Resample volume with unregular spacing

Support
1

Hi everyone,

I’m trying to resampled a volume with an unregular spacing along Z axis.
I followed this post but I encountered issue when resampling.
Here are the steps I followed:

  • Loading dicom volume as dicomVolume
  • It also creates an acquisition transform transform (vtkMRMLGridTransform)
  • I used Resample Scalar Volume by specifying output spacing (I’ll use the output as an input for the other Resample filter) with dicomVolume as an input and create a new volume tempResampledVolume
  • I launch the Resample Image (BRAINS) by setting:
    – ImageToWrap: dicomVolume
    – Reference image: tempResampledVolume
    – Transform file: transform
    The resampling fails with this error :
[FAILED]
Error while reading the the file C:/blablabla/Slicer/BJAIA_vtkMRMLGridTransformNodeB.h5

itk::ExceptionObject (000000D6A50FDA00)
Location: "unknown" 
File: D:\D\S\Slicer-1-build\ITK\Modules\IO\TransformBase\src\itkTransformIOBase.cxx
Line: 62
Description: itk::ERROR: itk::ERROR: HDF5TransformIOTemplate(0000024174726940): Could not create an instance of "InverseDisplacementFieldTransform_double_3_3"
The usual cause of this error is not registering the transform with TransformFactory
Currently registered Transforms: 
	"AffineTransform_double_2_2"
	"AffineTransform_double_3_3"
	"AffineTransform_double_4_4"
	"AffineTransform_float_2_2"
	"AffineTransform_float_3_3"
	"AffineTransform_float_4_4"
	"AzimuthElevationToCartesianTransform_double_3_3"
	"AzimuthElevationToCartesianTransform_float_3_3"
       .....

My understanding is that there are some issue with the transform but I don’t understand what exactly.
Thanks for your help.

2

Can you re-send the post you linked to? It’s not coming through.

As a workaround you can use the “harden transform” option in the transforms module.

3

Sorry for the fail.
Here is the link

4

Thanks! Yes, I figured it was that one or something similar.

For now I think hardening the volume through the transforms or data module is best. Passing the grid transform to the brains resampler really should work and I’m not sure why it doesn’t.

5

Thanks for your fast answer. Indeed, I was able to apply the harden transform. I didn’t remember how to do this. It seems to work well. Thanks !!