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Transforming image to world coordinates with negative z axis
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Transforming image to world coordinates with negative z axis
by John M. Drescher
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I am loading a dicom CT series in image # order
The first slice is: 0020|0032 Image Position (Patient) = -164.300\-169.500\-24.750 0020|0037 Image Orientation (Patient) = 1.000000\0.000000\0.000000\0.000000\1.000000\0.000000 And the last slice is: 0020|0032 Image Position (Patient) = -164.300\-169.500\-359.750 0020|0037 Image Orientation (Patient) = 1.000000\0.000000\0.000000\0.000000\1.000000\0.000000 The problem I am having is that TransformIndexToPhysicalPoint is returning Z values that are positive which is impossible because the z range is from -24.750 to -359.750. I thought it was the same problem as http://www.nabble.com/itk::Image-vs.-itk::OrientedImage-td19899159.html but my direction vector (examined while debugging) looks wrong to me: 1 0 0 0 1 0 0 0 1 Any ideas how to fix this so that I get the correct world coordinates? Or am I misunderstanding something? I am quite new at itk and vtk. I am using itk version is 3.10.2, and vtk-5.2.1. Thanks, John M. Drescher _____________________________________ 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 ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://www.itk.org/mailman/listinfo/insight-users |
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Re: Transforming image to world coordinates with negative z axis
by Luis Ibanez
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Hi John,
You are right, this looks strange. Please do the following: Just after you load your DICOM image into an ITK image, call the Print() method in the resulting image, and post the outcome to the mailing list. Your code should look something like imageSeriesReader->Update(); imageSeriesReader->GetOutput()->Print( std::cout ); The output of the Print() method will help us to locate the source of the problem. ---- BTW: Why do you say that the direction cosines > 1 0 0 > 0 1 0 > 0 0 1 look wrong to you ? Given that the direction cosines in the DICOM header are > 1.000000\0.000000\0.000000\0.000000\1.000000\0.000000 It seems normal to have the Direction matrix to be an identity matrix. Thanks Luis -------------------- John Drescher wrote: > I am loading a dicom CT series in image # order > > The first slice is: > 0020|0032 Image Position (Patient) = -164.300\-169.500\-24.750 > 0020|0037 Image Orientation (Patient) = > 1.000000\0.000000\0.000000\0.000000\1.000000\0.000000 > > And the last slice is: > 0020|0032 Image Position (Patient) = -164.300\-169.500\-359.750 > 0020|0037 Image Orientation (Patient) = > 1.000000\0.000000\0.000000\0.000000\1.000000\0.000000 > > The problem I am having is that TransformIndexToPhysicalPoint is > returning Z values that are positive which is impossible because the z > range is from -24.750 to -359.750. I thought it was the same problem > as > > http://www.nabble.com/itk::Image-vs.-itk::OrientedImage-td19899159.html > > but my direction vector (examined while debugging) looks wrong to me: > 1 0 0 > 0 1 0 > 0 0 1 > > Any ideas how to fix this so that I get the correct world coordinates? > Or am I misunderstanding something? I am quite new at itk and vtk. > > I am using itk version is 3.10.2, and vtk-5.2.1. > > Thanks, > John M. Drescher > _____________________________________ > 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 ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://www.itk.org/mailman/listinfo/insight-users > 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 ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://www.itk.org/mailman/listinfo/insight-users |
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Re: Transforming image to world coordinates with negative z axis
by John M. Drescher
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> You are right, this looks strange.
