Multimodal Registration of Dicom file in physical space (mm space)

I am new to simpleITK. My task is to register MR volume with CT volume. The CT volume is entire body while MR volume is abdomen only. Moreover MR volume is rotated i.e. direction cosines are not (1,0,0,1) from dicom IOP tag. My question is in registration example (Image Registration Method 4 β€” SimpleITK 2.0rc2 documentation) when dicom image is loaded and registration performed, is it done in Physical space(mm space) or in index space(pixel space)?

Hello @gaurav_patel,

ITK/SimpleITK always work in physical space so you don’t need to worry about the direction cosine matrix being different from identity. Please see the registration overview, and the toolkit’s Jupyer notebook repository, specifically the registration notebook series (6* prefix).

A key aspect of registration is the initialization (see this notebook). In your case, because of the significantly different image extents this will likely be a bit more complex than naively centering the two volumes. The initialization notebook illustrates various commonly used initialization strategies which you can readily evaluate for your needs.

Thank you very much for prompt reply. I will look into the resources you shared. Issue may be closed.

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