[ITK] [ITK-users] SimpleITK, read MHD volume and convert it into a numpy array respecting its transformation

[Lowekamp, Bradley (NIH/NLM/LHC) [C]]

Hello,

If I understand you correctly you want to rotate the image and pad it for visualization before exporting to numpy.

Have you looked into the ResampleImageFilter? It accepts a transform, along with output image geometry so that you can readily manipulate the image for display. You also may want to scale the image’s intensity with a WindowLevelImageFilter for better visualization of the range of interest.

HTH,
Brad

On May 4, 2016, at 1:14 PM, fausto milletarì <fausto.milletari at gmail.com<mailto:fausto.milletari at gmail.com>> wrote:

Hello everyone,

I have a probably naive question about simpleITK. I find simpleITK extremely useful to process medical data such as MRI scans but I would like also to enjoy being able to convert my images in numpy format while respecting the transformation of the volume.

In other words I would like to get the MRI image in numpy rotated by the correct amount around each axis with zero padding for example.

when i do simply sitk.GetArrayFromImage(imgResampledCropped)I get back the raw data itself, but what I would like to do is to have a numpy array that contains the data “ready to visualise” by simple slicing of the array itself.

Do you think this is doable? Is there a standard way of doing it?



Kind regards,

Fausto

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