How to preserve the direction cosine matrix

Development
1

Hi Guys,

Recently, I had write a batch to resample a series of MR volumes. However, there is one problem that the direction cosine matrix of the output volume is not the same as that of the input volume.
Thanks！

reader=sitk.ImageFileReader()
writer=sitk.ImageFileWriter()
reader.SetFileName(str(fi_d))
inputVolume=reader.Execute()
reader.ReadImageInformation()
if inputVolume is not None:
 			resample=sitk.ResampleImageFilter()
 			resample.SetInterpolator(sitk.sitkLinear)
 			resample.SetTransform(sitk.Transform(3,sitk.sitkIdentity))
 			resample.SetOutputDirection(reader.GetDirection())
 			print(reader.GetDirection())
 			resample.SetOutputOrigin(reader.GetOrigin())
 			out_spacing=[1.0,1.0,1.0]
 			resample.SetOutputSpacing(out_spacing)
 			original_spacing=reader.GetSpacing()
 			original_size=reader.GetSize()
 			out_size=[int(np.round(original_size[0]*(original_spacing[0]/out_spacing[0]))),int(np.round(original_size[1]*(original_spacing[1]/out_spacing[1]))),int(np.round(original_size[2]*(original_spacing[2]/out_spacing[2])))]
 			resample.SetSize(out_size)
 			resample.SetDefaultPixelValue(0.0)
 			out=resample.Execute(inputVolume)
 			prefix="%s_iso.nii"%fileName
 			resampleVolumeFilePath=os.path.join(self.saveVolumeDir,prefix)
 			writer.SetFileName(str(resampleVolumeFilePath))
 			writer.Execute(out)
2

This looks like a good question for the SimpleITK forum. From a quick look it seems you are setting the output direction to match the input, but maybe something else if going on.

3

Hi Pieper,

Thanks for your advice!