Hello AFNI-gurus!
I'm aligning EPI to anat using align_epi_anat.py. Here is the command I'm using:
align_epi_anat.py -anat ${Part[${SLURM_ID}]}_T1_S+orig \
-epi ${Let}_${run}_Cat_S_TS_VR+orig. \
-volreg off \
-epi_base 0 \
-deoblique off \
-tshift off \
-epi2anat \
-save_tsh \
-save_vr \
-cost lpc \
-giant_move \
-suffix _A+orig \
-epi_strip None \
-anat_has_skull no \
-overwrite


But after this step I'm getting stray voxels outside the brain (Aligned.png) that did not exist before alignment. This is happening in every subject, across all runs,. And I don't have any concerning movement (as seen from volreg, which I'm running separately) so the ghosting is likely not due to movement.

Additionally, normalising this data cause a lot of bleeding out of the brain(Normalised.png). That's concerning because when I run 3dDeconvolve on this data I'm getting (the much-elusive, corrected) "blobs" outside the brain. So I'm a little hesitant to ignore the problem! Does anyone have any suggestions about why this might be happening, and what I could do to prevent it?

Thanks a lot!
Mrinmayi