AFNI version info (afni -ver
):
Precompiled binary linux_openmp_64: Jan 18 2021 (Version AFNI_21.0.04 'Titus')
Hi AFNI experts,
I am attempting to coregister ASL to a skull stripped t1w image, and I have been having some trouble with alignment failing. The goal is to then align the coregistered ASL+t1w to MNI space.
I have been running align_epi_anat.py with the following commands:
align_epi_anat.py \
-anat t1_ss.nii \
-epi asl_orig.nii \
-epi_base 1 \
-epi2anat \
-big_move \
-partial_coverage \
-cost lpa \
-edge \
-anat_has_skull no \
-suffix _al
And this has worked for one or two participants, but the majority appear to have large misalignments, as you can see below.


even modifying with -ginormous_move and -Allineate_opts ‘-maxrot 50’, the alignment still does not look good. Is there something I am missing?
Thanks so much,
MK