add checks/warnings on ROI in STC

lib/petpvcSTCPVCImageFilter.h

@@ -44,6 +44,18 @@ using namespace itk;
 
 namespace petpvc
 {
+
+  /*! Single Target Correction (STC)
+
+    An Implementation of the STC Method, see<br>
+    Sari H, Erlandsson K, Law I, Larsson HB, Ourselin S, Arridge S, Atkinson D, Hutton BF.
+    Estimation of an image derived input function with MR-defined carotid arteries in FDG-PET human studies using a novel partial volume correction method. 
+    J Cereb Blood Flow Metab. 2017;37(4): 1398--409
+    <br>
+    Erlanddsson K and Hutton BF.
+    A novel voxel-based partial volume correction method for single regions of interest.
+    J Nucl Med Meeting Abstr 2014; 55: 2023.
+  */
 template< class TInputImage, typename TMaskImage>
 class STCPVCImageFilter:public ImageToImageFilter< TInputImage, TInputImage >
 {

lib/petpvcSTCPVCImageFilter.txx

@@ -26,6 +26,7 @@
 #include "itkObjectFactory.h"
 #include "itkImageRegionIterator.h"
 #include "itkImageRegionConstIterator.h"
+#include <stdexcept>
 
 using namespace itk;
 
@@ -64,6 +65,7 @@ void STCPVCImageFilter< TInputImage, TMaskImage>
     if (imageSize.Dimension != 3) {
         std::cerr << "[Error]\tMask file must be 3-D!"
                   << std::endl;
+        throw std::runtime_error("Mask file must be 3-D");
     }
 
     MaskSizeType desiredStart;
@@ -92,6 +94,11 @@ void STCPVCImageFilter< TInputImage, TMaskImage>
     int numOfLabels = labelStatsFilter->GetNumberOfLabels();
     nClasses = numOfLabels;
 
+    if ( numOfLabels < 2 ) {
+        std::cerr << "[Error]\tMask file contains only 1 label, implying zero voxels in the ROI"
+                << std::endl;
+        throw std::runtime_error("Mask file should contain at least 2 labels");
+    }
     if ( this->m_bVerbose )
         std::cout << "Number of labels: " << nClasses << std::endl;
 
@@ -230,6 +237,22 @@ void STCPVCImageFilter< TInputImage, TMaskImage>
             {
 
                 LabelPixelType labelValue = *vIt;
+
+                //checks on ROI size
+                if ( k == 1 ) {
+                    const typename LabelStatisticsFilterType::MapSizeType numOfVoxels = labelStatsFilter->GetCount( labelValue );
+                    if ( numOfVoxels == 0) {
+                        std::cerr << "[Error]\tMask file contains zero voxels in the ROI for label " << labelValue << "!"
+                                  << std::endl;
+                        throw std::runtime_error("Mask file contains zero voxels in the ROI");
+
+                    } else if ( numOfVoxels < 10 ) {
+                        std::cerr << "[Warning]\nMask file contains less than 10 voxels in the ROI. That is unlikely to work well.\n";
+                    }
+                    if ( this->m_bVerbose )
+                      std::cout << "Number of voxels in the ROI of label " << labelValue << ": " << numOfVoxels << std::endl;
+                }
+
                 binThreshFilter->SetLowerThreshold( labelValue );
                 binThreshFilter->SetUpperThreshold( labelValue );
 

src/STC.cxx

@@ -3,7 +3,7 @@
 
    Author:      Benjamin A. Thomas
 
-   Copyright 2017 Institute of Nuclear Medicine, University College London.
+   Copyright 2017, 2020 Institute of Nuclear Medicine, University College London.
 
    Licensed under the Apache License, Version 2.0 (the "License");
    you may not use this file except in compliance with the License.
@@ -18,7 +18,15 @@
    limitations under the License.
 
    This program implements the Single Target Correction (STC) partial volume correction
-   (PVC) technique. Please cite the following paper:
+   (PVC) technique. Please cite the following:
+
+   Sari H, Erlandsson K, Law I, Larsson HB, Ourselin S, Arridge S, Atkinson D, Hutton BF.
+   Estimation of an image derived input function with MR-defined carotid arteries in FDG-PET human studies using a novel partial volume correction method. 
+   J Cereb Blood Flow Metab. 2017;37(4): 1398--409
+
+   Erlanddsson K and Hutton BF.
+   A novel voxel-based partial volume correction method for single regions of interest.
+   J Nucl Med Meeting Abstr 2014; 55: 2023.
 
  */
 
@@ -125,6 +133,9 @@ int main(int argc, char *argv[])
     maskReader->SetFileName(sMaskFileName);
 
     //Try to read mask.
+    if ( bDebug )
+      std::cout << "Reading mask (making it binary by thresholding if it isn't yet)\n";
+
     try {
         maskReader->Update();
     } catch (itk::ExceptionObject & err) {
@@ -195,7 +206,13 @@ int main(int argc, char *argv[])
 std::string getAcknowledgments(void)
 {
     //Produces acknowledgments string for 3DSlicer.
-    std::string sAck = "This program implements the Single Target Correction (STC) partial volume correction (PVC) technique. Please cite the following paper:\n";
+    std::string sAck = "This program implements the Single Target Correction (STC) partial volume correction (PVC) technique. Please cite the following:\n"
+      "Sari H, Erlandsson K, Law I, Larsson HB, Ourselin S, Arridge S, Atkinson D, Hutton BF.\n"
+      "Estimation of an image derived input function with MR-defined carotid arteries in FDG-PET human studies using a novel partial volume correction method.\n"
+      "J Cereb Blood Flow Metab. 2017;37(4): 1398--409\n\n"
+      "Erlanddsson K and Hutton BF.\n"
+      "A novel voxel-based partial volume correction method for single regions of interest.\n"
+      "J Nucl Med Meeting Abstr 2014; 55: 2023.\n";
 
     return sAck;
 }