_’
When I execute sliceBySliceFilter-\>Update(); I get the following error:
‘_itk::ERROR: SliceBySliceImageFilter(000001630B273560): At least 2 of the first 2 indexed inputs are required but only 1 are specified. The required inputs are expected to be the first inputs_’
And I have no idea of what could it be. How can I solve it? Could I obtain what I want in a different way?
My ITK version is: 4.8.2
Thank you very much,
Cristina
---
### Author:  [@dzenanz](https://discourse.itk.org/u/dzenanz)
#### Post date: [October 17, 2022, 1:01pm UTC](https://discourse.itk.org/t/how-can-i-apply-a-2d-mask-in-a-3d-image-slicebysliceimagefilter/5418/2 "2022-10-17T13:01:56Z")
Maybe try `sliceBySliceFilter->SetInput(1, mask);`? Looking at the code, `SliceBySliceImageFilter` should be able to work with multiple inputs.
---
### Author:  [@dzenanz](https://discourse.itk.org/u/dzenanz)
#### Post date: [October 17, 2022, 1:06pm UTC](https://discourse.itk.org/t/how-can-i-apply-a-2d-mask-in-a-3d-image-slicebysliceimagefilter/5418/3 "2022-10-17T13:06:04Z")
But it expects all the inputs to have the same size (requested region). Depending on what you are trying to accomplish, it might be easier to construct a 3D mask using `TileImageFilter`, and use 3D variant of `MaskImageFilter`.
---
### Author:  [@cristinamontserrat](https://discourse.itk.org/u/cristinamontserrat)
#### Post date: [October 18, 2022, 10:47am UTC](https://discourse.itk.org/t/how-can-i-apply-a-2d-mask-in-a-3d-image-slicebysliceimagefilter/5418/4 "2022-10-18T10:47:04Z")
Thank you for the answer.
- **Firstly**
I have tried the first advice:
> auto mask = ITKImgLabelType2D::New();
> ITKImgLabelType2D::RegionType region = a\_pmask-\>GetLargestPossibleRegion();
>
> mask-\>SetRegions(region);
> mask-\>Allocate();
>
> ITKImgLabelType2D::SizeType regionSize = region.GetSize();
> itk::ImageRegionIterator imageIterator(mask, region);
>
> while (!imageIterator.IsAtEnd())
> {
> imageIterator.Set(itk::NumericTraits::max());
> ++imageIterator;
> }
>
> // We create the filter mask
> using MaskFilterType = itk::MaskImageFilter\;
> MaskFilterType::Pointer maskFilter3D = MaskFilterType::New();
> maskFilter3D-\>SetInput(a\_pmask);
> maskFilter3D-\>SetMaskImage(mask);
>
> // Apply a 2D mask to every slice of a 3D image
> typedef itk::SliceBySliceImageFilter\< ITKImgInType, ITKImgLabelType, MaskFilterType, MaskFilterType, ITKImgLabelType2D, ITKImgLabelType2D \> SliceBySliceImageFilter;
> SliceBySliceImageFilter::Pointer sliceBySliceFilter = SliceBySliceImageFilter::New();
> sliceBySliceFilter-\>SetFilter(maskFilter3D);
> **sliceBySliceFilter-\>SetInput(1, &a\_pimage3D);**
And I get another error, which is:
> itk::ERROR: SliceBySliceImageFilter(0000019653A533C0): Input Primary is required but not set.
* * *
- **Secondly**
I have tried to construct a 3D mask using `TileImageFilter` , and use 3D variant of `MaskImageFilter`.
