Dear AFNI experts,

I would like to ask for your advice on the spatial normalization of anatomical scans.

I warped the individual brains to the MNI template by setting the parameter “ -tlrc_base MNI_avg152T1+tlrc” in afni_proc.py. It worked well for most subjects, but I have a few participants for whom it failed.

The specific problems I have are:

1) The brain images are weirdly rotated/stretched out and completely miss the template (in 2/27 subjects -- see the top image for an example).

2) The parietal portion of the brain gets cut off after normalization, although the imaging volume included the entire cerebrum (in 3/27 subjects -- see the bottom image for an example); the anat-EPI alignment worked fine regardless, so this issue seems less critical, but I am still curious what could have gone wrong there.

Could you please recommend what preprocessing settings I could tweak to fix those issues?


Thank you!

Katya