Hi -
I am trying to interface FSL's applywarp tool with another registration toolkit, and for that it would be extremely helpful to understand how applywarp defines the coordinate systems of the input and reference images.
That is, for each pixel in the reference image, how is the spatial coordinate determined that is fed into the warp function, and for each mapped spatial coordinate in the input image space, how is its location in the input image's pixel grid determined?
Specifically, are the NIFTI qform/sform transformations respected for either image, or are the spatial coordinates based on (and aligned with) the image grid itself? Also, is there any image grid reorientation (e.g., to RAS space) or are the coordinates based on the physical storage order of pixels in the images?
Thanks!
Torsten
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