# correction of gantry tilted ct image

**URL:** https://discourse.itk.org/t/correction-of-gantry-tilted-ct-image/4841
**Category:** Beginner Questions
**Tags:** dicom
**Created:** [March 1, 2022, 9:43am UTC](https://discourse.itk.org/t/correction-of-gantry-tilted-ct-image/4841 "2022-03-01T09:43:50Z")
**Posts on this page:** 17
**Page:** 1

<div class="post-metadata">

### Author: ![csad6517](https://discourse.itk.org/letter_avatar_proxy/v4/letter/c/49beb7/32.png) [@csad6517](https://discourse.itk.org/u/csad6517)
#### Post date: [March 1, 2022, 9:43am UTC](https://discourse.itk.org/t/correction-of-gantry-tilted-ct-image/4841/1 "2022-03-01T09:43:50Z")

</div>

Hello,  
I need help by understanding the correct pipleline and determining the share factor of a gantry tilted ct dataset, so that I can apply a transform on it.  
I know the exact angle of the gantry over read out DICOM Tag (-15°) and that I can use the `Shear()` function from `itkAffineTransform` class for the correction:

```
const unsigned int dim= 3;
typedef itk::AffineTransform< float, dim> TransformType;

TransformType::Pointer transform = TransformType::New(); 
transform->Shear(int axis1, int axis2, TParametersValueType coef); // ?

itk::AffineTransform<float, dim>::OutputVectorType translation;
translation[0] = ;
translation[1] = ;
translation[2] = ;
transform->Translate(translation); //?

```

How can I determine the direction axis and shear factor for the `Shear()` function and in which direction should I translate the dataset?  
Thank you!

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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 1, 2022, 2:47pm UTC](https://discourse.itk.org/t/correction-of-gantry-tilted-ct-image/4841/2 "2022-03-01T14:47:20Z")

</div>

If you call `reader->ForceOrthogonalDirectionOff();`, the image direction should already be correct and you don’t need any manual processing. See the complete [example](https://itk.org/ITKExamples/src/IO/GDCM/ReadDICOMSeriesAndWrite3DImage/Documentation.html).

---

<div class="post-metadata">

### Author: ![csad6517](https://discourse.itk.org/letter_avatar_proxy/v4/letter/c/49beb7/32.png) [@csad6517](https://discourse.itk.org/u/csad6517)
#### Post date: [March 4, 2022, 7:36am UTC](https://discourse.itk.org/t/correction-of-gantry-tilted-ct-image/4841/3 "2022-03-04T07:36:01Z")

</div>

Thank you for your response. Does it mean that this function corrects the tilt already during reading of images and visualize them series correctly (square)?

`ForceOrthogonalDirectionOff()` is implemented in version 5.2.1 and if I understand correctly it calculates the position difference of the first and last image in the dataset and shifts the images properly in the correct direction?

```auto
if (!m_ForceOrthogonalDirection)
{
  for (j = 0; j < TOutputImage::ImageDimension; ++j)
  {
    direction[j][this->m_NumberOfDimensionsInImage] = dirN[j] / dirNnorm;
  }
}
output->SetOrigin(origin);
output->SetSpacing(spacing);
output->SetDirection(direction);
output->SetLargestPossibleRegion(largestRegion);

```

---

<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 4, 2022, 2:06pm UTC](https://discourse.itk.org/t/correction-of-gantry-tilted-ct-image/4841/4 "2022-03-04T14:06:50Z")

</div>

Yes. [That](https://github.com/InsightSoftwareConsortium/ITK/commit/23436a04c978d176b32775e97d2701d96d6d2dd6) was added specifically to correctly read gantry-tilted CT images. If other steps in the processing pipeline have trouble handling non-orthogonal images, you can resample the images into ortho-normal grid immediately after reading.