Here is my code:
> constexpr unsigned int InputDimension = 2;
> constexpr unsigned int OutputDimension = 3;
>
> using PixelType = unsigned char;
> using InputImageType = itk::Image\;
> using OutputImageType = itk::Image\;
>
> using FilterType = itk::TileImageFilter\;
> auto filter = FilterType::New();
>
> itk::FixedArray\ layout;
> layout[0] = 2;
> layout[1] = 2;
> layout[2] = 0;
>
> filter-\>SetLayout(layout);
>
> ITKImgInType::SizeType insize = a\_pimage3D.GetRequestedRegion().GetSize();
> int nImages = insize[2];
>
> for (int ii = 0; ii \<= nImages - 1; ++ii)
> {
> InputImageType::Pointer input = a\_pmask;
> filter-\>SetInput(ii, input);
> }
>
> constexpr PixelType defaultValue = 128;
> filter-\>SetDefaultPixelValue(defaultValue);
>
> filter-\>GetOutput()-\>SetSpacing(a\_pimage3D.GetSpacing());
> filter-\>GetOutput()-\>SetOrigin(a\_pimage3D.GetOrigin());
> filter-\>GetOutput()-\>SetDirection(a\_pimage3D.GetDirection());
>
> _if (f\_verbose)_
> _{_
> _a\_file \<\< "Spacing 3D mask after: " \<\< filter-\>GetOutput()-\>GetSpacing() \<\< std::endl;_
> _a\_file \<\< "Spacing 3D image: " \<\< a\_pimage3D.GetSpacing() \<\< std::endl \<\< std::endl;_
> _a\_file \<\< "Origin 3D mask after: " \<\< filter-\>GetOutput()-\>GetOrigin() \<\< std::endl;_
> _a\_file \<\< "Origin 3D image: " \<\< a\_pimage3D.GetOrigin() \<\< std::endl \<\< std::endl;_
> _}_
>
> // Apply a 3D mask to a 3D image
> using MaskFilterType = itk::MaskImageFilter\;
> MaskFilterType::Pointer maskFilter3D = MaskFilterType::New();
> maskFilter3D-\>SetInput(&a\_pimage3D);
> maskFilter3D-\>SetMaskImage(filter-\>GetOutput());
>
> try
> {
> maskFilter3D-\>Update();
> }
> catch (const itk::ExceptionObject& err)
I don’t understand what’s wrong, because if I print the origin and the spacing of the a\_image3D and the filter, as you can see in my code, I get the following information:
> Spacing 3D mask after: [0.847656, 0.847656, 2.98663]
> Spacing 3D image: [0.847656, 0.847656, 2.98663]
>
> Origin 3D mask after: [-208.208, -251.595, 1148.21]
> Origin 3D image: [-208.208, -251.595, 1148.21]
So, the spacing and the origin is the same. But then, when I execute maskFilter3D-\>Update(); I get the following error:
> ExceptionObject caught !Alma::SegmentationLib::ApplyMask3D
> C:\Dev\ITK\Modules\Core\Common\include\itkImageToImageFilter.hxx:248:
> itk::ERROR: MaskImageFilter(00000231EBE04390): Inputs do not occupy the same physical space!
> InputImage Origin: [-2.0820781e+02, -2.5159518e+02, 1.1482096e+03], InputImage\_1 Origin: [-2.0820781e+02, -2.5159518e+02, 0.0000000e+00]
> Tolerance: 8.4765559e-07
> InputImage Spacing: [8.4765559e-01, 8.4765559e-01, 2.9866300e+00], InputImage\_1 Spacing: [8.4765559e-01, 8.4765559e-01, 1.0000000e+00]
> Tolerance: 8.4765559e-07
What should I do?
Thank you very much,
Cristina
---
### Author:  [@dzenanz](https://discourse.itk.org/u/dzenanz)
#### Post date: [October 18, 2022, 2:57pm UTC](https://discourse.itk.org/t/how-can-i-apply-a-2d-mask-in-a-3d-image-slicebysliceimagefilter/5418/5 "2022-10-18T14:57:44Z")
> [@cristinamontserrat](#):
>
> TileImageFilter
From the docs: “The output image have a larger dimension than the input images. This filter can be used to create a volume from a series of inputs by specifying a layout of 1,1,0.” You are using a tile layout 2,2,0. Your mask is probably bigger than the image.
> _a\_file \<\< "Spacing 3D mask after: " \<\< filter-\>GetOutput()-\>GetSpacing() \<\< std::endl;_
You should print to the same or higher precision as the comparison tolerance (7-8 decimal places) in order to spot a possible problem here.
---
### Author:  [@cristinamontserrat](https://discourse.itk.org/u/cristinamontserrat)
#### Post date: [October 19, 2022, 7:02pm UTC](https://discourse.itk.org/t/how-can-i-apply-a-2d-mask-in-a-3d-image-slicebysliceimagefilter/5418/6 "2022-10-19T19:02:10Z")
Thanks!
I’ve changed the tile layout and I also get exactly the same error.
