# Beginner in ITK, Averaging Image

**URL:** <https://discourse.itk.org/t/beginner-in-itk-averaging-image/2328>\
**Category:** Beginner Questions\
**Created:** [October 16, 2019, 5:38pm UTC](https://discourse.itk.org/t/beginner-in-itk-averaging-image/2328 "2019-10-16T17:38:36Z")\
**Posts on this page:** 7\
**Page:** 1

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**Author:** ![banikr](https://discourse.itk.org/user_avatar/discourse.itk.org/banikr/32/3296_2.png) [@banikr](https://discourse.itk.org/u/banikr)\
**Post date:** [October 16, 2019, 5:38pm UTC](https://discourse.itk.org/t/beginner-in-itk-averaging-image/2328/1 "2019-10-16T17:38:36Z")

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Hello all,  
I am new in ITK and using it with CMAKE, GCC compiler. As a python/Matlab programmer, I am finding ITK a bit confusing. But I am trying to do a project that will help me to learn ITK in general. I find the project interesting.  
I have a public dataset of 21 3D MR images. I want to average those images and form a single one for registration purposes.  
How do I do that?  
And also would be helpful if anyone shares how to load class and header files for my purpose/need.

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**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:** [October 16, 2019, 8:41pm UTC](https://discourse.itk.org/t/beginner-in-itk-averaging-image/2328/2 "2019-10-16T20:41:10Z")

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If you want to use your average image for registration purposes, then you have a chicken and egg problem. To get a good average image, you first need to register images together.

You could use ordinary registration techniques to register all images to one which is most average-looking to you. Let’s call that image atlas master. Then you could resample the images onto the pixel grid of the atlas master. Then you could finally make pixel-wise averages.

But before starting it, maybe you should read some [groupwise registration](https://scholar.google.com/scholar?q=groupwise+image+registration) papers. [This one](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105200/) is freely accessible.

As for the ITK code, you could look at the [examples](https://itk.org/ITKExamples/src/Registration/index.html) and pick one to start from.

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**Author:** ![banikr](https://discourse.itk.org/user_avatar/discourse.itk.org/banikr/32/3296_2.png) [@banikr](https://discourse.itk.org/u/banikr)\
**Post date:** [October 16, 2019, 9:06pm UTC](https://discourse.itk.org/t/beginner-in-itk-averaging-image/2328/3 "2019-10-16T21:06:24Z")

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Thanks for your reply.  
I wanted to add the images and divide it by the number of images added. Though I mentioned registration but in the second step I will use registration for comparison.  
How do I add the 21 images from my local directory?

I am trying the following codes to add the images…let me know but ending up with some errors

\<

> int  
> main (int argc, char \*argv)  
> {  
> // Setup types  
> const unsigned int nDims = 3;  
> typedef itk::Image\<int, nDims\> ImageType;

// Create and setup a reader from argv[1]  
typedef itk::ImageFileReader ImageReaderType;

ImageReaderType::Pointer readers[21];  
for (size\_t i = 0; i \< 21; i++)  
{  
readers[i] = ImageReaderType::New ();  
readers[i]-\>SetFileName (“KKI2009-” + std::to\_string (files[i])  
+ “-MPRAGE.nii”);  
readers[i]-\>Update ();  
}

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**Author:** ![matt.mccormick](https://discourse.itk.org/user_avatar/discourse.itk.org/matt.mccormick/32/7_2.png) [@matt.mccormick](https://discourse.itk.org/u/matt.mccormick)\
**Post date:** [October 16, 2019, 9:25pm UTC](https://discourse.itk.org/t/beginner-in-itk-averaging-image/2328/4 "2019-10-16T21:25:11Z")

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Welcome to ITK, Rana! ☀

A good resource to be aware of is [The ITK Software Guide](https://itk.org/ItkSoftwareGuide.pdf).

Also, note that ITK also [has a Python interface](https://itkpythonpackage.readthedocs.io/en/latest/Quick_start_guide.html).

To achieve your goal in C++, one possible approach is to:

1. Create an `itk::ImageFileReader`, set the filename for the first file, then call `Update()`. Get the output image _SmartPointer_, e.g. `outputImage`, with `reader->GetOutput()`, then call `DisconnectPipeline()` on the image. Call `FillBuffer(0)` on the image to start with an image of 0’s.
2. Create an `itk::AddImageFilter`. The inputs are the `outputImage` and the ImageFileReader.
3. Looping over the filenames, call `SetFileName()` on the ImageFileReader. Then call `Update()` on the AddImageFilter. Then assign the `outputImage` SmartPointer to `addImageFilter->GetOutput()`. Then, call `outputImage->DisconnectPipeline();`.
4. Use _itk::MultipleImageFilter_, which [also works with scalars](https://itk.org/ITKExamples/src/Filtering/ImageIntensity/MultiplyImageByScalar/Documentation.html) to divide by the number of images.

