# registration
if [ "$method" == "blutdir" ]; then
- registration_blutdir $reference_in $target_in $mask_ref_in $mask_targ_in $vf_in $result_in $params $log_in $coeff_in $init_coeff_in
- registration_blutdir $reference_out $target_out $mask_ref_out $mask_targ_out $vf_out $result_out $params $log_out $coeff_out $init_coeff_out
+ registration_blutdir $reference_in $target_in $mask_ref_in $mask_targ_in $vf_in $result_in $params $log_in $coeff_in
+ registration_blutdir $reference_out $target_out $mask_ref_out $mask_targ_out $vf_out $result_out $params $log_out $coeff_out
elif [ "$method" == "elastix" ]; then
registration_elastix $reference_in $target_in $mask_ref_in $mask_targ_in $vf_in $result_in $params $log_in
registration_elastix $reference_out $target_out $mask_ref_out $mask_targ_out $vf_out $result_out $params $log_out
# combine in and out results
out_result=$output_dir/result_${ref_phase_nb}_$phase_nb.mhd
- clitkCombineImage -i $result_in -j $result_out -m $motion_mask -o $out_result
+ # clitkCombineImage -i $result_in -j $result_out -m $motion_mask -o $out_result
+ combine_image $result_in $result_out $out_result $motion_mask
abort_on_error registration $? clean_up_registration
# combine in and out vf
vf_result=$vf_dir/vf_${ref_phase_nb}_$phase_nb.mhd
- clitkCombineImage -i $vf_in -j $vf_out -m $motion_mask -o $vf_result
+ #clitkCombineImage -i $vf_in -j $vf_out -m $motion_mask -o $vf_result
+ combine_image $vf_in $vf_out $vf_result $motion_mask
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
- clitkCombineImage -i $vf_result -j vf_zero.mhd -m $patient_mask -o $vf_result
+ #clitkCombineImage -i $vf_result -j vf_zero.mhd -m $patient_mask -o $vf_result
+ combine_image $vf_result vf_zero.mhd $vf_result $patient_mask
abort_on_error registration $? clean_up_registration
rm vf_zero.*
reference_in=$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
- clitkCombineImage -i $reference_in -j $reference_out -m $motion_mask -o $out_result
+ #clitkCombineImage -i $reference_in -j $reference_out -m $motion_mask -o $out_result
+ combine_image $reference_in $reference_out $out_result $motion_mask
abort_on_error registration $? clean_up_registration
# create 4D vf
create_mhd_4D_pattern.sh $vf_dir/vf_inside_${ref_phase_nb}_
create_mhd_4D_pattern.sh $vf_dir/vf_outside_${ref_phase_nb}_
+ # create 4D coeffs
+ create_mhd_4D_pattern.sh $vf_dir/coeff_inside_${ref_phase_nb}_ _0
+ create_mhd_4D_pattern.sh $vf_dir/coeff_outside_${ref_phase_nb}_ _0
+
# create 4D result image
create_mhd_4D_pattern.sh $output_dir/result_inside_${ref_phase_nb}_
create_mhd_4D_pattern.sh $output_dir/result_outside_${ref_phase_nb}_
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
- clitkAverageTemporalDimension -i $vf_dir/vf_${ref_phase_nb}_4D.mhd -o $vf_midp
+ #clitkAverageTemporalDimension -i $vf_dir/vf_${ref_phase_nb}_4D.mhd -o $vf_midp
+ average_temporal_dimension $vf_dir/vf_${ref_phase_nb}_4D.mhd $vf_midp
abort_on_error midp $? clean_up_midp
# invert the vf (why?)
create_mhd_4D_pattern.sh $midp_dir/vf_midp_
echo "Calculating midp_avg.mhd..."
- clitkAverageTemporalDimension -i $midp_dir/midp_4D.mhd -o $midp_dir/midp_avg.mhd
+ #clitkAverageTemporalDimension -i $midp_dir/midp_4D.mhd -o $midp_dir/midp_avg.mhd
+ average_temporal_dimension $midp_dir/midp_4D.mhd $midp_dir/midp_avg.mhd
abort_on_error midp $? clean_up_midp
echo "Calculating midp_med.mhd..."
echo "Calculating midp_$phase_nb.mhd..."