---

<div class="post-metadata">

### Author: ![csad6517](https://discourse.itk.org/letter_avatar_proxy/v4/letter/c/49beb7/32.png) [@csad6517](https://discourse.itk.org/u/csad6517)
#### Post date: [March 4, 2022, 3:38pm UTC](https://discourse.itk.org/t/correction-of-gantry-tilted-ct-image/4841/5 "2022-03-04T15:38:53Z")

</div>

Since I am using an older version of the itk, I have implemented the `ForceOrthogonalDirectionOff()` function in my source code same as in `itkImagesSeriesReader.hxx`. As expected the image direction matrix is shifted:

Image direction before applying `ForceOrthogonalDirectionOff` on the image:

```auto
1 0 0
0 1 0
0 0 1

```

Image direction after applying `ForceOrthogonalDirectionOff`:

```auto
1 0 0
0 0.984808 0.173648
0 -0.173648 0.984808

```

The values in matrix `-0.173648` and `0.173648` is exactly the `sin` of the tilt angle in radiance, if I calculate it separately:  
`float sinOfTiltAngle = sin(vtkMath::RadiansFromDegrees(-10.0));`

The image origin and spacing are remaining unchanged after applying the function. I guess it is ok? My goal is, doing the tilt correction on the fly without needing to save and load the ct dataset again. I will try this resampling ([Resample](https://itk.org/ITKExamples/src/Filtering/ImageGrid/ResampleAnImage/Documentation.html)), if you have no other recommendation.  
Thank you!

---

<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 4, 2022, 3:44pm UTC](https://discourse.itk.org/t/correction-of-gantry-tilted-ct-image/4841/6 "2022-03-04T15:44:47Z")

</div>

When I was writing this, I had plenty of data to work with. Some of the series had 2D X-rays which allowed me to check whether the data looked correct for rendering and resampling into ortho-normal images.

I don’t remember whether the spacing changes, but it is computed by this line `spacing[this->m_NumberOfDimensionsInImage] = dirNnorm / ( numberOfFiles - 1 );`.

---

<div class="post-metadata">

### Author: ![csad6517](https://discourse.itk.org/letter_avatar_proxy/v4/letter/c/49beb7/32.png) [@csad6517](https://discourse.itk.org/u/csad6517)
#### Post date: [March 7, 2022, 3:14pm UTC](https://discourse.itk.org/t/correction-of-gantry-tilted-ct-image/4841/7 "2022-03-07T15:14:28Z")

</div>

After resampling the image dataset as following and connecting it to the visualization pipeline, I get only a black the screen, which does not contains any oriented image (axial, sagittal,cornal). What I am doing wrong during resampling?

```
typedef short PixelType;
const unsigned int Dimension = 3;

typedef itk::OrientedImage<PixelType, Dimension> OutputImageType;
const OutputImageType* first = firstReader->GetOutput();
typedef itk::ResampleImageFilter<OutputImageType, OutputImageType> ResampleFilterType;

ResampleFilterType::Pointer resampleFilter = ResampleFilterType::New();
resampleFilter->SetInput(seriesReader->GetOutput());
resampleFilter->SetOutputOrigin(imOrigin); // does not change
resampleFilter->SetOutputSpacing(imSpacing); // does not chaneg
resampleFilter->SetOutputDirection(imDirection); // shifted in correct direction
resampleFilter->SetSize(imOutputSize); // same as series reader size (512x512xnumberOfImages)
resampleFilter->Update();    

ItkImageType::Pointer itkIm = seriesReader->GetOutput();
itkIm = resampleFilter->GetOutput();
itkIm ->Update();

itk::VTKImageExport<ItkImageType>::Pointer exporter = itk::VTKImageExport<ItkImageType>::New();
exporter->SetInput(itkIm);
exporter->ReleaseDataFlagOn();
exporter->Update();
```

---

<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 7, 2022, 3:59pm UTC](https://discourse.itk.org/t/correction-of-gantry-tilted-ct-image/4841/8 "2022-03-07T15:59:41Z")

</div>

Do you get a non-black image if you replace `exporter->SetInput(itkIm);` by `exporter->SetInput(seriesReader->GetOutput());`?

What if you replace it by `exporter->SetInput(resampleFilter->GetOutput());`?

