Hi Afni Experts,

I wanted to follow up with questions about oblique datasets. I have EPI and T1 scans that were both taken at slightly different oblique angles. I want to keep the EPI scan as is so that I minimize any steps that would alter the raw data (oblique angle 12.44). I have a T1 image which I processed through freesurfer and want to use 3dAllineate to move the anatomical scan to the last time point of the EPI scan for alignment. Even though I run 3dAllineate and apply the transformation matrix I will still get a warning about the datasets being oblique (1.96 deg). Now if I used 3dAllineate to coregister the two images I do not know why I would even be getting this error....shouldn't the two images be aligned resulting in no error messages, as there should not be a difference in angles between them? Does the warning stem for the fact that I aligned to the last timepoint and the first timepoint may have the oblique angle difference of 1.96 that the software is picking up? Additionally, when applying 3dWarp - deoblique to the T1 or both datasets, the alignment looks much worse in the afni viewer. Please let me know if these popups can be ignored or if there is someting I can do to fix this issue.

Thanks,
Ajay