abort_on_error registration $? clean_up_registration
# combine in and out vf
vf_result=$vf_dir/vf_${ref_phase_nb}_$phase_nb.mhd
abort_on_error registration $? clean_up_registration
# combine in and out vf
vf_result=$vf_dir/vf_${ref_phase_nb}_$phase_nb.mhd
abort_on_error registration $? clean_up_registration
clitkZeroVF -i $vf_in -o vf_zero.mhd
abort_on_error registration $? clean_up_registration
patient_mask=$mask_dir/patient_mask_$phase_nb.mhd
abort_on_error registration $? clean_up_registration
clitkZeroVF -i $vf_in -o vf_zero.mhd
abort_on_error registration $? clean_up_registration
patient_mask=$mask_dir/patient_mask_$phase_nb.mhd
reference_in=$mask_dir/${banded}inside_${ref_phase_nb}.mhd
reference_out=$mask_dir/${banded}outside_$ref_phase_nb.mhd
out_result=$output_dir/result_${ref_phase_nb}_${ref_phase_nb}.mhd
reference_in=$mask_dir/${banded}inside_${ref_phase_nb}.mhd
reference_out=$mask_dir/${banded}outside_$ref_phase_nb.mhd
out_result=$output_dir/result_${ref_phase_nb}_${ref_phase_nb}.mhd
vf_midp=$midp_dir/vf_midp_$phase_nb.mhd
midp=$midp_dir/midp_$phase_nb.mhd
# average the vf's from reference phase to phase
vf_midp=$midp_dir/vf_midp_$phase_nb.mhd
midp=$midp_dir/midp_$phase_nb.mhd
# average the vf's from reference phase to phase
coeff_midp_out=$midp_dir/coeff_outside_midp_$phase_nb.mhd
# average the vf's from reference phase to phase
# clitkAverageTemporalDimension -i $vf_dir/vf_inside_${ref_phase_nb}_4D.mhd -o $vf_midp_in
coeff_midp_out=$midp_dir/coeff_outside_midp_$phase_nb.mhd
# average the vf's from reference phase to phase
# clitkAverageTemporalDimension -i $vf_dir/vf_inside_${ref_phase_nb}_4D.mhd -o $vf_midp_in
abort_on_error midp $? clean_up_midp
# clitkAverageTemporalDimension -i $vf_dir/vf_outside_${ref_phase_nb}_4D.mhd -o $vf_midp_out
abort_on_error midp $? clean_up_midp
# clitkAverageTemporalDimension -i $vf_dir/vf_outside_${ref_phase_nb}_4D.mhd -o $vf_midp_out
ref_vf_midp_in=$vf_midp_in
ref_vf_midp_out=$vf_midp_out
vf_midp=$midp_dir/vf_midp_$phase_nb.mhd
ref_vf_midp_in=$vf_midp_in
ref_vf_midp_out=$vf_midp_out
vf_midp=$midp_dir/vf_midp_$phase_nb.mhd
# create the midp by warping the reference phase with the reference vf
midp=$midp_dir/midp_$phase_nb.mhd
# create the midp by warping the reference phase with the reference vf
midp=$midp_dir/midp_$phase_nb.mhd