[ITK-users] [ITK] Extract slice from ResampleFilter

[Dženan Zukić]

Hi Sidartha,

the code looks OK. The index is [0,0,0] by default, so just setting size is
enough. My idea was not to apply translation2, then you would not have to
set origin on the resample filter (it would start from [0,0,0]).

I think you are forgetting to apply second translation, and you are not
applying any transformation to the resample filter. Something like this is
needed:
filter->SetTransform(eulerTransform);

What results are you getting?

Regards,
Dženan Zukić, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)

On Thu, Apr 13, 2017 at 9:04 AM, sidharta <sidharta.gupta93 at gmail.com>
wrote:

> Hi Dženan,
>
> So I am doing something as follows:
>
> // Vectors for calculating normal_to_plane - The plane/slice I want to
> extract
>
> Vector3d ST, SP, normal_to_plane; // This is a custom 3D Vector library
> ST = traj_start - traj_end; // start and end of the trajectory - vector 1
> SP = traj_start - third_point; // start and third point gives another
> vector
> - vector 2
> // Now with two vectors I can get the direction of the normal to the plane
> normal_to_plane = ST.cross(SP); // cross product essentially
>
> // Getting angles between normal to the plane and the coordinate axes
> double angle_plane_z = std::acos((normal_to_plane[2] * 1) /
> norm(normal_to_plane)); // angle between plane and z axis
> double angle_plane_y = std::acos((normal_to_plane[1] * 1) /
> norm(normal_to_plane)); // angle between plane and y axis
> double angle_plane_x = std::acos((normal_to_plane[0] * 1) /
> norm(normal_to_plane)); // angle between plane and x axis
>
> // Instantiate an Euler Transform
> typedef itk::Euler3DTransform<double> ETransformType;
> ETransformType::Pointer eulerTransform = ETransformType::New();
>
> // This because - Quote from ITKSoftwareGuide "Rotations are performed
> around the origin of physical coordinates—not the image origin nor the
> image
> center"
> ETransformType::OutputVectorType translation1;
> translation1[0] = -origin_dcm[0]; // origin_dcm is the origin of the dicom
> translation1[1] = -origin_dcm[1];
> translation1[2] = -origin_dcm[2];
> eulerTransform->Translate(translation1);
> eulerTransform->SetRotation(angle_plane_x, angle_plane_y, angle_plane_z);
>
> // Get back to the origin of the dicom
> ETransformType::OutputVectorType translation2;
> translation2[0] = origin_dcm[0];
> translation2[1] = origin_dcm[1];
> translation2[2] = origin_dcm[2];
>
> // Instantiate the ResampleFilter
> // typedef double InternalPixelType;
> // typedef itk::Image< InternalPixelType, Dimension > InternalImageType; //
> For clarity
> typedef itk::ResampleImageFilter<InternalImageType, InternalImageType>
> ResampleFilterType;
>
> ResampleFilterType::Pointer filter = ResampleFilterType::New();
>
> typedef itk::NearestNeighborInterpolateImageFunction<
>                 InternalImageType, double> InterpolatorType;
> InterpolatorType::Pointer interpolator = InterpolatorType::New();
> filter->SetInterpolator(interpolator);
>
> filter->SetDefaultPixelValue(0);
> filter->SetOutputSpacing(image->GetSpacing());
> filter->SetOutputOrigin(image->GetOrigin()); // If I change this to
> traj_start, the dicom looks completely off, as in not intended.
> filter->SetOutputDirection(image->GetDirection()); // I have my doubts
> about
> this too
> filter->SetSize(image->GetSize()); // Of course, as you suggested, I would
> set the thickness here as 1, but I was doing this for testing purposes.
> filter->SetInput(image);
>
> So, what do you think about this code? Am I doing it correctly? I feel
> really dumb asking you to check my code but unfortunately I can't find any
> relevant example for 3D resampling. Additionally, (no offense) but I don't
> get what you mean by "target region index" with respect to the resampling
> filter? Do you mean the SetOrigin()? As you also see, I am essentially not
> applying any translation to the origin. Just a rotation for testing
> purposes.
>
> Thank you for your time.
> Best Regards,
> Sidharta
>
>
>
>
>
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