My code now is:
> using PixelType = unsigned char;
> using InputImageType = ITKImgLabelType2D;
> using OutputImageType = ITKImgLabelType;
>
> using FilterType = itk::TileImageFilter\;
> auto filter = FilterType::New();
>
> itk::FixedArray\ layout;
> layout[0] = 1;
> layout[1] = 1;
> layout[2] = 0;
>
> filter-\>SetLayout(layout);
>
> ITKImgInType::SizeType insize = a\_pimage3D.GetRequestedRegion().GetSize();
> int nImages = insize[2];
>
> unsigned int inputImageNumber = 0;
>
> for (int ii = 1; ii \< nImages-1; ++ii)
> {
> InputImageType::Pointer input = a\_pmask;
> input-\>DisconnectPipeline();
> filter-\>SetInput(inputImageNumber++, input);
> }
>
> constexpr PixelType defaultValue = 128;
> filter-\>SetDefaultPixelValue(defaultValue);
>
> filter-\>GetOutput()-\>SetSpacing(a\_pimage3D.GetSpacing());
> filter-\>GetOutput()-\>SetOrigin(a\_pimage3D.GetOrigin());
> filter-\>GetOutput()-\>SetDirection(a\_pimage3D.GetDirection());
>
> if (f\_verbose)
> {
> a\_file \<\< std::fixed \<\< std::setprecision(9) \<\< std::endl;
> a\_file \<\< "Spacing 3D mask after: " \<\< filter-\>GetOutput()-\>GetSpacing() \<\< std::endl;
> a\_file \<\< "Spacing 3D image: " \<\< a\_pimage3D.GetSpacing() \<\< std::endl \<\< std::endl;
> a\_file \<\< "Origin 3D mask after: " \<\< filter-\>GetOutput()-\>GetOrigin() \<\< std::endl;
> a\_file \<\< "Origin 3D image: " \<\< a\_pimage3D.GetOrigin() \<\< std::endl \<\< std::endl;
> }
>
> // Apply a 3D mask to a 3D image
> using MaskFilterType = itk::MaskImageFilter\;
> MaskFilterType::Pointer maskFilter3D = MaskFilterType::New();
> maskFilter3D-\>SetInput1(&a\_pimage3D);
> maskFilter3D-\>SetInput2(filter-\>GetOutput());
>
> try
> {
> maskFilter3D-\>Update();
> }
> catch (const itk::ExceptionObject& err)
What exactly do the layout values 1,1,0 mean?
Could it be possible that the error is related to the different input pixels type of the `MaskImageFilter` function?
Thank you,
Cristina
---
### Author:  [@dzenanz](https://discourse.itk.org/u/dzenanz)
#### Post date: [October 19, 2022, 7:25pm UTC](https://discourse.itk.org/t/how-can-i-apply-a-2d-mask-in-a-3d-image-slicebysliceimagefilter/5418/7 "2022-10-19T19:25:42Z")
Have you tried `filter->Update();` before `if (f_verbose)`? Are size, bufferedRegion and direction same, too? You could inspect that using a debugger, instead of printing to console.
---
### Author:  [@cristinamontserrat](https://discourse.itk.org/u/cristinamontserrat)
#### Post date: [October 20, 2022, 4:29pm UTC](https://discourse.itk.org/t/how-can-i-apply-a-2d-mask-in-a-3d-image-slicebysliceimagefilter/5418/8 "2022-10-20T16:29:10Z")
Yes, I have tried that. And I also have checked that the inputs have the same size, bufferedRegion and direction too.
As a possible solution, I have changed the way of resampling the image.
I have replaced this:
> filter-\>GetOutput()-\>SetSpacing(a\_pimage3D.GetSpacing());
> filter-\>GetOutput()-\>SetOrigin(a\_pimage3D.GetOrigin());
> filter-\>GetOutput()-\>SetDirection(a\_pimage3D.GetDirection());
For this:
> using ResampleFilterType = itk::ResampleImageFilter\;
> auto resampleFilter = ResampleFilterType::New();
>
> resampleFilter-\>SetInput(filter-\>GetOutput());
> resampleFilter-\>SetOutputSpacing(a\_pimage3D.GetSpacing());
> resampleFilter-\>SetOutputOrigin(a\_pimage3D.GetOrigin());
> resampleFilter-\>SetOutputDirection(a\_pimage3D.GetDirection());
This way, I don’t get the error: `Inputs do not occupy the same physical space!`, but I do get the following error: `Requested region is (at least partially) outside the largest possible region.`
Do you know the reason for this?
Thank you for your dedication.
Cristina
---
### Author:  [@dzenanz](https://discourse.itk.org/u/dzenanz)
#### Post date: [October 20, 2022, 4:37pm UTC](https://discourse.itk.org/t/how-can-i-apply-a-2d-mask-in-a-3d-image-slicebysliceimagefilter/5418/9 "2022-10-20T16:37:16Z")
You need to invoke `filter->Update()`, or at least `filter->UpdateOutputInformation()` before `filter->GetOutput()` will have meaningful data.
---
### Author:  [@cristinamontserrat](https://discourse.itk.org/u/cristinamontserrat)
#### Post date: [October 25, 2022, 6:00pm UTC](https://discourse.itk.org/t/how-can-i-apply-a-2d-mask-in-a-3d-image-slicebysliceimagefilter/5418/10 "2022-10-25T18:00:50Z")
Hi!
I have tried that and it didn’t work for me. But I have also tried another thing, that consists in “resampling” the mask with the `ResampleImageFilter` instead of manually. This way, I have fixed the error. But now another thing is happening.