> > > Please do the following: > > Just after you load your DICOM image into an ITK image, > call the Print() method in the resulting image, and post > the outcome to the mailing list. > > Your code should look something like > > imageSeriesReader->Update(); > > imageSeriesReader->GetOutput()->Print( std::cout ); > > > The output of the Print() method will help us to locate > the source of the problem. > > OrientedImage (01D5C650) RTTI typeinfo: class itk::OrientedImage<short,3> Reference Count: 1 Modified Time: 2757 Debug: Off Observers: none Source: (01D5C508) Source output index: 0 Release Data: Off Data Released: False Global Release Data: Off PipelineMTime: 30 UpdateMTime: 2758 LargestPossibleRegion: Dimension: 3 Index: [0, 0, 0] Size: [512, 512, 107] BufferedRegion: Dimension: 3 Index: [0, 0, 0] Size: [512, 512, 107] RequestedRegion: Dimension: 3 Index: [0, 0, 0] Size: [512, 512, 107] Spacing: [0.626953, 0.626953, 2.5] Origin: [-174.6, -160.5, -35.685] Direction: 1 0 0 0 1 0 0 0 1 IndexToPointMatrix: 0.626953 0 0 0 0.626953 0 0 0 2.5 PointToIndexMatrix: 1.59502 0 0 0 1.59502 0 0 0 0.4 PixelContainer: ImportImageContainer (01D5C8A0) RTTI typeinfo: class itk::ImportImageContainer<unsigned long,short> Reference Count: 1 Modified Time: 81 Debug: Off Observers: none Pointer: 03410040 Container manages memory: true Size: 28049408 Capacity: 28049408 > ---- > > > BTW: Why do you say that the direction cosines > >> 1 0 0 >> 0 1 0 >> 0 0 1 > > look wrong to you ? > 1 0 0 0 1 0 0 0 -1 so that the z axis coordinate conversion would be handled correctly. > Given that the direction cosines in the DICOM header > are > >> 1.000000\0.000000\0.000000\0.000000\1.000000\0.000000 > > It seems normal to have the Direction matrix to be an > identity matrix. > Looks like I have to do some reading. Thanks for your help, John _____________________________________ 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 ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://www.itk.org/mailman/listinfo/insight-users |
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Re: Transforming image to world coordinates with negative z axis
by Luis Ibanez
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Hi John,
Thanks a lot for posting the output of the Print() method. It seems that the image is not being read as the last slice begin located at: Z = -359.750 Instead it is located at: Z = -35.685 + 2.5 * 107 = +231.81 and... even if the spacing was negative, it could have only got to: Z = -35.685 - 2.5 * 107 = -303.18 This raises suspicion about what you call the "last DICOM slice..." Are you sure that it belongs to the same Series as the first slice ? Also, If you visualize the image that you can read with ITK, does it look ok ? BTW: As DICOM readers/viewers you may want to try: A) Slicer http://www.slicer.org B) VV http://www.midasjournal.org/browse/publication/288 Please let us know what you find. Thanks Luis ------------------- John Drescher wrote: >>You are right, this looks strange. >> >> >>Please do the following: >> >>Just after you load your DICOM image into an ITK image, >>call the Print() method in the resulting image, and post >>the outcome to the mailing list. >> >>Your code should look something like >> >> imageSeriesReader->Update(); >> >> imageSeriesReader->GetOutput()->Print( std::cout ); >> >> >>The output of the Print() method will help us to locate >>the source of the problem. >> >> > > > OrientedImage (01D5C650) > RTTI typeinfo: class itk::OrientedImage<short,3> > Reference Count: 1 > Modified Time: 2757 > Debug: Off > Observers: > none > Source: (01D5C508) > Source output index: 0 > Release Data: Off > Data Released: False > Global Release Data: Off > PipelineMTime: 30 > UpdateMTime: 2758 > LargestPossibleRegion: > Dimension: 3 > Index: [0, 0, 0] > Size: [512, 512, 107] > BufferedRegion: > Dimension: 3 > Index: [0, 0, 0] > Size: [512, 512, 107] > RequestedRegion: > Dimension: 3 > Index: [0, 0, 0] > Size: [512, 512, 107] > Spacing: [0.626953, 0.626953, 2.5] > Origin: [-174.6, -160.5, -35.685] > Direction: > 1 0 0 > 0 1 0 > 0 0 1 > > IndexToPointMatrix: > 0.626953 0 0 > 0 0.626953 0 > 0 0 2.5 > > PointToIndexMatrix: > 1.59502 0 0 > 0 1.59502 0 > 0 0 0.4 > > PixelContainer: > ImportImageContainer (01D5C8A0) > RTTI typeinfo: