hi Daniel,

thanks for the explanation. I'm still a bit confused though.

In my analyses, I want to keep spatial interpolation of the functional data minimal - motion correction only (after slice time correction of course).
As input I have epi+orig (oblique) and anat+orig (plump) that are aligned in MRIcron but not aligned in the afni viewer. Using

3dWarp -oblique_parent epi+orig -prefix anat_al+orig anat+orig

the volumes are aligned in the AFNI viewer. If I understand your message and the page you referred to correctly though, this alignment should only work if both anat_al+orig and epi+orig have the same 'obliqueness'. According to 3dinfo, however, anat_al+orig is plump but epi+orig is oblique. There are no headers in either file that describe an affine transformation except for the IJK_TO_DICOM{_REAL} ones. So *if* the obliqueness of the epi+orig volume were to be taken into account, would that mean that in reality these volumes are not aligned?

To make things more complicated, I also use a (what I believe is a) non-standard approach to freesurfer surfaces. Rather than using the ones directly from the make_spec script, I apply an affine transformation to the node coordinates to align them with the oblique epi+orig. I also use the matlab toolbox to extract voxel values from the epi+orig based on surface coordinates.

In the AFNI viewer everything seems to be aligned (anatomical, epi, and the surfaces) and also my analyses give sensible results. However, if "under the hood" the oblique transformation of the epi+orig is not taken into account, how I can be sure that I take the correct values from voxels based on a certain spatial location? Is there a "sanity check" that you can recommend? Or am I just too worried and should everything be fine?

Thanks,
Nick