[Python] MRI Resampling

When to Resample?

Anytime we use two datasets with different sized voxels

Dicom Attributes to use

1. Slice Thickess

2. PixelSpacing (width, height)

Calcuate new size

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])))]

How to resample with SimpleITK

def resample_img(itk_image, out_spacing=[2.0, 2.0, 2.0], is_label=False):
    # resample images to 2mm spacing with simple itk

    original_spacing = itk_image.GetSpacing()
    original_size = itk_image.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 = sitk.ResampleImageFilter()
    resample.SetOutputSpacing(out_spacing)
    resample.SetSize(out_size)
    resample.SetOutputDirection(itk_image.GetDirection())
    resample.SetOutputOrigin(itk_image.GetOrigin())
    resample.SetTransform(sitk.Transform())
    resample.SetDefaultPixelValue(itk_image.GetPixelIDValue())

    if is_label:
        resample.SetInterpolator(sitk.sitkNearestNeighbor)
    else:
        resample.SetInterpolator(sitk.sitkBSpline)

    return resample.Execute(itk_image)

How to resample with Python - Skimage resize

def interpolate(img, new_size):
    new_img = resize(img, new_size, order=1, anti_aliasing=False, clip=False, preserve_range=True)
    return new_img

 

reference

https://f-i-tushar-eee.medium.com/3d-medical-imaging-pre-processing-all-you-need-6ba981738877