class itk::ImportImageContainer<unsigned long,short> > Reference Count: 1 > Modified Time: 81 > Debug: Off > Observers: > none > Pointer: 03410040 > Container manages memory: true > Size: 28049408 > Capacity: 28049408 > > >>---- >> >> >>BTW: Why do you say that the direction cosines >> >> >>>1 0 0 >>>0 1 0 >>>0 0 1 >> >>look wrong to you ? >> > > I thought it should be > > 1 0 0 > 0 1 0 > 0 0 -1 > > so that the z axis coordinate conversion would be handled correctly. > > >>Given that the direction cosines in the DICOM header >>are >> >> >>>1.000000\0.000000\0.000000\0.000000\1.000000\0.000000 >> >>It seems normal to have the Direction matrix to be an >>identity matrix. >> > > Looks like I have to do some reading. > > Thanks for your help, > John > 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 ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://www.itk.org/mailman/listinfo/insight-users |
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Re: Transforming image to world coordinates with negative z axis
by John M. Drescher
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Luis,
I am Sorry. I will have to get you new output. The debug output I posted for GetOutput()->Print( std::cout ) was not the same as the original post. John On Thu, Mar 12, 2009 at 4:35 PM, Luis Ibanez <luis.ibanez@...> wrote: > Hi John, > > Thanks a lot for posting the output of the Print() method. > > It seems that the image is not being read as the last slice > begin located at: > > Z = -359.750 > > Instead it is located at: > > > Z = -35.685 + 2.5 * 107 = +231.81 > > and... even if the spacing was negative, > it could have only got to: > > Z = -35.685 - 2.5 * 107 = -303.18 > > > > This raises suspicion about what you call the > > > "last DICOM slice..." > > > Are you sure that it belongs to the same Series > as the first slice ? > > > Also, > If you visualize the image that you can read with ITK, > does it look ok ? > > > BTW: As DICOM readers/viewers you may want to try: > > > A) Slicer > http://www.slicer.org > > B) VV > http://www.midasjournal.org/browse/publication/288 > > > > Please let us know what you find. > > > Thanks > > > Luis > > > ------------------- > John Drescher wrote: >>> >>> You are right, this looks strange. >>> >>> >>> Please do the following: >>> >>> Just after you load your DICOM image into an ITK image, >>> call the Print() method in the resulting image, and post >>> the outcome to the mailing list. >>> >>> Your code should look something like >>> >>> imageSeriesReader->Update(); >>> >>> imageSeriesReader->GetOutput()->Print( std::cout ); >>> >>> >>> The output of the Print() method will help us to locate >>> the source of the problem. >>> >>> >> >> >> OrientedImage (01D5C650) >> RTTI typeinfo: class itk::OrientedImage<short,3> >> Reference Count: 1 >> Modified Time: 2757 >> Debug: Off >> Observers: >> none >> Source: (01D5C508) >> Source output index: 0 >> Release Data: Off >> Data Released: False >> Global Release Data: Off >> PipelineMTime: 30 >> UpdateMTime: 2758 >> LargestPossibleRegion: >> Dimension: 3 >> Index: [0, 0, 0] >> Size: [512, 512, 107] >> BufferedRegion: >> Dimension: 3 >> Index: [0, 0, 0] >> Size: [512, 512, 107] >> RequestedRegion: >> Dimension: 3 >> Index: [0, 0, 0] >> Size: [512, 512, 107] >> Spacing: [0.626953, 0.626953, 2.5] >> Origin: [-174.6, -160.5, -35.685] >> Direction: >> 1 0 0 >> 0 1 0 >> 0 0 1 >> >> IndexToPointMatrix: >> 0.626953 0 0 >> 0 0.626953 0 >> 0 0 2.5 >> >> PointToIndexMatrix: >> 1.59502 0 0 >> 0 1.59502 0 >> 0 0 0.4 >> >> PixelContainer: >> ImportImageContainer (01D5C8A0) >> RTTI typeinfo: class itk::ImportImageContainer<unsigned long,short> >> Reference Count: 1 >> Modified Time: 81 >> Debug: Off >> Observers: >> none >> Pointer: 03410040 >> Container manages memory: true >> Size: 28049408 >> Capacity: 28049408 >> >> >>> ---- >>> >>> >>> BTW: Why do you say that the direction cosines >>> >>> >>>> 1 0 0 >>>> 0 1 0 >>>> 0 0 1 >>> >>> look wrong to you ? >>> >> >> I thought it should be >> >> 1 0 0 >> 0 1 0 >> 0 0 -1 >> >> so that the z axis coordinate conversion would be handled correctly. >> >> >>> Given that the direction cosines in the DICOM header >>> are >>> >>> >>>> 1.000000\0.000000\0.000000\0.000000\1.000000\0.000000 >>> >>> It seems normal to have the Direction matrix to be an >>> identity matrix. >>> >> >> Looks like I have to do some reading. >> >> Thanks for your help, >> John >> > -- John M. Drescher _____________________________________ 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 ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://www.itk.org/mailman/listinfo/insight-users |