---

<div class="post-metadata">

### Author: ![csad6517](https://discourse.itk.org/letter_avatar_proxy/v4/letter/c/49beb7/32.png) [@csad6517](https://discourse.itk.org/u/csad6517)
#### Post date: [March 8, 2022, 8:08am UTC](https://discourse.itk.org/t/correction-of-gantry-tilted-ct-image/4841/9 "2022-03-08T08:08:03Z")

</div>

If I use following pipeline as you mentioned, I get colored backgrounds without any image on them. I guess what I represented is only renderer from vtk:

```
ItkImageType::Pointer itkIm = seriesReader->GetOutput();
itkIm ->SetDirection(direction);
itkIm ->SetSpacing(spacing);
itkIm ->SetOrigin(origin);

ResampleFilterType::Pointer resampleFilter = ResampleFilterType::New();
resampleFilter->SetInput(itkIm);
resampleFilter->SetOutputOrigin(origin);
resampleFilter->SetOutputSpacing(spacing);
resampleFilter->SetOutputDirection(direction);
resampleFilter->SetSize(outputSize);
resampleFilter->Update();

//itkIm = resampleFilter->GetOutput();
//itkIm->Update();

itk::VTKImageExport<ItkImageType>::Pointer exporter = itk::VTKImageExport<ItkImageType>::New();
exporter->SetInput(resampleFilter->GetOutput());
exporter->ReleaseDataFlagOn();
exporter->Update();

```

 ![image](https://discourse.itk.org/uploads/default/original/2X/e/e466139fcc565d7bc804c2733a6fe018b603bf3e.png)

If I set following pipeline, I get only black backgrounds

```
ItkImageType::Pointer itkIm = seriesReader->GetOutput();
itkIm ->SetDirection(direction);
itkIm ->SetSpacing(spacing);
itkIm ->SetOrigin(origin);

ResampleFilterType::Pointer resampleFilter = ResampleFilterType::New();
resampleFilter->SetInput(seriesReader->GetOutput());
resampleFilter->SetOutputOrigin(origin);
resampleFilter->SetOutputSpacing(spacing);
resampleFilter->SetOutputDirection(direction);
resampleFilter->SetSize(outputSize);
resampleFilter->Update();

itkIm = resampleFilter->GetOutput();
itkIm->Update();

itk::VTKImageExport<ItkImageType>::Pointer exporter = itk::VTKImageExport<ItkImageType>::New();
exporter->SetInput(resampleFilter->GetOputput());
exporter->ReleaseDataFlagOn();
exporter->Update();

```

 ![image](https://discourse.itk.org/uploads/default/original/2X/3/30585ffca934b98f8128535b0f68e31bc1397f14.png)

If I set following pipeline, I can not read the image dataset:

```
ItkImageType::Pointer itkIm = seriesReader->GetOutput();
itkIm ->SetDirection(direction);
itkIm ->SetSpacing(spacing);
itkIm ->SetOrigin(origin);

ResampleFilterType::Pointer resampleFilter = ResampleFilterType::New();
resampleFilter->SetInput(seriesReader->GetOutput());
resampleFilter->SetOutputOrigin(origin);
resampleFilter->SetOutputSpacing(spacing);
resampleFilter->SetOutputDirection(direction);
resampleFilter->SetSize(outputSize);
resampleFilter->Update();

itkIm = resampleFilter->GetOutput();
itkIm->Update();

itk::VTKImageExport<ItkImageType>::Pointer exporter = itk::VTKImageExport<ItkImageType>::New();
exporter->SetInput(itkIm);
exporter->ReleaseDataFlagOn();
exporter->Update();

```

**EDIT**  
What if I use the `itkIm`, which contains new `direction` as a reference image in `resampleFilter` and give still the `seriesReader` as input?

```
ItkImageType::Pointer itkIm = seriesReader->GetOutput();
itkIm ->SetDirection(direction);
itkIm ->SetSpacing(spacing);
itkIm ->SetOrigin(origin);

ResampleFilterType::Pointer resampleFilter = ResampleFilterType::New();
resampleFilter->SetInput(seriesReader->GetOutput());
resampleFilter->UseReferenceImageOn();
resampleFilter->SetReferenceImage(itkIm);
resampleFilter->SetOutputOrigin(origin);
resampleFilter->SetOutputSpacing(spacing);
resampleFilter->SetOutputDirection(direction);
resampleFilter->SetSize(outputSize);
resampleFilter->Update();

itk::VTKImageExport<ItkImageType>::Pointer exporter = itk::VTKImageExport<ItkImageType>::New();
exporter->SetInput(resampleFilter->GetOputput());
exporter->ReleaseDataFlagOn();
exporter->Update();

```

So I can read and visualize images and the `image direction` in `resamleFilter` is still correct:

```
DIRECTION in resampleFilter : 
1 0 0
0 0.984808 0.173648
0 -0.173648 0.984808
```

---

<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 8, 2022, 4:10pm UTC](https://discourse.itk.org/t/correction-of-gantry-tilted-ct-image/4841/10 "2022-03-08T16:10:23Z")

</div>

Does resample filter work correctly? Try [writing](https://github.com/InsightSoftwareConsortium/ITK/blob/v5.3rc03/Modules/IO/ImageBase/include/itkImageFileWriter.h#L247) it via `itk::WriteImage(resampleFilter->Update(), "temp.nrrd");` and visualize it using Slicer or ITK-SNAP.

