I recently added this variable, AFNI_NIFTI_VIEW, to control the default view for NIFTI datasets with a qform or sform code set to "aligned" (2). Note this only applies to NIFTI codes set to "aligned"=2 and not to "TLRC"=3 or "MNI"=4. Use nifti_tool to determine the space code in your dataset.
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Variable: AFNI_NIFTI_VIEW
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The default view extension used for output when creating AFNI format datasets
from NIFTI datasets.This variable is only applicable for sform and qform codes
that do not have clearly defined views (sform/qform code = 2). Set to "tlrc"
or "orig". See also AFNI_DEFAULT_STD_SPACE and AFNI_NIFTI_PRIORITY.