> Hi Woo Hyoung Kim,
>
> I was wondering how you managed to calculate all this in the end?
> Currently I am doing my own research and I am struggling with same problem
> as you. I need to know what amount of visceral fat can be found on a CT,
> based upon 3 slices of CT of the abdomen.
>
> My range of interest would be between -90 and -130 HU but I am not sure how
> to do that with ImageJ.
> This is my first research project I am doing alone so I am at a loss of
> where to find the correct information.
>
> Hopefully you can help me out!
>
> Thanks in advance,
>
> Matthijs Engbrenghof
> 4th year medical student
> Netherlands
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Dear-Image-J-Volume-measurement-of-pixels-in-exact-range-of-CT-numbers-gray-number-or-gray-scale-tp3687659p5006464.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html