If it does, this is more of a question for [VTK](https://discourse.vtk.org/) than ITK.

---

<div class="post-metadata">

### Author: ![csad6517](https://discourse.itk.org/letter_avatar_proxy/v4/letter/c/49beb7/32.png) [@csad6517](https://discourse.itk.org/u/csad6517)
#### Post date: [March 9, 2022, 9:07am UTC](https://discourse.itk.org/t/correction-of-gantry-tilted-ct-image/4841/11 "2022-03-09T09:07:40Z")

</div>

I don’t think that resample filter works as expected. The written `nrrd` data is visualized as black (without any image) in slicer. Please see my whole code block:

```
if (gantry != 0.0)
{
  ItkImageType::Pointer itkIm = seriesReader->GetOutput();

  bool reverseOrder = true;
  const auto numberOfFiles = static_cast<int>(m_Filenames.size());
  const int firstFileName = (reverseOrder ? numberOfFiles - 1 : 0);
  const int lastFileName = (reverseOrder ? 0 : numberOfFiles - 1);

  typedef itk::OrientedImage<short, 3> ItkImageType;
  using ReaderType = itk::ImageFileReader<ItkImageType>;
  ReaderType::Pointer firstReader = ReaderType::New();
  ReaderType::Pointer lastReader = ReaderType::New();

  firstReader->SetFileName(m_Filenames[firstFileName].toStdString().c_str());
  firstReader->Update();
  firstReader->UpdateOutputInformation();

  lastReader->SetFileName(m_Filenames[lastFileName].toStdString().c_str());
  lastReader->Update();
  lastReader->UpdateOutputInformation();

  const ItkImageType *firstImage = firstReader->GetOutput();

  typename ItkImageType::SpacingType spacing = firstImage->GetSpacing();
  typename ItkImageType::PointType origin = firstImage->GetOrigin();
  typename ItkImageType::DirectionType direction = firstImage->GetDirection();
  typename ItkImageType::RegionType::ImageRegion largestRegion = firstImage->GetLargestPossibleRegion();

  // Set size of the processed dataset same as the original dataset
  ItkImageType::SizeType outputSize;
  typedef ItkImageType::SizeType::SizeValueType SizeValueType;
  const ItkImageType::SizeType &inputSize = largestRegion.GetSize();
  outputSize[0] = inputSize[0];
  outputSize[1] = inputSize[1];
  outputSize[2] = numberOfFiles;

  using SpacingScalarType = typename ItkImageType::SpacingValueType;
  itk::Array<SpacingScalarType> position1(ItkImageType::ImageDimension);
  position1.Fill(0.0f);
  itk::Array<SpacingScalarType> positionN(ItkImageType::ImageDimension);
  positionN.Fill(0.0f);

  // Initialize the position to the origin returned by the reader
  unsigned int j;
  for (j = 0; j < ItkImageType::ImageDimension; j++)
  {
    position1[j] = static_cast<SpacingScalarType>(origin[j]);
  }
  const ItkImageType* last = lastReader->GetOutput();

  // Initialize the position to the origin returned by the reader
  for (j = 0; j < ItkImageType::ImageDimension; j++)
  {
    positionN[j] = static_cast<SpacingScalarType>(last->GetOrigin()[j]);
  }

  // Compute and set the inter slice spacing and last (usually third) axis of direction
  itk::Vector<SpacingScalarType, ItkImageType::ImageDimension> dirN;
  for (j = 0; j < ItkImageType::ImageDimension; ++j)
  {
    dirN[j] = positionN[j] - position1[j];
  }

  SpacingScalarType dirNnorm = dirN.GetNorm();
  unsigned int numberOfDimensionsInImage = firstReader->GetImageIO()->GetNumberOfDimensions();
  spacing[numberOfDimensionsInImage] = dirNnorm / (numberOfFiles - 1);
  
  // Shift the image direction and set it to the output image
  for (j = 0; j < ItkImageType::ImageDimension; ++j)
  {
	direction[j][numberOfDimensionsInImage] = dirN[j] / dirNnorm;
  }

  itkIm->SetDirection(direction); //Corrected image direction matrix
  itkIm->SetSpacing(spacing);

  resampleFilter = ResampleFilterType::New();
  resampleFilter->SetInput(itkIm);
  //resampleFilter->UseReferenceImageOn();
  //resampleFilter->SetReferenceImage(itkIm);
  resampleFilter->SetOutputOrigin(itkIm->GetOrigin());
  resampleFilter->SetOutputSpacing(itkIm->GetSpacing());
  resampleFilter->SetOutputDirection(itkIm->GetDirection());
  resampleFilter->SetSize(outputSize);
  resampleFilter->Update();

  //itk::WriteImage(resampleFilter->Update(), "temp.nrrd");
  using WriterType = itk::ImageFileWriter<ItkImageType>;
  WriterType::Pointer writer = WriterType::New();
  writer->SetFileName("temp.nrrd");
  writer->SetInput(resampleFilter->GetOutput());
  writer->Update();

  //itkIm = resampleFilter->GetOutput();
  //itkIm->Update();
  
  itk::VTKImageExport<ItkImageType>::Pointer exporter = itk::VTKImageExport<ItkImageType>::New();
  exporter->SetInput(resampleFilter->GetOutput());
  exporter->ReleaseDataFlagOn();
  exporter->Update();
}
```

