# with the specified preffix, which is interesting for debugging.
# if blank, it means that the original images (those without bands)
# will be used (see create_midP_masks-2.0.sh for details).
- banded="banded_"
+ banded=""
# params read from conf file
params="$nb_iter $nb_samples $sampling_algo $nb_hist_bins $nb_levels $bspline_spacing $metric $optimizer $interpolator"
registration_elastix $reference_out $target_out $mask_ref_out $mask_targ_out $vf_out $result_out $params $log_out
fi
- # combine in and out vf
motion_mask=$mask_dir/mm_$phase_nb.mhd
+
+ # combine in and out results
+ out_result=$output_dir/result_${ref_phase_nb}_$phase_nb.mhd
+ clitkCombineImage -i $result_in -j $result_out -m $motion_mask -o $out_result
+ 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
+ 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
+ abort_on_error registration $? clean_up_registration
+
rm vf_zero.*
# save for later...
fi
done
- # create (zero) vf from reference to reference
+ # create (zero) vf from reference to reference and associated images
+ vf_in=$vf_dir/vf_inside_${ref_phase_nb}_${ref_phase_nb}.mhd
+ vf_out=$vf_dir/vf_outside_${ref_phase_nb}_${ref_phase_nb}.mhd
clitkZeroVF -i $vf_ref -o $vf_dir/vf_${ref_phase_nb}_${ref_phase_nb}.mhd
+ clitkZeroVF -i $vf_ref -o $vf_in
+ clitkZeroVF -i $vf_ref -o $vf_out
+ abort_on_error registration $? clean_up_registration
+
+ motion_mask=$mask_dir/mm_${ref_phase_nb}.mhd
+ reference_in=$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
+ clitkCombineImage -i $reference_in -j $reference_out -m $motion_mask -o $out_result
+ abort_on_error registration $? clean_up_registration
# create 4D vf
create_mhd_4D_pattern.sh $vf_dir/vf_${ref_phase_nb}_
+ 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 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}_
+ create_mhd_4D_pattern.sh $output_dir/result_${ref_phase_nb}_
echo
echo "-------- Registration done ! --------"
########### calculate the midp wrt the reference phase
phase_nb=$ref_phase_nb
echo "Calculating midp_$phase_nb.mhd..."
- vf_midp=$midp_dir/vf_$phase_nb\_midp.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
clitkAverageTemporalDimension -i $vf_dir/vf_${ref_phase_nb}_4D.mhd -o $vf_midp
+ abort_on_error midp $? clean_up_midp
+
# invert the vf (why?)
clitkInvertVF -i $vf_midp -o $vf_midp
+ abort_on_error midp $? clean_up_midp
+
# create the midp by warping the reference phase with the reference vf
clitkWarpImage -i $ref_phase_file -o $midp --vf=$vf_midp -s 1
+ abort_on_error midp $? clean_up_midp
ref_vf_midp=$vf_midp
ref_midp=$midp
clitkImageConvert -i $ref_midp -o $ref_midp -t float
+ abort_on_error midp $? clean_up_midp
########### calculate the midp wrt the other phases
for i in $( seq 0 $((${#phase_files[@]} - 1))); do
phase_file=${phase_files[$i]}
phase_nb=${phase_nbs[$i]}
- vf_midp=$midp_dir/vf_$phase_nb\_midp.mhd
+ vf_midp=$midp_dir/vf_midp_$phase_nb.mhd
midp=$midp_dir/midp_$phase_nb.mhd
if [ "$phase_nb" != "$ref_phase_nb" ]; then
# calculate vf from phase to midp, using the vf from reference phase to midp (-i)
# and the vf from reference phase to phase (-j)
clitkComposeVF -i $ref_vf_midp -j $vf_dir/vf_$ref_phase_nb\_$phase_nb.mhd -o $vf_midp
+ abort_on_error midp $? clean_up_midp
+
clitkWarpImage -i $phase_file -o $midp --vf=$vf_midp -s 1
+ abort_on_error midp $? clean_up_midp
+
clitkImageConvert -i $midp -o $midp -t float
+ abort_on_error midp $? clean_up_midp
fi
done
+ # create 4D midp
create_mhd_4D_pattern.sh $midp_dir/midp_
+ 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
+ abort_on_error midp $? clean_up_midp
+
echo "Calculating midp_med.mhd..."
clitkMedianTemporalDimension -i $midp_dir/midp_4D.mhd -o $midp_dir/midp_med.mhd
+ abort_on_error midp $? clean_up_midp
# clean-up
- rm $midp_dir/vf_*
+ #rm $midp_dir/vf_*
echo
echo "-------- Mid-position done ! --------"
conf=$3
source $conf
+cd `dirname $mhd4d`
+
mkdir -p $log_dir
mask_dir="MASK-${mask_interpolation_spacing}mm-$mask_interpolation_algorithm"