afni.nimh.nih.gov

When you say these datasets are not aligned, are you viewing with the afni GUI or something else? I don't think I've seen this particular problem, but try these things, one at a time, and let me know which step, if any, works.

1. Update AFNI to latest version, "@update.afni.binaries -d"
2. 3drefit -deoblique anat_fs_al.nii
3. 3drefit -deoblique anat_fs.nii