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**Author:** ![banikr](https://discourse.itk.org/user_avatar/discourse.itk.org/banikr/32/3296_2.png) [@banikr](https://discourse.itk.org/u/banikr)\
**Post date:** [October 18, 2019, 8:59pm UTC](https://discourse.itk.org/t/beginner-in-itk-averaging-image/2328/5 "2019-10-18T20:59:18Z")

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Hello Matt,  
Thanks for the suggestion. Unfortunately, I ran some codes myself and it worked pretty much as I expected so I couldn’t see your suggestion otherwise I would’ve tried yours. Could you please take a look at the following code:

```auto
#include "itkImage.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkDivideImageFilter.h"
#include "itkNaryAddImageFilter.h"
#include <string< //double bracket does not print here

int
main(int argc, char * argv[])
{
  // Setup types
  const unsigned int nDims = 3 ;
  typedef itk::Image< double, nDims > ImageType;

  // Create and setup readers for images:
  typedef itk::ImageFileReader< ImageType > readerType;
  readerType::Pointer readers[21];

  for (int i = 1; i<=21; i = i+1)
    {
      std::string digit="";
      if(i<10)
      {
       digit = "0";
      }
      readers[i-1] = readerType::New();
      readers[i-1]-> SetFileName("../MPRAGE21_copy/KKI2009-"+digit + std::to_string(i)+"-MPRAGE.nii");
      readers[i-1]->Update();
    }

  typedef itk::NaryAddImageFilter<ImageType, ImageType>NAddImageFilterType;
  NAddImageFilterType::Pointer nAddImage = NAddImageFilterType::New();
  for (int i =0;i<=20;i++)
    {
      nAddImage->SetInput(i, readers[i]->GetOutput());
    }
  nAddImage->Update();

  typedef itk::DivideImageFilter<ImageType, ImageType, ImageType>DivideImageFilterType;
  DivideImageFilterType::Pointer divider = DivideImageFilterType::New();
  divider->SetInput (nAddImage->GetOutput());
  divider-> SetConstant(21.0);
  divider->Update();

  // write out the result to:
  typedef itk::ImageFileWriter < ImageType > writerType;
  writerType::Pointer writer = writerType::New();
  //writer->SetInput ( divider->GetOutput());
  writer->SetFileName ("Sum21.nii" );
  writer->SetInput(divider->GetOutput());
  writer->Update();

  // Done.
  return 0 ;
}

```

What I want to do is now choose one image as a fixed image and affinely register other 20 ones to the fixed image and average all 21 again.  
Which will give me affine template.

How do I perform affine registration in my case?

Thanks in advance.

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<div class="post-metadata">

**Author:** ![matt.mccormick](https://discourse.itk.org/user_avatar/discourse.itk.org/matt.mccormick/32/7_2.png) [@matt.mccormick](https://discourse.itk.org/u/matt.mccormick)\
**Post date:** [October 21, 2019, 4:48pm UTC](https://discourse.itk.org/t/beginner-in-itk-averaging-image/2328/6 "2019-10-21T16:48:31Z")

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> [@banikr](#):
>
> Could you please take a look at the following code:

@banikr looks great 👏

> [@banikr](#):
>
> How do I perform affine registration in my case?

The choice of similarity metric, optimization strategy, etc. depends on your data. A good general starting place is the ITK-based [elastix](http://elastix.isi.uu.nl/).

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<div class="post-metadata">

**Author:** ![banikr](https://discourse.itk.org/user_avatar/discourse.itk.org/banikr/32/3296_2.png) [@banikr](https://discourse.itk.org/u/banikr)\
**Post date:** [October 21, 2019, 5:11pm UTC](https://discourse.itk.org/t/beginner-in-itk-averaging-image/2328/7 "2019-10-21T17:11:09Z")

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Hello Matt,

Thanks for the reply. I have tried writing some codes and shared for help in another post.

> [@Affine Registration 3D for beginner](https://discourse.itk.org/t/affine-registration-3d-for-beginner/2337):
>
> Hello All, I have 21 3D MR brain images… as a format …/MPRAGE\_copy/KKI-2009-01-MPRAGE.nii for one image in MPRAGE\_copy folder… Out of the 21 images I would like to use the first image as fixed image and register the rest of the 20 images on that reference fixed image. I want to write the code in self-dependent where I do not have to provide any input. I am using GCC/6.0.0 compiler… have four folders: ITKAffReg3: where the code will be named ITKAffReg3.cxx and CMakeLists.txt which will c…

Could you take a look and may be suggest ?

Thanks