I create the 3D mask correctly, but then, when I “resample” it, the 3D mask disappears.
I’m going to explain myself with my code.
First of all I create a 3D mask from the 2D mask:
> using PixelType = unsigned char;
> using InputImageType = ITKImgLabelType2D;
> using OutputImageType = ITKImgLabelType;
>
> using FilterType = itk::TileImageFilter\;
> auto filter = FilterType::New();
>
> itk::FixedArray\ layout;
> layout[0] = 1;
> layout[1] = 1;
> layout[2] = 0;
>
> filter-\>SetLayout(layout);
>
> ITKImgInType::SizeType insize = a\_pimage3D.GetRequestedRegion().GetSize();
> int nImages = insize[2];
>
> unsigned int inputImageNumber = 0;
> InputImageType::Pointer input = a\_pmask;
>
> WriteImage(a\_pmask, “a\_pmask.jpg”, a\_file);
> for (int ii = 0; ii \< nImages; ++ii)
> {
> input-\>DisconnectPipeline();
> filter-\>SetInput(inputImageNumber++, a\_pmask);
> }
>
> try
> {
> filter-\>UpdateOutputInformation();
> filter-\>UpdateLargestPossibleRegion();
> }
> catch (const itk::ExceptionObject& err)
> {
> if (f\_verbose)
> {
> a\_file \<\< “ExceptionObject caught !” \<\< **func** \<\< std::endl;
> a\_file \<\< err.what() \<\< std::endl;
> }
> }
That’s done correctly, because if I print the image I can see the 2D mask in every slice of the 3D mask.
Then, I “resample” the mask:
> ITKImgInType::SizeType outputSize = a\_pimage3D.GetLargestPossibleRegion().GetSize();
> ITKImgLabelType::SpacingType outputSpacing = a\_pimage3D.GetSpacing();
>
> using ScalarType = double;
>
> using NearestNeighborInterpolatorType = itk::NearestNeighborInterpolateImageFunction\;
> auto nearestNeighborInterpolator = NearestNeighborInterpolatorType::New();
>
> using ResampleImageFilterType = itk::ResampleImageFilter\;
> ResampleImageFilterType::Pointer resample = ResampleImageFilterType::New();
>
> resample-\>SetInput(filter-\>GetOutput());
> resample-\>SetReferenceImage(&a\_pimage3D);
> resample-\>SetInterpolator(nearestNeighborInterpolator);
> resample-\>UseReferenceImageOn(); // spacing, origin and direction of the reference image will be used
> resample-\>SetSize(outputSize);
>
> try
> {
> resample-\>UpdateOutputInformation();
> resample-\>UpdateLargestPossibleRegion();
> }
> catch (const itk::ExceptionObject& err)
> {
> if (f\_verbose)
> {
> a\_file \<\< “ExceptionObject caught !” \<\< **func** \<\< std::endl;
> a\_file \<\< err.what() \<\< std::endl;
> }
> }
Now, if I print the 3D mask, is wholly or partially black. So, when I do apply this mask to my original 3D image it does not do anything.
Am I missing something?
Thank you very much for your time,
Cristina
---
### Author:  [@dzenanz](https://discourse.itk.org/u/dzenanz)
#### Post date: [October 25, 2022, 8:18pm UTC](https://discourse.itk.org/t/how-can-i-apply-a-2d-mask-in-a-3d-image-slicebysliceimagefilter/5418/11 "2022-10-25T20:18:22Z")
Why are you resampling? And if you are resampling, you should pay attention to spatial extent of your images, their overlap etc.
You could take a look at a [tutorial](https://insightsoftwareconsortium.github.io/GetYourBrainStraight/HCK01_2022_Virtual/Tutorials/MetadataPreservation/MetadataPreservation.html) from earlier this year, or its [video recording](https://drive.google.com/file/d/14-Kgt-VoqAHKJHLQBVuOAB-u7w7ve2N4/view?usp=sharing). Of particular interest would be [ITK image grid](https://mybinder.org/v2/gh/InsightSoftwareConsortium/GetYourBrainStraight/main?filepath=HCK01_2022_Virtual/Tutorials/MetadataPreservation/ITK_image_grid.ipynb) notebook.
---
### Author:  [@cristinamontserrat](https://discourse.itk.org/u/cristinamontserrat)
#### Post date: [November 7, 2022, 8:56am UTC](https://discourse.itk.org/t/how-can-i-apply-a-2d-mask-in-a-3d-image-slicebysliceimagefilter/5418/12 "2022-11-07T08:56:24Z")
Thank you very much!
I actually don’t know why I was resampling. I finally managed to fix the problem by changing the
`ResampleImageFilter` to `ChangeInformationImageFilter`.