# How to get voxel coordinates(as in ITK snap ) from vtkimage viewer from mouse click

**URL:** https://discourse.itk.org/t/how-to-get-voxel-coordinates-as-in-itk-snap-from-vtkimage-viewer-from-mouse-click/4719
**Category:** Engineering
**Tags:** itk, vtk, cpp
**Created:** [January 11, 2022, 3:27pm UTC](https://discourse.itk.org/t/how-to-get-voxel-coordinates-as-in-itk-snap-from-vtkimage-viewer-from-mouse-click/4719 "2022-01-11T15:27:28Z")
**Posts on this page:** 7
**Page:** 1

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### Author: ![SREERAG\_H](https://discourse.itk.org/user_avatar/discourse.itk.org/sreerag_h/32/2486_2.png) [@SREERAG\_H](https://discourse.itk.org/u/SREERAG_H)
#### Post date: [January 11, 2022, 3:27pm UTC](https://discourse.itk.org/t/how-to-get-voxel-coordinates-as-in-itk-snap-from-vtkimage-viewer-from-mouse-click/4719/1 "2022-01-11T15:27:28Z")

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Hello,  
I am trying to use ITK’s region growing algorithm for medical image segmentation. So to put the seedpoint i need exact voxel coordinates of the mouse click position in my vtkimageviewer. So how can I get those voxel coordinates(as in ITK snap tool) from my vtkimageviewer. Currently I am able to get VTK World Coordinates using pick point picker . Now how to convert this vtk world coordinates to voxel coordinates as in ITK snap tool …  
Please help me with this information.

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<div class="post-metadata">

### Author: ![dzenanz](https://discourse.itk.org/user_avatar/discourse.itk.org/dzenanz/32/1093_2.png) [@dzenanz](https://discourse.itk.org/u/dzenanz)
#### Post date: [January 11, 2022, 3:42pm UTC](https://discourse.itk.org/t/how-to-get-voxel-coordinates-as-in-itk-snap-from-vtkimage-viewer-from-mouse-click/4719/2 "2022-01-11T15:42:39Z")

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Have you tried [my suggestion at stack overflow](https://stackoverflow.com/a/70653739/276168)? If so, why doesn’t that work?

