[ITK-users] [ITK] Resizing DICOM images

[Yaniv, Ziv Rafael (NIH/NLM/LHC) [C]]

Hello Tony,

Short answer is yes.

To shrink a volume using integral sizes, use the BinShrinkImageFilter (https://itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1BinShrinkImageFilter.html).
Using the procedural interface to shrink an image by 4 in x, by 4 in y and by 2 in z would be:
bShrinkImage = sitk.BinShrink(img, [4,4,2])

The BinShrink filter also averages the neighborhood, so it deals to some extent with potential aliasing. Don’t use this filter if your volume represents a discrete set of labels (i.e. segmentation).


Longer answer:

For truly arbitrary resizing use the ResampleImageFilter (https://itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1ResampleImageFilter.html).

Using the procedural interface to modify the original (style is verbose for clarity):

new_x_size = 700 #upsample
new_y_size = 64 #downsample
new_z_size = 5 #downsample
new_size = [new_x_size, new_y_size, new_z_size]
new_spacing = [old_sz*old_spc/new_sz  for old_sz, old_spc, new_sz in zip(img.GetSize(), img.GetSpacing(), new_size)]

interpolator_type = sitk.sitkLinear

new_img = sitk.Resample(img, new_size, sitk.Transform(), interpolator_type, img.GetOrigin(), new_spacing, img.GetDirection(), 0.0, img.GetPixelIDValue())

The ResampleImageFilter does not deal with aliasing, so if you are downsampling it is recommended to blur prior to resampling. If you are resampling a volume with discrete labels you would use the sitk.sitkNearestNeighbor
interpolator type.

    hope this helps
            Ziv




From: G Reina <greina at eng.ucsd.edu>
Date: Monday, July 17, 2017 at 6:52 PM
To: "insight-users at itk.org" <insight-users at itk.org>
Subject: [ITK] [ITK-users] Resizing DICOM images

I've seen in pydicom and opencv how to resize a DICOM image to an arbitrary pixel resolution (e.g. going from 512x512 down to 128x128).

Does SimpleITK have a way to do this for 3D image volumes (i.e. rescale height, width, and slice at the same time?

I'm looking to have a method to make my DICOM volumes uniform in shape.

Thanks.
-Tony

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