[vtkusers] How get DICOM image intensity?
Italo Ribeiro
italo.ribeiro at gmail.com
Mon Sep 13 21:52:53 EDT 2010
Hi Jim,
I get the solution, the problem is that i am dont select position correctly
with mouse. I stop use integer and use now float for get position the mouse
cilck and i now i get the correct values.
One observation, the positions the ITKsnap and vtk are be differents. The Y
axi is inverted.
Thank you for everything.
2010/9/13 Jim Peterson <jimcp at cox.net>
> Italo,
> I am not sure what I am supposed to "look very close" at, nor what actual
> problem we are addressing. What you have raised is a technical need to
> access the scalar data for an image in vtk, could easily be a classroom
> assignment, and not a problem I have any great interest in.
> Have you implemented a point picker in vtk to interact with the 3d model in
> vtk to access the scalar values for selected points? I believe you will find
> each structured grid "point" to be a 3d space location derived from the row
> and column location in a dicom image file, the combination of row, column
> and file number times the sample spacing results in a location is space for
> the point. the radio intensity value results in a scalar. at a sufficient
> scaling a point scalar is a voxel scalar is a pixel scalar, depending on
> whether we are talking the structured grid in 3d space, a surface element in
> the space or a row and column in a single dicom image file.
>
> The image of the dicom data loaded is generated in itk and vtk by similar
> "surface generating" algorithms that construct polygon defined surfaces
> connecting points with similar scalar values. So if ITKSnap and vtk both
> generate similar images, they are both finding similar scalar data.
> I am afraid I am at the end if my interest in this problem,
> Jim
>
> Italo Ribeiro wrote:
>
>> 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 <mailto:
>> 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
>> <mailto: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>
>> <mailto: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>>
>> >> <mailto: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>>>
>> >> <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
>> <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>>>
>> >> <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
>> <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>
>> >> <http://ogre.irados.org>
>> >>
>> >>
>> >>
>> >>
>> >> -- Ítalo Mendes
>> >>
>> >> ogre.irados.org <http://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> <http://ogre.irados.org>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >> --
>> >> Ítalo Mendes
>> >> ogre.irados.org <http://ogre.irados.org> <http://ogre.irados.org>
>> >
>> > _______________________________________________
>> > Powered by www.kitware.com <http://www.kitware.com>
>> >
>> > Visit other Kitware open-source projects at
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>>
>>
>>
>> --
>> Ítalo Mendes
>> ogre.irados.org <http://ogre.irados.org>
>>
>
>
--
Ítalo Mendes
ogre.irados.org
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