There was an example which I wrote:  
[https://itk.org/Wiki/ITK/Examples/IO/itkVtkImageConvertDICOM](https://itk.org/Wiki/ITK/Examples/IO/itkVtkImageConvertDICOM)  
It has been since deleted as unmaintained. Here is the code:

```cpp
#include <itkRandomImageSource.h>
#include "itkImageToVTKImageFilter.h"
 
#include "vtkVersion.h"
#include <vtkSmartPointer.h>
#include <vtkGPUVolumeRayCastMapper.h>
#include <vtkColorTransferFunction.h>
#include <vtkPiecewiseFunction.h>
#include <vtkRenderer.h>
#include <vtkRenderWindow.h>
#include <vtkRenderWindowInteractor.h>
#include <vtkVolumeProperty.h>
#include <vtkMatrix4x4.h>
#include <vtkAxesActor.h>

using VisualizingImageType = itk::Image<unsigned char, 3>;

VisualizingImageType::Pointer createImage()
{
    itk::Size<3> size;
    size[0]=512;
    size[1]=512;
    size[2]=16;
 
    itk::RandomImageSource<VisualizingImageType>::Pointer randomImageSource =
        itk::RandomImageSource<VisualizingImageType>::New();
    randomImageSource->SetNumberOfThreads(1); // to produce non-random results
    randomImageSource->SetSize(size);
    randomImageSource->Update();
    
    VisualizingImageType::Pointer image=randomImageSource->GetOutput();
    double t[3]={0, -200, 150};
    image->SetOrigin(t);
    t[0]=0.68;
    t[1]=0.68;
    t[2]=4.4;
    image->SetSpacing(t);

    VisualizingImageType::DirectionType m;
    m(0,0)=0;
    m(0,1)=1;
    m(0,2)=0;
    m(1,0)=0.707;
    m(1,1)=0;
    m(1,2)=-0.707;
    m(2,0)=-0.707;
    m(2,1)=0;
    m(2,2)=-0.707;
    m=m.GetTranspose();
    image->SetDirection(m);
    return image;
}

int main(int argc, char *argv[])
{
  VisualizingImageType::Pointer image=createImage();
 
  vtkSmartPointer<vtkRenderWindow> renWin = vtkSmartPointer<vtkRenderWindow>::New();
  vtkSmartPointer<vtkRenderer> ren1 = vtkSmartPointer<vtkRenderer>::New();
  ren1->SetBackground(0.5f,0.5f,1.0f);
 
  renWin->AddRenderer(ren1);
  renWin->SetSize(1280,1024);
  vtkSmartPointer<vtkRenderWindowInteractor> iren =
      vtkSmartPointer<vtkRenderWindowInteractor>::New();
  iren->SetRenderWindow(renWin);
  renWin->Render(); // make sure we have an OpenGL context.
 
  using itkVtkConverter = itk::ImageToVTKImageFilter<VisualizingImageType>;
  itkVtkConverter::Pointer conv=itkVtkConverter::New();
  conv->SetInput(image);
 
  vtkSmartPointer<vtkGPUVolumeRayCastMapper> volumeMapper =
      vtkSmartPointer<vtkGPUVolumeRayCastMapper>::New();
#if VTK_MAJOR_VERSION <= 5
  volumeMapper->SetInput(conv->GetOutput());
#else
  conv->Update();
  volumeMapper->SetInputData(conv->GetOutput());
#endif
 
  vtkSmartPointer<vtkVolumeProperty> volumeProperty =
  vtkSmartPointer<vtkVolumeProperty>::New();
 
  vtkSmartPointer<vtkPiecewiseFunction> compositeOpacity =
  vtkSmartPointer<vtkPiecewiseFunction>::New();
  compositeOpacity->AddPoint(0.0,0.1);
  compositeOpacity->AddPoint(80.0,0.2);
  compositeOpacity->AddPoint(255.0,0.1);
  volumeProperty->SetScalarOpacity(compositeOpacity);
 
  vtkSmartPointer<vtkColorTransferFunction> color =
  vtkSmartPointer<vtkColorTransferFunction>::New();
  color->AddRGBPoint(0.0 ,0.0,0.0,1.0);
  color->AddRGBPoint(40.0 ,1.0,0.0,0.0);
  color->AddRGBPoint(255.0,1.0,1.0,1.0);
  volumeProperty->SetColor(color);
 
  vtkSmartPointer<vtkVolume> volume =
  vtkSmartPointer<vtkVolume>::New();
  volume->SetMapper(volumeMapper);
  volume->SetProperty(volumeProperty);
 
  // Here we take care of position and orientation
  // so that volume is in DICOM patient physical space
  VisualizingImageType::DirectionType d=image->GetDirection();
  vtkMatrix4x4 *mat=vtkMatrix4x4::New(); //start with identity matrix
  for (int i=0; i<3; i++)
      for (int k=0; k<3; k++)
          mat->SetElement(i,k, d(i,k));
 
  // Counteract the built-in translation by origin
  VisualizingImageType::PointType origin=image->GetOrigin();
  volume->SetPosition(-origin[0], -origin[1], -origin[2]);
 
  // Add translation to the user matrix
  for (int i=0; i<3; i++)
    {
    mat->SetElement(i,3, origin[i]);
    }
  volume->SetUserMatrix(mat);
 
  // Add coordinate system axes, so we have a reference for position and orientation
  vtkSmartPointer<vtkAxesActor> axes = vtkSmartPointer<vtkAxesActor>::New();
  axes->SetTotalLength(250,250,250);
  axes->SetShaftTypeToCylinder();
  axes->SetCylinderRadius(0.01);
  ren1->AddActor(axes);
 
  ren1->AddVolume( volume );
  ren1->ResetCamera();
 
  renWin->Render();
  renWin->Render();
  renWin->Render();
 
  iren->Start();
 
  return EXIT_SUCCESS;
}

```

You might need something akin to `volume->SetUserMatrix(mat);` for `ijkIndex = itkImage->TransformPhysicalPointToIndex(worldCoordinates);` to work directly. Or an inverse version of that, going from VTK’s world coordinates to ITK’s DICOM Image Position Patient coordinate system before you can use those coordinates in `TransformPhysicalPointToIndex`.

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<div class="post-metadata">

### Author: ![SREERAG\_H](https://discourse.itk.org/user_avatar/discourse.itk.org/sreerag_h/32/2486_2.png) [@SREERAG\_H](https://discourse.itk.org/u/SREERAG_H)
#### Post date: [January 12, 2022, 7:59am UTC](https://discourse.itk.org/t/how-to-get-voxel-coordinates-as-in-itk-snap-from-vtkimage-viewer-from-mouse-click/4719/3 "2022-01-12T07:59:20Z")

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Thank you so much for your response… I will be trying this soon and will give you the update.

