Dear Afni developers,

Previously, I was using 3dQwarp on oblique PLUS-MINUS phase-encode direction data for distortion correction within a custom semi automatic pipeline, and it worked fine.

I recently updated my afni from the 32-bit version to the 64-bit version (see: [afni.nimh.nih.gov]) to fix some other problem with warp inversion in 3dQwarp.

Now, 3dQwarp produces warped images on grids with the same dimensions as the original images, but with orientations at 0 (plumb). The warp is defined on a larger grid than the original and also as plumb orientation.

I guess 3dQwarp is producing a warp that not only deforms the source to the base (or in my case to the mid-point between the source and the base), but also displaces it to plumb orientation.

Problems come when overlaying with freesurfer, which resamples considering the orientation information. See following image.

Note that when the original and warped images are overlaid without consideration for orientations (e.g. fslview), the results are perfectly fine.

More importantly, applying registration matrices computed on other images with freesurfer functions in my pipeline doesn't work anymore.

Is there a way to turn off this silent auto-registration-to-plumb-orientation (that is indeed what is hapening)? or should I look for workarounds?

Thanks a lot for your help and
Have a very good day!
Sébastien Proulx