Hi pt.
I finally figured out why some of those files were on different grids. When I transformed the freesurfer file to AFNI, I used the transformation matrix based on oblique dwi data rather than the de-obliqued (3dWarp) data. Thus, this should solve my problem.
It seems like you suggest that I should not use 3dAllineate. Ok.
Further, our collaborators sent their pipeline for dwi pre-processing (not in AFNI, though). The first step is the equivalent of 3dWarp. However, I didn't perform the equivalent of the last 3 steps in AFNI. Would you suggest I could just use their pre-proprocessed data, or should I do this in AFNI or can I just forget them all?
1. aligning and centering (pnlNipype and ANTS v2.3.4) --- deoblique
2. denoising with dwidenoise (MRtrix3 v3.0.1)
3. unringing with mrdegibbs (MRtrix3 v3.0.1)
4. head motion correction with eddy (FSL v.6.0.1) --- originally I thought 3dAllineate took care of this but now it seems not.
