calculation of an RTstruct's motion amplitude

diff --git a/scripts/calculate_motion_amplitude.sh b/scripts/calculate_motion_amplitude.sh
new file mode 100755 (executable)
index 0000000..9fa0aa9
--- /dev/null
+++ b/scripts/calculate_motion_amplitude.sh
@@ -0,0 +1,52 @@
+#! /bin/bash +x 
+
+############# main 
+
+if echo $* | grep "\-h"; then
+  echo Usage: calculate_motion_amplitude.sh VECTOR_FILE RTSTRUCT_FILE RTSTRUCT_ROI_NUMBER RTSTRUCT_REF_IMAGE
+  echo "  VECTOR_FILE: mhd of the vector field from where to extract motion information (may also be 4D)"
+  echo "  RTSTRUCT_FILE: dicom with contours"
+  echo "  RTSTRUCT_ROI: number of the contour whose motion to analyze"
+  echo "  RTSTRUCT_REF_IMAGE: mhd of the reference image used in the contour delineation"
+
+  exit 0
+fi
+
+if [ $# != 4 ]; then
+  echo Invalid arguments. Type \'`basename $0` -h\' for help
+  exit -1
+fi
+
+vector_file=$1
+rtstruct_file=$2
+rtstruct_roi=$3
+rtstruct_ref_image=$4
+
+if ! cat $vector_file | grep -q "Channels = 3"; then
+  echo Vector file must have 3 channels.
+  exit -2
+fi
+
+# create ROI mask from rtstruct
+roi_mask=roi_${rtstruct_roi}.mhd
+clitkDicomRTStruct2BinaryImage -i ${rtstruct_file} -o ${roi_mask} -j ${rtstruct_ref_image} -r ${rtstruct_roi} 2> /tmp/err.txt
+if cat /tmp/err.txt | grep -q "No ROI"; then
+  echo Invalid contour number.
+  exit -3
+fi
+
+# guarantees the same sampling for roi mask and vector image
+roi_mask2=resampled_${roi_mask}
+clitkResampleImage -i ${roi_mask} -o ${roi_mask2} --like ${vector_file}
+
+# calculate motion amplitudes along the 3 image axes
+dir=( sagittal coronal axial )
+for i in 0 1 2; do
+  echo Motion along ${dir[$i]} direction
+  clitkImageStatistics -i ${vector_file} -m ${roi_mask2} -c $i --verbose 2> /dev/null | tail -n 8 | head -n 6
+  echo
+done
+
+rm `basename $roi_mask .mhd`.{mhd,raw}
+rm `basename $roi_mask2 .mhd`.{mhd,raw}
+rm /tmp/err.txt