[vtkusers] ISO-Value of bones

[samo]

Thanks Stephen for your answer. I didn't know so much about *dicom and *raw
formats, I just used them. In my files I got from my dicom converter, there
are no IntensityScale and IntensityOffset tags. Maybe I should use another
converter. But as you said, the bone density can vary from CT to CT and from
patient to patient, so I will continue to use 1500 as a good guess. It
worked most of the times for my files, sometimes I get holes in my
reconstructed surface. I just thought there might be a possibility to
calculate a good value, but now I understand that it is not as easy as I
thought.

Thank you!



Stephen R. Aylward wrote:
> 
> Hi Sandra,
> 
> CT images are ACQUIRED in Hounsfield units.  These units (unlike, for 
> example, MR) are on a absolute scale that has physical meaning, i.e., 
> the radiodensity of the material.   The radiodensity of air is -1000 HU, 
> water is 0 HU, and bone is about +1000 HU.   There will be variations 
> between and within patients as bone density changes, but 1000 HU is a 
> good start.
> 
> CT images are typically STORED in dicom files using unsigned shorts. 
> So, the negative recorded values of HU units cannot be directly 
> represented in the DICOM files.   Therefore, two additional fields are 
> also stored in the dicom files when they contain CT data: RescaleSlope 
> and RescaleIntercept.  For CT images, these additional values are 
> typically set to 1 and -1000.  That is, an offset of -1000 must be 
> applied to the recorded values in the dicom files to convert them to the 
> acquired HU values.
> 
> MetaImages store dicom's RescaleSlope and RescaleIntercept values in the 
> tags IntensityScale and IntensityOffset.  However, it is up to the DICOM 
> to MetaImage converter to correctly fill-in and use those values - some 
> converters don't do this :(.   Also, until recently (last month) VTK was 
> using a VERY old versions of metaImage that did not support those tags. 
>    ITK's (www.itk.org) version (the 'official' version of ITK) has been 
> supporting them for years.   Last month we synchronized ITK and VTK's 
> versions of MetaImage.
> 
> So, if (the tags IntensityScale and IntensityOffset are in the text 
> header of your MetaImage file and the element type is unsigned shorts) 
> or if (the element is signed shorts), you should probably use 1000 as a 
> guess for bone density.   Otherwise, you should probably use 2000 for
> bone.
> 
> To account for inter- and intra-patient variation, you may want to also 
> follow with a simple connectedness filter from ITK.
> 
> Also, if this is a contrast study (gastro has been injected prior to the 
> scan to accentuate vasculature), then some vessels may be nearly as 
> bright as the bone...and without a pre-contrast study, your job becomes 
> a nice research topic.
> 
> Stephen
> 
> 
> 
> samo wrote:
>> 
>> Sorry, I have to correct myself, I am not looking for the iso-value, I am
>> looking for the contour values I have to set in the marching cubes
>> algorithm. 
>> 
>> 
>> 
>> samo wrote:
>>>
>>> Hi 
>>>
>>> I would like to o know whether it is possible to calculate the iso-value
>>> of an image for the marching cubes algorithm. I have different MetaImage
>>> files (which represent different CT-data-files) which I use in a
>>> program.
>>> I contruct the bone surface via marching cubes. There, I set the value
>>> with cubes->SetValue(0,value). The optimal value changes for every file.
>>> Is there a possibility to calculate the optimal value for representing
>>> the
>>> bones out of the information I get from the MetaImage-file?
>>>
>>> Thanks for your help!
>>>
>>> samo
>>>
>> 
> 
> -- 
> =============================================================
> Stephen R. Aylward, Ph.D.
> Chief Medical Scientist
> Kitware, Inc. - Chapel Hill Office
> http://www.kitware.com
> Phone: (518)371-3971 x300
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