Output orientation same as input?

[gdevenyi]

When I write something like:

    inp.open(input_files, "mask.mnc")
    out.open(outfilename, "mask.mnc")

I would've expected that outfilename would have the same orientation and size/shape as the input_files.

Instead it's A-P and L-R flipped.

I guess this is due to the RAS/LPS confusion underlying ITK/EZMinc?

[vfonov]

No, it has nothing to do with ITK.
It's due to the fact that pyezminc normalizes data internally, to have consistent representation.