[Elastix] Deformation field - pixel spacing swapped

Catarina De Brito Carvalho Catarina.DeBritoCarvalho at esat.kuleuven.be
Wed May 28 14:16:39 CEST 2014

Dear elastix users,

I’m working with elastix and transformix to obtain deformation fields.
I write the images I'm working either in nifty or in mhd format (specifying the pixel spacing in the associated header files).

If I use transformix (with a previously defined transformation parameter) to “Transform” my moving image (i.e. to create the deformed moving image), the output is correct having the same image properties then the input (i.e. the image dimensions and pixel size is the same).

The problem is that, if I use the same transformation parameters but I select “Deformation Field” instead, the output image has the same dimensions as the input BUT the pixel spacing in x and y are swapped.
Perhaps the problem is caused by the anatomical orientation used by nifti and mhd formats versus the anatomical orientation used by itk.

I tried to write my images using both RAI and ASL orientation but nothing seems to work.

So, in conclusion, I would like to know your opinion about this matter. Is the problem caused by the anatomical plane I’m writing my images? If it is an orientation problem, shouldn’t the pixel dimension be swapped also? Finally, why does it work with every image format when doing the transformation and not when asking for the deformation field?

Many thanks in advance,


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