Hi, One possible issue - make sure that the image viewer applied is displaying the correct dynamic range so it does just not appear that there are only zeros after interpolation. 3D Slicer, ITK-SNAP, etc. support this.
HTH, Matt On Sat, Sep 9, 2017 at 1:49 AM, Pfaehler, EAG (ngmb) <e.a.g.pfaeh...@umcg.nl> wrote: > Hey, > > thanks. I did this, but it did not change anything. However, I used another > image (with some higher intensity values) and then I got an image with only > 1s. > > Can it be the problem that my images have only values from 0-5? > I also tried an image with only 0 and 1, but als here I get only zeros after > interpolation. > > ________________________________________ > Van: Matt McCormick [matt.mccorm...@kitware.com] > Verzonden: vrijdag 8 september 2017 21:27 > Aan: Pfaehler, EAG (ngmb) > CC: Samuel Gerber; insight-developers@itk.org > Onderwerp: Re: [ITK-dev] [ITK] problems itk resample filter > > Hi, > > The Origin should be the same in the resampled image. > > HTH, > Matt > > On Fri, Sep 8, 2017 at 3:12 PM, Pfaehler, EAG (ngmb) > <e.a.g.pfaeh...@umcg.nl> wrote: >> Thanks Samuel and Matt for the help. However, it is unfortunatly still not >> working. >> >> I deleted the line resizeFilter->SetTransform, but unfortunately it did not >> change anything. >> >> Then I tried to set the direction and the origin. But maybe here is the >> problem. I set as direction the same direction as in the original image >> because I do not want to have any rotation. >> >> But I am a bit insecure how to set the origin. First I set the origin in the >> resampled image to the same as in the original image, what did not work. >> Then I tried different things, e.g >> >> origin[0] = origin[0] + inputSpacing[0] * (newWidth - oldWidth); >> origin[1] = origin[1] + inputSpacing[1] * (newHeight - oldHeight); >> origin[2] = origin[2] + inputSpacing[2] * (newDepth - oldDepth); >> >> where newWidth etc is the width of the new image and oldWidth of the >> original image. And origin[0] is the x value of the original origin etc. >> >> But this was also not working. ( In all of these cases I get an image full >> of zeros. >> >> If I make originalImage->Print(std::cout) I get the following: >> >> Image (000000000282A800) >> RTTI typeinfo: class itk::Image<float,3> >> Reference Count: 3 >> Modified Time: 705 >> Debug: Off >> Object Name: >> Observers: >> none >> Source: (none) >> Source output name: (none) >> Release Data: Off >> Data Released: False >> Global Release Data: Off >> PipelineMTime: 692 >> UpdateMTime: 704 >> RealTimeStamp: 0 seconds >> LargestPossibleRegion: >> Dimension: 3 >> Index: [0, 0, 0] >> Size: [11, 11, 19] >> BufferedRegion: >> Dimension: 3 >> Index: [0, 0, 0] >> Size: [11, 11, 19] >> RequestedRegion: >> Dimension: 3 >> Index: [0, 0, 0] >> Size: [11, 11, 19] >> Spacing: [3.1819, 3.1819, 2] >> Origin: [48.5757, -171.979, 20.5] >> Direction: >> 1 0 0 >> 0 1 0 >> 0 0 1 >> >> IndexToPointMatrix: >> 3.1819 0 0 >> 0 3.1819 0 >> 0 0 2 >> >> PointToIndexMatrix: >> 0.314278 0 0 >> 0 0.314278 0 >> 0 0 0.5 >> >> Inverse Direction: >> 1 0 0 >> 0 1 0 >> 0 0 1 >> >> PixelContainer: >> ImportImageContainer (00000000027B59F0) >> RTTI typeinfo: class itk::ImportImageContainer<unsigned >> __int64,float> >> Reference Count: 1 >> Modified Time: 701 >> Debug: Off >> Object Name: >> Observers: >> none >> Pointer: 00000000028542E0 >> Container manages memory: true >> Size: 2299 >> Capacity: 2299 >> >> If I do the same for the resampled image I get: >> >> Image (000000000282B100) >> RTTI typeinfo: class itk::Image<float,3> >> Reference Count: 2 >> Modified Time: 11626 >> Debug: Off >> Object Name: >> Observers: >> none >> Source: (000000000282BB80) >> Source output name: Primary >> Release Data: Off >> Data Released: False >> Global Release Data: Off >> PipelineMTime: 11614 >> UpdateMTime: 11627 >> RealTimeStamp: 0 seconds >> LargestPossibleRegion: >> Dimension: 3 >> Index: [0, 0, 0] >> Size: [17, 17, 19] >> BufferedRegion: >> Dimension: 3 >> Index: [0, 0, 0] >> Size: [17, 17, 19] >> RequestedRegion: >> Dimension: 3 >> Index: [0, 0, 0] >> Size: [17, 17, 19] >> Spacing: [2, 2, 2] >> Origin: [67.6671, -152.888, 20.5] >> Direction: >> 1 0 0 >> 0 1 0 >> 0 0 1 >> >> IndexToPointMatrix: >> 2 0 0 >> 0 2 0 >> 0 0 2 >> >> PointToIndexMatrix: >> 0.5 0 0 >> 0 0.5 0 >> 0 0 0.5 >> >> Inverse Direction: >> 1 0 0 >> 0 1 0 >> 0 0 1 >> >> PixelContainer: >> ImportImageContainer (00000000027B5EC0) >> RTTI typeinfo: class itk::ImportImageContainer<unsigned >> __int64,float> >> Reference Count: 1 >> Modified Time: 11625 >> Debug: Off >> Object Name: >> Observers: >> none >> Pointer: 0000000002A8D520 >> Container manages memory: true >> Size: 5491 >> Capacity: 5491 >> >> Does that maybe help to find out whats going wrong? >> >> Thanks in advance >> >> >> >> ________________________________________ >> Van: Matt McCormick [matt.mccorm...