vf_midp_in=$midp_dir/vf_inside_midp_$phase_nb.mhd
vf_midp_out=$midp_dir/vf_outside_midp_$phase_nb.mhd
+ coeff_midp_in=$midp_dir/coeff_inside_midp_$phase_nb.mhd
+ 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
+ # clitkAverageTemporalDimension -i $vf_dir/vf_inside_${ref_phase_nb}_4D.mhd -o $vf_midp_in
+ #clitkAverageTemporalDimension -i $vf_dir/coeff_inside_${ref_phase_nb}_4D_0.mhd -o $coeff_midp_in
+ average_temporal_dimension $vf_dir/coeff_inside_${ref_phase_nb}_4D_0.mhd $coeff_midp_in
abort_on_error midp $? clean_up_midp
- clitkAverageTemporalDimension -i $vf_dir/vf_outside_${ref_phase_nb}_4D.mhd -o $vf_midp_out
+ # clitkAverageTemporalDimension -i $vf_dir/vf_outside_${ref_phase_nb}_4D.mhd -o $vf_midp_out
+ #clitkAverageTemporalDimension -i $vf_dir/coeff_outside_${ref_phase_nb}_4D_0.mhd -o $coeff_midp_out
+ average_temporal_dimension $vf_dir/coeff_outside_${ref_phase_nb}_4D_0.mhd $coeff_midp_out
abort_on_error midp $? clean_up_midp
- # invert the vf (why?)
- clitkInvertVF -i $vf_midp_in -o $vf_midp_in
+ # invert the vf
+ # clitkInvertVF -i $vf_midp_in -o $vf_midp_in
+ clitkInvertVF -i $coeff_midp_in -o $vf_midp_in --type 1 --like $ref_phase_file
abort_on_error midp $? clean_up_midp
- clitkInvertVF -i $vf_midp_out -o $vf_midp_out
+ # clitkInvertVF -i $vf_midp_out -o $vf_midp_out
+ clitkInvertVF -i $coeff_midp_out -o $vf_midp_out --type 1 --like $ref_phase_file
abort_on_error midp $? clean_up_midp
# combine in and out VF's
ref_vf_midp_in=$vf_midp_in
ref_vf_midp_out=$vf_midp_out
vf_midp=$midp_dir/vf_midp_$phase_nb.mhd
- clitkCombineImage -i $vf_midp_in -j $vf_midp_out -o $vf_midp -m $mask_dir/mm_$phase_nb.mhd
+ #clitkCombineImage -i $vf_midp_in -j $vf_midp_out -o $vf_midp -m $mask_dir/mm_$phase_nb.mhd
+ combine_image $vf_midp_in $vf_midp_out $vf_midp $mask_dir/mm_$phase_nb.mhd
clitkZeroVF -i $vf_midp -o vf_zero.mhd
- clitkCombineImage -i $vf_midp -j vf_zero.mhd -o $vf_midp -m $mask_dir/patient_mask_$phase_nb.mhd
+ #clitkCombineImage -i $vf_midp -j vf_zero.mhd -o $vf_midp -m $mask_dir/patient_mask_$phase_nb.mhd
+ combine_image $vf_midp vf_zero.mhd $vf_midp $mask_dir/patient_mask_$phase_nb.mhd
# create the midp by warping the reference phase with the reference vf
midp=$midp_dir/midp_$phase_nb.mhd
# combine in and out VF's
vf_midp=$midp_dir/vf_midp_$phase_nb.mhd
- clitkCombineImage -i $vf_midp_in -j $vf_midp_out -o $vf_midp -m $mask_dir/mm_$phase_nb.mhd
+ #clitkCombineImage -i $vf_midp_in -j $vf_midp_out -o $vf_midp -m $mask_dir/mm_$phase_nb.mhd
+ combine_image $vf_midp_in $vf_midp_out $vf_midp $mask_dir/mm_$phase_nb.mhd
clitkZeroVF -i $vf_midp -o vf_zero.mhd
- clitkCombineImage -i $vf_midp -j vf_zero.mhd -o $vf_midp -m $mask_dir/patient_mask_$phase_nb.mhd
+ #clitkCombineImage -i $vf_midp -j vf_zero.mhd -o $vf_midp -m $mask_dir/patient_mask_$phase_nb.mhd
+ combine_image $vf_midp vf_zero.mhd $vf_midp $mask_dir/patient_mask_$phase_nb.mhd
midp=$midp_dir/midp_$phase_nb.mhd
clitkWarpImage -i $phase_file -o $midp --vf=$vf_midp -s 1
create_mhd_4D_pattern.sh $midp_dir/vf_outside_midp_
echo "Calculating midp_avg.mhd..."
- clitkAverageTemporalDimension -i $midp_dir/midp_4D.mhd -o $midp_dir/midp_avg.mhd
+ #clitkAverageTemporalDimension -i $midp_dir/midp_4D.mhd -o $midp_dir/midp_avg.mhd
+ average_temporal_dimension $midp_dir/midp_4D.mhd $midp_dir/midp_avg.mhd
abort_on_error midp $? clean_up_midp
echo "Calculating midp_med.mhd..."