Hi Stefano,
Hmm, it seems you are right about this. I haven't tracked this down to where it happens inside 3dSkullstrip, but it's not too bad a workaround using the recommended code for masking the original volume that comes at the end of its terminal output:
3dcalc -a anat_oblique.nii.gz -b anat_ns_notoblique.nii.gz -expr 'a*step(b)' -prefix anat_ns_oblique.nii.gz
The obliquity will come from the original dataset. The other way to do this is to use either nifti_tool to modify the header or 3dinfo to modify the AFNI header which propagates from AFNI's IJK_TO_DICOM_REAL attribute down to the NIFTI header's sform matrix.
3drefit -atrcopy IJK_TO_DICOM_REAL original_dset modified_dset
Thanks for letting me know about this. I'll look into this some more.