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Re: Transforming image to world coordinates with negative z axis
by John M. Drescher
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Here is output from 1 series:
0020|0013 Instance Number = 1 0020|0032 Image Position (Patient) = -174.600006\-160.500000\-35.685001 0020|0037 Image Orientation (Patient) = 1.000000\0.000000\0.000000\0.000000\1.000000\0.000000 0020|0013 Instance Number = 107 0020|0032 Image Position (Patient) = -174.600006\-160.500000\-300.684998 0020|0037 Image Orientation (Patient) = 1.000000\0.000000\0.000000\0.000000\1.000000\0.000000 OrientedImage (02606C90) RTTI typeinfo: class itk::OrientedImage<short,3> Reference Count: 1 Modified Time: 2757 Debug: Off Observers: none Source: (02606B88) Source output index: 0 Release Data: Off Data Released: False Global Release Data: Off PipelineMTime: 30 UpdateMTime: 2758 LargestPossibleRegion: Dimension: 3 Index: [0, 0, 0] Size: [512, 512, 107] BufferedRegion: Dimension: 3 Index: [0, 0, 0] Size: [512, 512, 107] RequestedRegion: Dimension: 3 Index: [0, 0, 0] Size: [512, 512, 107] Spacing: [0.626953, 0.626953, 2.5] Origin: [-174.6, -160.5, -35.685] Direction: 1 0 0 0 1 0 0 0 1 IndexToPointMatrix: 0.626953 0 0 0 0.626953 0 0 0 2.5 PointToIndexMatrix: 1.59502 0 0 0 1.59502 0 0 0 0.4 PixelContainer: ImportImageContainer (02606F30) RTTI typeinfo: class itk::ImportImageContainer<unsigned long,short> Reference Count: 1 Modified Time: 81 Debug: Off Observers: none Pointer: 05660040 Container manages memory: true Size: 28049408 Capacity: 28049408 John _____________________________________ 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 ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://www.itk.org/mailman/listinfo/insight-users |
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Re: Transforming image to world coordinates with negative z axis, from DICOM image
by Luis Ibanez
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Hi John, This looks strange. Is there a chance that you could send us the DICOM images ? You will have to de-identify the image by first removing all patient information. Thanks Luis ---------------------- John Drescher wrote: > Here is output from 1 series: > > 0020|0013 Instance Number = 1 > 0020|0032 Image Position (Patient) = -174.600006\-160.500000\-35.685001 > 0020|0037 Image Orientation (Patient) = > 1.000000\0.000000\0.000000\0.000000\1.000000\0.000000 > > 0020|0013 Instance Number = 107 > 0020|0032 Image Position (Patient) = -174.600006\-160.500000\-300.684998 > 0020|0037 Image Orientation (Patient) = > 1.000000\0.000000\0.000000\0.000000\1.000000\0.000000 > > OrientedImage (02606C90) > RTTI typeinfo: class itk::OrientedImage<short,3> > Reference Count: 1 > Modified Time: 2757 > Debug: Off > Observers: > none > Source: (02606B88) > Source output index: 0 > Release Data: Off > Data Released: False > Global Release Data: Off > PipelineMTime: 30 > UpdateMTime: 2758 > LargestPossibleRegion: > Dimension: 3 > Index: [0, 0, 0] > Size: [512, 512, 107] > BufferedRegion: > Dimension: 3 > Index: [0, 0, 0] > Size: [512, 512, 107] > RequestedRegion: > Dimension: 3 > Index: [0, 0, 0] > Size: [512, 512, 107] > Spacing: [0.626953, 0.626953, 2.5] > Origin: [-174.6, -160.5, -35.685] > Direction: > 1 0 0 > 0 1 0 > 0 0 1 > > IndexToPointMatrix: > 0.626953 0 0 > 0 0.626953 0 > 0 0 2.5 > > PointToIndexMatrix: > 1.59502 0 0 > 0 1.59502 0 > 0 0 0.4 > > PixelContainer: > ImportImageContainer (02606F30) > RTTI typeinfo: class itk::ImportImageContainer<unsigned long,short> > Reference Count: 1 > Modified Time: 81 > Debug: Off > Observers: > none > Pointer: 05660040 > Container manages memory: true > Size: 28049408 > Capacity: 28049408 > > John > 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 ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://www.itk.org/mailman/listinfo/insight-users |
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