Problems in reading Hounsfield units from a DICOM image (Fiji)

Posted by Shreyakanakiya on Feb 26, 2017; 5:20am
URL: http://imagej.273.s1.nabble.com/Problems-in-reading-Hounsfield-units-from-a-DICOM-image-Fiji-tp5018195.html

Hello,

I have a set of DICOM images. When I import them as an image sequence I believe that Fiji reads the slope and intercept from the DICOM header and converts the raw pixel values to Hounsfield units (HU). In my header file, however, the rescale slope = 1 and rescale intercept = 0. Thus by the formula,

Hounsfield unit = pixel value*slope+intercept

My Hounsfield units are the same as pixel values. I want to segment the image using the Hounsfield scale (air = -1000 HU, water = 0 HU). But since all my values are positive I am unable to use it directly. I have attached a histogram of my DICOM image stack for reference.  The left peak represents the background (air) and the right peak represents the grayscale distribution of my data (rock).

I'm not aware of a calibration to have only positive HU but am new to this field and wanted to know if such a calibration exists ? If yes, is there a way I can rescale them such that air = -1000 HU, water = 0 HU and so on?  

Thanks in advance.

-Shreya