@kitware.com] >> Verzonden: vrijdag 8 september 2017 15:32 >> Aan: Pfaehler, EAG (ngmb) >> CC: Samuel Gerber; insight-developers@itk.org >> Onderwerp: Re: [ITK-dev] [ITK] problems itk resample filter >> >> Hi Elli, >> >> The OutputOrigin and OutputDirection may need to be set so the >> sampling grids overlap. >> >> HTH, >> Matt >> >> On Fri, Sep 8, 2017 at 9:13 AM, Pfaehler, EAG (ngmb) >> <e.a.g.pfaeh...@umcg.nl> wrote: >>> Thanks, I did this. Now I get an image, with the desired size, but there all >>> image values are 0. I get the same when I use linear interpolation… >>> >>> Does someone know, what could be the reason? >>> >>> >>> >>> Thanks in advance, >>> >>> >>> >>> Regards >>> >>> >>> >>> Elli >>> >>> >>> >>> Van: Samuel Gerber [mailto:samuel.ger...@kitware.com] >>> Verzonden: vrijdag 8 september 2017 14:51 >>> Aan: Pfaehler, EAG (ngmb) >>> CC: insight-developers@itk.org >>> Onderwerp: Re: [ITK] [ITK-dev] problems itk resample filter >>> >>> >>> >>> I believe you might need to call resizeFilter2->Update() >>> >>> >>> >>> >>> >>> >>> >>> On Fri, Sep 8, 2017 at 8:32 AM, Pfaehler, EAG (ngmb) >>> <e.a.g.pfaeh...@umcg.nl> wrote: >>> >>> Dear all, >>> >>> >>> >>> I would need some help to resample so that it has isotropic voxels in the >>> end. >>> >>> For this, I wanted to use the Nearest Neighbor Interpolator and the >>> ResampleFilterType. >>> >>> My code is running, but the output of the filter has always the dimensions >>> [0 0 0], so is not existent. >>> >>> What am I doing wrong? (see code below) >>> >>> >>> >>> Thanks in advance! >>> >>> Elli >>> >>> >>> >>> typedef itk::NearestNeighborInterpolateImageFunction<ImageType, T> >>> NearestNeighborInterpolatorType; >>> >>> typedef itk::ResampleImageFilter<ImageType, ImageType> >>> ResampleFilterType; >>> >>> typedef itk::AffineTransform <double, 3> TransformType; >>> >>> //use nearest neighbor interpolation >>> >>> typename NearestNeighborInterpolatorType::Pointer >>> nearestNeighborInterpolator = NearestNeighborInterpolatorType::New(); >>> >>> typename ImageType::DirectionType direction; >>> >>> typename TransformType::Pointer transform = TransformType::New(); >>> >>> //transform->SetIdentity(); >>> >>> typedef itk::NearestNeighborInterpolateImageFunction<ImageType, double> >>> InterpolatorType; >>> >>> //typedef itk::LinearInterpolateImageFunction<ImageType, double > >>> InterpolatorType; >>> >>> typename InterpolatorType::Pointer interpolator = InterpolatorType::New(); >>> >>> >>> >>> typename ResampleFilterType::Pointer resizeFilter2 = >>> ResampleFilterType::New(); >>> >>> resizeFilter2->SetTransform(transform); >>> >>> >>> >>> resizeFilter2->SetInterpolator( interpolator ); >>> >>> resizeFilter2->SetDefaultPixelValue(0); >>> >>> //resizeFilter2->SetInterpolator(); >>> >>> >>> >>> const typename ImageType::SpacingType& inputSpacing = image->GetSpacing(); >>> >>> //sampling >>> >>> double outputSpacing[3]; >>> >>> // Fetch original image size >>> >>> const typename ImageType::RegionType& inputRegion = >>> image->GetLargestPossibleRegion(); >>> >>> const typename ImageType::SizeType& inputSize = inputRegion.GetSize(); >>> >>> unsigned int oldWidth = inputSize[0]; >>> >>> unsigned int oldHeight = inputSize[1]; >>> >>> unsigned int oldDepth = inputSize[2]; >>> >>> unsigned int newWidth; >>> >>> unsigned int newHeight; >>> >>> unsigned int newDepth; >>> >>> //get the new height etc of image >>> >>> double minimum = inputSpacing[0]; >>> >>> if (inputSpacing[1]<minimum){ >>> >>> minimum = inputSpacing[1]; >>> >>> } >>> >>> if (inputSpacing[2] < minimum){ >>> >>> minimum = inputSpacing[2]; >>> >>> } >>> >>> outputSpacing[0] = minimum; >>> >>> outputSpacing[1] = minimum; >>> >>> outputSpacing[2] = minimum; >>> >>> newWidth = (double) oldWidth * inputSpacing[0]/minimum; >>> >>> ewHeight = (double) oldHeight * inputSpacing[1]/minimum; >>> >>> newDepth = (double) oldDepth * inputSpacing[2]/minimum; >>> >>> // Set