[slicer-users] Help regarding DICOM files

Andriy Fedorov fedorov at bwh.harvard.edu
Mon Jul 12 08:56:39 EDT 2010

Hi Saurabh,

I will try to answer, but for the future please direct these kind of
questions to the Slicer user list: slicer-users at bwh.harvard.edu

On Mon, Jul 12, 2010 at 08:12, Saurabh Gupta 402549
<Saurabh_402549 at infosys.com> wrote:
> Hi Andriy Fedorov
> You might remember that I sent a mail regarding the error in loading the
> DICOM files in Slicer. I converted the DICOM files into NRRD and it loads
> fine. However, since I am new to this, I had certain queries. I would be
> really thankful if you can answer them.
> 1.       Is there a way by which we can read the HU values from the DICOM
> images (pixel by pixel)?

The NRRD file you load should contain the same HU values as in the
original DICOM file.

If you want to simply "read" these values, you can do so by moving the
mouse pointer over the specific pixel, and reading the value Slicer
reports to you in the slice viewer.

If you want to compute statistics over the HU values in a region, you
can do this by creating a label image in the editor module


and use Label Statistics module


to get the mean and variance for the HU values within the label you created.

> 2.       Since there are other regions as well apart from the required
> portion, I created a label in Slicer and marked the areas. I then converted
> it into a model using Model Maker. However it seems that this creates a
> solid model and the original intensity/ grey value information is lost. Is
> it possible to know the HU value from this vtk file ?

There is no need to create a model to calculate greylevel statistics.
Please follow the approach I described above. If I misunderstood your
question, please reply to the list.

> I know my doubts might sound naïve but I am unable to get a clear
> understanding of this thing. My objective is to get the HU values from the
> areas of interest but I am unsure how to do that.

No problem.

Please let us know if this does not answer your question.


> Regards
> Saurabh

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