Output images have incorrect headers or otherwise do not match the applied transform

ITK-SNAP uses similar I/O to ANTs, and is very useful for testing how ANTs will interpret the image header. See the page on Using ITK-SNAP with ANTs.

Some potential causes of problems with output images being flipped or translated:

NIfTI header codes not set appropriately for ANTs

ITK, and therefore ANTs, only supports a rigid transform to physical space. It prefers qform over sform. See

https://github.com/ANTsX/ANTs/wiki/How-does-ANTs-handle-qform-and-sform-in-NIFTI-1-images%3F

Dimension mismatch

If you pass a 4D image where a 3D image is expected, the transform of the output image may not be correct. See

https://github.com/ANTsX/ANTs/wiki/Dimensionality-of-ANTs-algorithms