I will preface by apologizing for the silly question…
My general pipeline uses the align_epi_anat.py script, however, I have 2 animals where the original EPI and anatomical images have better alignment than the output from the align_epi_anat script. Is it necessary to perform alignment between those images prior to registering to a template if it doesn’t align as well as the originals do?
The contrast in the EPI dataset doesn’t have bright CSF relative to the tissue, and the default alignment relies on that. However, the alignment works well with lpa or nmi cost functions instead of the default for anat to epi alignment cost function of lpc or lpc+ZZ.
The
National Institute of Mental Health (NIMH) is part of the National Institutes of
Health (NIH), a component of the U.S. Department of Health and Human
Services.