Great. The outputs for the rigid registration are quite different.

In the v1.4.1_RHL6 folder:

111312_T1_stx.nii.gz
111312_T1_stx_T2JointT1_tmp1_mask.nii.gz
111312_T1_stx.nrrd
111312_T1_stx_T2JointT1_tmp2.nii.gz
111312_T1_stx_255.nii.gz
111312_T1_stx_T2JointT1_tmp2_mask.nii.gz
111312_T1_stx_255_Skull.nii.gz
111312_T2_stx.nii.gz
111312_T1_stx_T2JointT1_mask.nii.gz
111312_T2_stx.nrrd
111312_T1_stx_T2JointT1_tmp1.nii.gz

In the v1.7.7 folder:

111312_T1_stx.nrrd
111312_T2_stx.nii.gz
111312_T2_stx.nrrd