[ITK] SimpleITK - Resizing MRI scan with slice thickness and slice gap parameters

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

Hello,

I am not sure what you mean by you “re-arranged  the coronal scan to be in the axial view”. I hope you did it in a way to preserve the meta-data and the direction cosine matrix. You should be able to do this all in what step with the resample filter.

You need to use the input’s direction matrix for the OutputDirection of the resample filter. Next set the OutputSize, and then correctly calculate the OutputSpacing so that the result has the same physical extent as the input.

If you need further help, perhaps sharing a snip-it of code would help.

HTH,
Brad

On Jun 19, 2016, at 10:22 PM, Sara Gh <sg.ele.eng at gmail.com<mailto:sg.ele.eng at gmail.com>> wrote:

Hello experts,

I have two MRI scans: axial (256x256x56) and coronal (68x256x256). For both of them, slice thickness and slice gap parameters are 2 and 1, respectively.
I have re-arranged the coronal scan to be in the axial view. Therefore, the new coronal scan (with the axial view) is 256x256x68.
Now, I am trying to use SimpleITK to resize/upsample both scans to 256x256x256. Considering slice gap and slice thickness parameters, how can I perform this 3D-resizing in SimpleITK?

Thanks,
Sara Gh
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