the output spacing as specified on the command line >>> >>> resizeFilter2->SetOutputSpacing(outputSpacing); >>> >>> // Set the computed size >>> >>> itk::Size<3> outputSize = { {newWidth, newHeight, newDepth} }; >>> >>> resizeFilter2->SetSize(outputSize); >>> >>> // Specify the input for the resamplers >>> >>> resizeFilter2->SetInput(image); >>> >>> ImageType::Pointer imageNew = resizeFilter2->GetOutput(); >>> >>> const typename ImageType::RegionType& outputRegion = >>> imageNew->GetLargestPossibleRegion(); >>> >>> const typename ImageType::SizeType& outputSize2 = >>> outputRegion.GetSize(); >>> >>> >>> >>> ________________________________ >>> >>> De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de >>> geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken >>> van dit bericht, het niet openbaar maken of op enige wijze verspreiden of >>> vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een >>> incomplete aankomst of vertraging van dit verzonden bericht. >>> >>> The contents of this message are confidential and only intended for the eyes >>> of the addressee(s). Others than the addressee(s) are not allowed to use >>> this message, to make it public or to distribute or multiply this message in >>> any way. The UMCG cannot be held responsible for incomplete reception or >>> delay of this transferred message. >>> >>> >>> _______________________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://kitware.com/products/protraining.php >>> >>> 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://public.kitware.com/mailman/listinfo/insight-developers >>> >>> _______________________________________________ >>> Community mailing list >>> commun...@itk.org >>> http://public.kitware.com/mailman/listinfo/community >>> >>> >>> >>> >>> >>> -- >>> >>> Samuel Gerber >>> R&D Engineer >>> Kitware, Inc. >>> >>> ________________________________ >>> De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de >>> geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken >>> van dit bericht, het niet openbaar maken of op enige wijze verspreiden of >>> vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een >>> incomplete aankomst of vertraging van dit verzonden bericht. >>> >>> The contents of this message are confidential and only intended for the eyes >>> of the addressee(s). Others than the addressee(s) are not allowed to use >>> this message, to make it public or to distribute or multiply this message in >>> any way. The UMCG cannot be held responsible for incomplete reception or >>> delay of this transferred message. >>> >>> _______________________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://kitware.com/products/protraining.php >>> >>> 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://public.kitware.com/mailman/listinfo/insight-developers >>> >> ________________________________ >> De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de >> geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken >> van dit bericht, het niet openbaar maken of op enige wijze verspreiden of >> vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een >> incomplete aankomst of vertraging van dit verzonden bericht. >> >> The contents of this message are confidential and only intended for the eyes >> of the addressee(s). Others than the addressee(s) are not allowed to use >> this message, to make it public or to distribute or multiply this message in >> any way. The UMCG cannot be held responsible for incomplete reception or >> delay of this transferred message. > ________________________________ > De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de > geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken > van dit bericht, het niet openbaar maken of op enige wijze verspreiden of > vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een > incomplete aankomst of vertraging van dit verzonden bericht. > > The contents of this message are confidential and only intended for the eyes > of the addressee(s). Others than the addressee(s) are not allowed to use this > message, to make it public or to distribute or multiply this message in any > way. The UMCG cannot be held responsible for incomplete reception or delay of > this transferred message. _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php 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://public.kitware.com/mailman/listinfo/insight-developers