---

<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 9, 2022, 2:34pm UTC](https://discourse.itk.org/t/correction-of-gantry-tilted-ct-image/4841/12 "2022-03-09T14:34:17Z")

</div>

How about an even simpler test then: `itk::WriteImage(itkIm, "temp.mha");`. Then visualize this image in slicer. It should be correctly visualized with shear (gantry tilt). Current preview release handles such images correctly, and I think that was true for 5 years if not more.

---

<div class="post-metadata">

### Author: ![csad6517](https://discourse.itk.org/letter_avatar_proxy/v4/letter/c/49beb7/32.png) [@csad6517](https://discourse.itk.org/u/csad6517)
#### Post date: [March 9, 2022, 2:53pm UTC](https://discourse.itk.org/t/correction-of-gantry-tilted-ct-image/4841/13 "2022-03-09T14:53:15Z")

</div>

`itk::WriteImage` does not exist in version 3.20 therefore I had used `itk::ImageFileWriter`

---

<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 9, 2022, 3:00pm UTC](https://discourse.itk.org/t/correction-of-gantry-tilted-ct-image/4841/14 "2022-03-09T15:00:35Z")

</div>

Sure, you can use `ImageFileWriter`. Can you write the image just after reading the DICOM series, before you try to resample it? I suspect that your backporting of this feature to version 3.20 is not quite correct.

---

<div class="post-metadata">

### Author: ![csad6517](https://discourse.itk.org/letter_avatar_proxy/v4/letter/c/49beb7/32.png) [@csad6517](https://discourse.itk.org/u/csad6517)
#### Post date: [March 9, 2022, 3:33pm UTC](https://discourse.itk.org/t/correction-of-gantry-tilted-ct-image/4841/15 "2022-03-09T15:33:47Z")

</div>

Does not matter if I write the `nrrd` image before or after tilt correction, the images are represented in slicer correctly. How it is possible?

---

<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 9, 2022, 3:47pm UTC](https://discourse.itk.org/t/correction-of-gantry-tilted-ct-image/4841/16 "2022-03-09T15:47:04Z")

</div>

Maybe the code was modified to force orthogonal orientation with ITKv4, so 3.20 doesn’t have it?

---

<div class="post-metadata">

### Author: ![csad6517](https://discourse.itk.org/letter_avatar_proxy/v4/letter/c/49beb7/32.png) [@csad6517](https://discourse.itk.org/u/csad6517)
#### Post date: [March 9, 2022, 4:38pm UTC](https://discourse.itk.org/t/correction-of-gantry-tilted-ct-image/4841/17 "2022-03-09T16:38:30Z")

</div>

The version 3.20 does also the same mathematical operations as version 4 to correct the tilt in series reader 🙂 Therefore the tilt is corrected automatically after reading it, without applying any additional operations. It means I had to be more careful during checking the functionality. Thank you for your support.