: RE CAlibration of density RE: IMAGEJ Digest - 5 Nov 2005 t o 6 Nov 2005 (#2005-298)

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: RE CAlibration of density RE: IMAGEJ Digest - 5 Nov 2005 t o 6 Nov 2005 (#2005-298)

Goldsmith, Noel
Hi,
I suspect the images are being loaded as 16 bit grey images, and the
calibration you are attempting is for 8 bit.
I suspect when you load the images into imageJ you need to make sure that
they are imported as 8 bit images if that is what they are.
If they are 16 bit images then I am not sure about the calibration working
with such images.
If the images loaded as 8 bits look funny, then maybe the byte ordering is
switched, or there is some header which is different.
Hope this helps a  bit.
Noel


>   1. Calibration with Image J
>  
> Subject: Calibration with Image J
>
> 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  
>
>