Howdy-
It is likely because that anatomical has obliquity in it, and you have added these options:
-deoblique \
-deoblique_refitly \
Actually, those are not meant to both be applied together, and I should make that an error if both are called in the same command. The first one -deoblique applies the obliquity information, rotating/shifting the dataset (and regridding+interpolating+blurring it slightly) so it appears to be where it should be from the original scanner coordinates; this is what 3dWarp -deoblique .. would do. The second one -deoblique_refitly purges obliquity information, so the brain won't appear where it was originally in the scanner coordinates, but it won't be regridded. More details in the SSW help:
-deoblique :(opt) apply obliquity information to deoblique the input
volume ('3dWarp -deoblique -wsinc5 ...'), as an initial step.
This might introduce the need to overcome a large rotation
during the alignment, though
-deoblique_refitly :(opt) purge obliquity information to deoblique
the input volume (copy, and then '3drefit -deoblique ...'),
as an initial step. This might help when data sets are
very... oblique.
Normally, we would remove the obliquity before running @SSwarper; this will be quite helpful if also using FreeSurfer on the anatomical dataset, for example. That software will apply the obliquity when recon-all is applied.
What are your plans for this dataset, in your full pipeline?
--pt