Problems in reading Hounsfield units from a DICOM image

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Problems in reading Hounsfield units from a DICOM image


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

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.


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