[vtkusers] How get DICOM image intensity?
Italo Ribeiro
italo.ribeiro at gmail.com
Mon Sep 13 07:00:56 EDT 2010
Hi Jim and Bill,
Look very closed, in ITKsnap the slice 1 is slice 107 in my code, but when i
get the value, i am getting the same slice.
I are begining think that i must get values intensity of voxel and not
point. Look for cell data in vtk, i dont find one function that
"GetScalarCell()", so how i get cell data in vtk? I must use
"GetCell(100)->Derivatives()"? Cell = Voxel?
thanks
2010/9/12 Bill Lorensen <bill.lorensen at gmail.com>
> 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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> >>
> >>
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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>
> >
> > _______________________________________________
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> >
> > Please keep messages on-topic and check the VTK FAQ at:
> > http://www.vtk.org/Wiki/VTK_FAQ
> >
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>
--
Ítalo Mendes
ogre.irados.org
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