Calibration with Image J

Posted by Soljanlahti Sami on Nov 02, 2005; 11:17am
URL: http://imagej.273.s1.nabble.com/Calibration-with-Image-J-tp3704525.html

Hi,

I have been trying to measure velocity of the blood flow from phase encoded
MRI images. On these images the different shades represent different
velocities. In our case black represent a flow velocity of 1.5 m/s and white
-1.5 m/s. On our last project we used NIH image but now don´t have Macs
anymore at our institution and we changed to Image J. I have done the
calibration for the measurements the same way I did with NIH image. First I
draw a white and a black spot to one of the images. Then I measure the mean
grey value of these. Then I use the calibrate command from analyze menu. I
use the straight line function.

My problem is that although white should represent one end of the scale of
pixel values in the picture and black the other there seems to be a lot more
values beyond this range. In other words when I measure my white spot it
represents mean gray value of 2558 and the black one represents 0. On the
calibration function the scale goes up 65535 which in thery is the maximum
of different shades in a 16-bit-picture. When I try to measure my pictures
after calibration the values are not even between 1.5 and -1.5.

If I change my images to 8-bit ones the calibration seems to work but my
images don´t look like they should anymore. So I think that the problem has
something to do with colour depth of the images (is it the right term when
talking about black& white images?).

I don´t know if I managed to describe my problem properly but I thank you in
advance for any suggestions that would solve the problem.

Yours,

           Sami Soljanlahti, MD
           Helsinki Medical Imaging Center
           Helsinki, Finland