[vtkusers] How get DICOM image intensity?

[Bill Lorensen]

vtk images are flipped in the y -direction. This is because vtk takes
a "computer graphics" view of images while itk takes a "medical" view.

In itk, the first pixel in memory is the first pixel on disk. In vtk,
the first pixel in memory is the first pixel of the last y "line".

On Sun, Sep 12, 2010 at 11:37 AM, Jim Peterson <jimcp at cox.net> wrote:
> ok, I believe we have a registration problem between the vtk model
> coordinates and the ITKSnap model coordinates. if I understand the data you
> have given, we have some point data like:
>
> tested point
>        ITKSnap value
>        ITK Snap Material
>        VTK Value
>        Vtk Material
> pt1
>        2318
>        dense bone
>        -1024
>        air (-1000 is air at STP calibration)
> pt2
>        2210
>        dense bone
>        1023
>        soft bone
> pt3
>        2410
>        dense bone
>        41
>        watery liquid (0 is water at STP calibration)
> pt4
>        2130
>        dense bone
>        993
>        soft bone
>
>
> We agree all of these values are reasonable for some location in a dental
> scan. I believe the problem is, in spite of expectations and intentions, the
> location tested are not from the same input data, maybe the coordinate
> schemes in vtk and itk do not match. Can you find corresponding values in
> the ITKSnap? perhaps by transposing a coordinate location? can we find
> locations to "sample" in the vtk model that produce the dense bone values?
>
> does that make sense?
> Hope that helps,
> Jim
>
> Italo Ribeiro wrote:
>>
>> Hi Jim,
>>
>> The value not is same the entire tooth, the diferents values are the same
>> point. In point (226, 100, 1) the values are:
>>
>> ITKsnap : 2130
>> Mycode: 993
>>
>> 2010/9/12 Jim Peterson <jimcp at cox.net <mailto:jimcp at cox.net>>
>>
>>    Hi Italo,
>>
>>    I am not an ITKSnap user myself, you are suggesting ITKSnap
>>    reports the same value for the entire tooth? I think you would
>>    have to iterate over the points in the tooth to find the maximum
>>    value in vtk to duplicate that if it is true. Can you display the
>>    point coordinates that have that value in ITKSnap? Then see if vtk
>>    has the same value at that point? I have trouble believing vtk has
>>    incorrect pixel data by point for imaging content.
>>
>>    Jim
>>
>>    Italo Ribeiro wrote:
>>
>>        Hi Jim,
>>
>>        I have dicom image with teeth, i am looking intensity values
>>        of 2 front teeth.
>>
>>        But some happen very strange, the tooth the left have greater
>>        intensity in ITKsnap 2518 and my code -1024. The tooth the
>>        right side have in ITKsnap 2402 and in my code 41. I do not
>>        know why the values are different.
>>
>>        In my code i get 255 points of heigh and width, but when i get
>>        dimension the image, vtk show 512 x 512, same dimesion show in
>>        ITKsnap. ITKsnap get dimension of voxels, so i must get
>>        information the intensity value voxel of volume and no pixel
>>        the image?
>>
>>        thanks.
>>
>>        2010/9/11 Jim Peterson <jimcp at cox.net <mailto:jimcp at cox.net>
>>        <mailto:jimcp at cox.net <mailto:jimcp at cox.net>>>
>>
>>
>>           Personally, I am sorry, but there is not enough information in
>>           your description of the problem to be sure you have a
>>        legitimate
>>           complaint. does your dicom data consist of only one point?
>>        how are
>>           you certain you have selected the exact same location?
>>
>>           in my mainframe programming life we have a saying:
>>
>>           "when expected results do not match observed results, check the
>>           library concatenation"
>>
>>           .... in my opinion, chances are you are looking at
>>        different points.
>>
>>           sorry, Hoping to be helpful not critical.
>>           Jim
>>
>>           Italo Ribeiro wrote:
>>
>>               No more ideas?
>>
>>               2010/9/10 Italo Ribeiro <italo.ribeiro at gmail.com
>>        <mailto:italo.ribeiro at gmail.com>
>>               <mailto:italo.ribeiro at gmail.com
>>        <mailto:italo.ribeiro at gmail.com>>
>>               <mailto:italo.ribeiro at gmail.com
>>        <mailto:italo.ribeiro at gmail.com>
>>               <mailto:italo.ribeiro at gmail.com
>>        <mailto:italo.ribeiro at gmail.com>>>>
>>
>>
>>                  I am expecting MIP of image point. In my program the
>>        value
>>               for one
>>                  point is 1023 and ITKsnap show 2210.
>>
>>                  Why the value is different?
>>
>>                  2010/9/10 John Drescher <drescherjm at gmail.com
>>        <mailto:drescherjm at gmail.com>
>>               <mailto:drescherjm at gmail.com <mailto:drescherjm at gmail.com>>
>>                  <mailto:drescherjm at gmail.com
>>        <mailto:drescherjm at gmail.com> <mailto:drescherjm at gmail.com
>>        <mailto:drescherjm at gmail.com>>>>
>>
>>
>>
>>                      > Using GetScalarType the type returned is
>>        short, i was
>>               using
>>                      int. But the
>>                      > value maximum showed is 1024 and i see the
>>        maximum short
>>                      value is 32767 and
>>                      > the intensity value is not corret.
>>                      >
>>
>>                      Depending on how you read the dicom file the value
>>               should be in
>>                      hounsfield units. I am confused on whether you
>>        mean you
>>               were
>>                      expecting
>>                      32767 or hounsfield.
>>
>>                      John
>>
>>
>>
>>
>>                  --     Ítalo Mendes
>>                  ogre.irados.org <http://ogre.irados.org>
>>        <http://ogre.irados.org>
>>               <http://ogre.irados.org>
>>
>>
>>
>>
>>               --         Ítalo Mendes
>>
>>               ogre.irados.org <http://ogre.irados.org>
>>        <http://ogre.irados.org> <http://ogre.irados.org>
>>
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>>
>>        --         Ítalo Mendes
>>        ogre.irados.org <http://ogre.irados.org> <http://ogre.irados.org>
>>
>>
>>
>>
>>
>> --
>> Ítalo Mendes
>> ogre.irados.org <http://ogre.irados.org>
>
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