Hi, Philipp-

Focusing first on the img_epi_anat_olap.jpg: what EPI did you input there? Your DSET_EPI should be the "raw" or non-deobliqued one---the one that still has obliquity information---and then the output image of interest should be called img_epi_anat_olap_DEOB.jpg (created by "deobliquing" the dataset in the sense of applying the obliquity information).

From these images, including the APQC HTML ones after afni_proc.py, it appears that you are not use the original EPI datasets that I was suggesting should be used here, because the EPIs don't have obliquity information in them still.

For most EPI-anatomical alignment in afni_proc.py, one would not find benefit from using the lpa cost function---that is useful when the datasets have similar contrast to each other. But again, I think that a different EPI dataset should be used here---the one that still has its original obliquity (so, if "3dinfo -obliquity DSET_EPI" is nonzero, in your case).

--pt