[Insight-users] DICOM : ITK or VTK
Ana Sandro
garufa7000 at hotmail.com
Wed Mar 15 05:21:30 EST 2006
I'm so glad,it works!Thank you,thank you,thank you.I love this community,VTK
wouldn't be the same without this.
Thank you Andinet for your explanation,now I understand what was happening
before.
Enjoy VTK!
>From: "Frank Gao" <gao at mdimaging.com>
>Reply-To: <gao at mdimaging.com>
>To: "Andinet Enquobahrie" <andinet.enqu at kitware.com>,"Ana Sandro"
><garufa7000 at hotmail.com>
>CC: <mathieu.malaterre at kitware.com>,<insight-users at itk.org>
>Subject: RE: [Insight-users] DICOM : ITK or VTK
>Date: Mon, 13 Mar 2006 10:33:08 -0800
>
>This does fix the problem!
>
>Thanks to all of you. It's a lot of fun in this community.
>
>Frank
>
>-----Original Message-----
>From: Andinet Enquobahrie [mailto:andinet.enqu at kitware.com]
>Sent: Monday, March 13, 2006 7:28 AM
>To: Ana Sandro
>Cc: mathieu.malaterre at kitware.com; gao at mdimaging.com; insight-users at itk.org
>Subject: Re: [Insight-users] DICOM : ITK or VTK
>
>Hi Ana,
>
>When reading dicom images you have to use the correct data type that
>corresponds to the modality type. CT values measured in HU can be
>negative as you can see from the HU values of typical materials listed in
>
>http://www.itk.org/Wiki/ITK_Hounsfield_Units
>
>Linear transformation is applied to the CT values when the data is
>written to a dicom file (intercept and slope dicom tags in the header
>correspond to this transformation). When you read a dicom image in ITK
>using GDCM, the image are rescaled back to the HU unit range.
>Therefore, you should use a signed short type to correctly visualize
>your CT image. If you use unsigned short type, the pixels in the
>negative HU range will be casted to a large positive value and that is
>the reason why you are getting a white background...
>
>Having said that, if you would like to do your image analysis task on a
>different data type, you can use one of the intensity mapping filters
>available in ITK to rescale your data.
>
> itk::RrescaleIntensityImageFilter
> itk::ShiftScaleImageFilter...
>etc...
>
>
>HTH,
>-Andinet
>
>
>
> > Hello,i'm vtkuser too and I've exactly the same problem.I read Dicom
> > files of a CT study using ITK and I convert them to VTK with the same
> > classes that Frank ( you can see that fragment code below). I don´t
> > understand what the solution is,Do I have to convert them to png files
> > with DicomImageReadWrite?
> > I've observed that if I read them like images of signed short type
> > there's no problem and I can see them whit the correct gray map but if
> > I read them like images of unsigned short type (and that's what I
> > need) I see them with the inverted gray map as Frank does. The code I
> > use is:
> >
> > typedef itk::Image<unsigned short,2> ImageType; //if I use here signed
> > short there's no problem.
> > typedef itk::ImageFileReader<ImageType> ReaderType;
> > typedef itk::ImageToVTKImageFilter<ImageType> ConnectorType;
> >
> > ReaderType::Pointer reader= ReaderType::New();
> > ConnectorType::Pointer connector= ConnectorType::New();
> > reader->SetFileName( argv[1]);
> > connector->SetInput( reader->GetOutput() );
> >
> > Could you help me?I don't understan what have you done to correct it?
> > Thank you very much.
> > Regards.
> >
> >
> >
> >> From: Mathieu Malaterre <mathieu.malaterre at kitware.com>
> >> To: gao at mdimaging.com
> >> CC: insight-users at itk.org
> >> Subject: Re: [Insight-users] DICOM : ITK or VTK
> >> Date: Fri, 10 Mar 2006 17:17:10 -0500
> >>
> >> Frank,
> >>
> >> Thanks for tending the image, it makes testing much easier.
> >> Without any change I ran the DicomImageReadWrite.cxx example,
> >> like this:
> >>
> >> $ ./bin/DicomImageReadWrite IM-0001-0052.dcm my.dcm my.png my2.dcm
> >>
> >> Looking at the file my.png I don't anything odd with it. Could
> >> you confirm ?
> >>
> >> Thanks
> >> Mathieu
> >>
> >> Frank Gao wrote:
> >>
> >>> Hi Mathieu,
> >>>
> >>> Attached please find the source code, the picture in pic.doc, and
> >>> the dicom
> >>> file I used.
> >>>
> >>> I am using VTK 5.0, ITK 2.4.0.
> >>>
> >>> By the way, I went to ITK download web page, filled in all the data,
> >>> but
> >>> could never get out of the page to start downloading.
> >>>
> >>> Thanks,
> >>>
> >>> Frank
> >>>
> >>> -----Original Message-----
> >>> From: Mathieu Malaterre [mailto:mathieu.malaterre at kitware.com]
> >>> Sent: Thursday, March 09, 2006 5:34 AM
> >>> To: gao at mdimaging.com
> >>> Cc: insight-users at itk.org
> >>> Subject: Re: [Insight-users] DICOM : ITK or VTK
> >>>
> >>> Frank,
> >>>
> >>> Do you have permission to share this image ? If so could you
> >>> send it
> >>> to
> >>> me ? That'd be the easiest way.
> >>>
> >>> If not, could you send us a dump of the header using
> >>> 'DicomImageReadPrintTags' (you can find it in the Examples/IO dir).
>And
> >>> parallel to that send us how you instanciate the itk::Image.
> >>>
> >>> Thanks
> >>> Mathieu
> >>>
> >>> Frank Gao wrote:
> >>>
> >>>> Hi,
> >>>>
> >>>>
> >>>>
> >>>> Can anyone please help with this?
> >>>>
> >>>>
> >>>>
> >>>> First, I use VTK to load 2D DICOM file and display it. Everything
> >>>> is good.
> >>>>
> >>>>
> >>>>
> >>>> Then I try to read 2D DICOM file with itkImageFileReader, and then
>use
> >>>> itkImageTOVTKImagefilter to load the data into VTK and display it.
> >>>> I got
> >>>> a picture with inverted gray maps (black turns into white).
> >>>>
> >>>>
> >>>>
> >>>> Is there any option in either ITK or VTK side to correct this? Do I
> >>>> have
> >>>> to use any filter to reverse the picture?
> >>>>
> >>>>
> >>>>
> >>>> Your help is really appreciated.
> >>>>
> >>>>
> >>>>
> >>>> Frank
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
>-----------------------------------------------------------------------
>-
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> Insight-users mailing list
> >>>> Insight-users at itk.org
> >>>> http://www.itk.org/mailman/listinfo/insight-users
> >>>
> >>
> >> _______________________________________________
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> >
> >
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