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<div class="post-metadata">

### Author: ![SREERAG\_H](https://discourse.itk.org/user_avatar/discourse.itk.org/sreerag_h/32/2486_2.png) [@SREERAG\_H](https://discourse.itk.org/u/SREERAG_H)
#### Post date: [January 18, 2022, 4:57am UTC](https://discourse.itk.org/t/how-to-get-voxel-coordinates-as-in-itk-snap-from-vtkimage-viewer-from-mouse-click/4719/4 "2022-01-18T04:57:47Z")

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Hi ,  
I am really sorry for the late reply. I tried what you suggested but still it is not giving me the exact coordinates. I don’t know where I am going wrong. What I was doing was,  
I am having multiplanar reconstruction window(MPR) and I am using vtkResliceCursorWidget for getting the coordinates . I have tried two methods ,  
1)

this-\>RCW[i]-\>GetResliceCursorRepresentation()-\>GetPlaneSource()-\>GetOrigin(Origin);

this-\>RCW[i]-\>GetResliceCursorRepresentation()-\>GetPlaneSource()-\>GetPoint1(Point1);

this-\>RCW[i]-\>GetResliceCursorRepresentation()-\>GetPlaneSource()-\>GetPoint2(Point2);

And then passing these points to TransformPhysicalPointToIndex() .

1. 

int evenposition[3];  
this-\>Interactor-\>GetEventPosition(evenposition);  
vtkSmartPointer vtkCellPicker pickerr = vtkSmartPointer vtkCellPicker ::New();  
this-\>Interactor-\>SetPicker(pickerr);  
pickerr-\>Pick(evenposition[0], evenposition[1], 0, this-\>Interactor-\>GetRenderWindow()-\>GetRenderers()-\>GetFirstRenderer());  
double datacoordinates[3];  
pickerr-\>GetMapperPosition(datacoordinates);

Then passing these points to TransformPhysicalPointToIndex() .

Both of the above methods are not giving me any transformations for getting voxel coordinates as in ITK SNAP.  
Could you please tell me where I am going wrong and help me to get the voxel coordinates.

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<div class="post-metadata">

### Author: ![dzenanz](https://discourse.itk.org/user_avatar/discourse.itk.org/dzenanz/32/1093_2.png) [@dzenanz](https://discourse.itk.org/u/dzenanz)
#### Post date: [January 18, 2022, 2:42pm UTC](https://discourse.itk.org/t/how-to-get-voxel-coordinates-as-in-itk-snap-from-vtkimage-viewer-from-mouse-click/4719/5 "2022-01-18T14:42:22Z")

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I don’t have a ready solution for that. Maybe try looking at source code of ITK-SNAP? [This](https://sourceforge.net/p/itk-snap/src/ci/master/tree/GUI/Renderer/Window3DPicker.cxx) seems to be a part of it. Or look at source of [Slicer](https://github.com/Slicer/Slicer/) or [MITK](https://github.com/MITK/MITK)? Or use one of those for UI, so you don’t have to make your own GUI?

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<div class="post-metadata">

### Author: ![SREERAG\_H](https://discourse.itk.org/user_avatar/discourse.itk.org/sreerag_h/32/2486_2.png) [@SREERAG\_H](https://discourse.itk.org/u/SREERAG_H)
#### Post date: [March 3, 2022, 9:55am UTC](https://discourse.itk.org/t/how-to-get-voxel-coordinates-as-in-itk-snap-from-vtkimage-viewer-from-mouse-click/4719/6 "2022-03-03T09:55:04Z")

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Hello ,  
Could you please tell is there any other way to solve this issue other than using other GUI. Please see the below code which is my current status.

```
                    int evenpos[3];
		this->Interactor->GetEventPosition(evenpos);
		vtkSmartPointer<vtkCellPicker> pickerr = vtkSmartPointer<vtkCellPicker>::New();
		this->Interactor->SetPicker(pickerr);
		pickerr->Pick(evenpos[0], evenpos[1], 0, this->GetDefaultRenderer());
		double picked[3];
		pickerr->GetPickPosition(picked);

```

Now this picked[3] I need to convert to voxel coordinates. Please help me with this

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<div class="post-metadata">

### Author: ![dzenanz](https://discourse.itk.org/user_avatar/discourse.itk.org/dzenanz/32/1093_2.png) [@dzenanz](https://discourse.itk.org/u/dzenanz)
#### Post date: [March 3, 2022, 4:25pm UTC](https://discourse.itk.org/t/how-to-get-voxel-coordinates-as-in-itk-snap-from-vtkimage-viewer-from-mouse-click/4719/7 "2022-03-03T16:25:34Z")

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Have you tried [vtkImageData::TransformPhysicalPointToContinuousIndex()](https://vtk.org/doc/nightly/html/classvtkImageData.html#aa37a2184cb38394a8828d4998f0628fc)?

If that is not enough, you might need to transform your point `picked` using the same transforms you apply to your image in VTK scene. Or maybe the inverse of that. Apply transforms before passing the point to `TransformPhysicalPointToContinuousIndex`.