Merge pull request CBICA#1493 from AlexanderGetka-cbica/add-ibsi2-gui

[BraTSPipeline] Move brain-masked image write to Skull Stripping instead of Brain Tumor step

src/applications/BraTSPipeline.cxx

@@ -365,34 +365,35 @@ int main(int argc, char** argv)
       cbica::ReadImage< TImageType >(brainMaskFile),
       finalBrainMask
       );
-  }
-
-  if (brainTumor)
-  {
-    /// [6] Brain Tumor Segmentation
-    auto brainTumorMaskFile = outputDir + "/dmOut_tumor/tumors_SRI.nii.gz";
 
-    if (!cbica::exists(brainTumorMaskFile))
+    // iterate over outputRegisteredMaskedImages to write brain-masked images before brain-tumor step
+    for (auto it = outputRegisteredMaskedImages.begin(); it != outputRegisteredMaskedImages.end(); it++)
     {
-      // iterate over outputRegisteredMaskedImages
-      for (auto it = outputRegisteredMaskedImages.begin(); it != outputRegisteredMaskedImages.end(); it++)
-      {
         auto modality = it->first;
         auto maskFilter = itk::MaskImageFilter< ImageType, ImageType >::New();
         maskFilter->SetInput(cbica::ReadImage< ImageType >(outputRegisteredImages[modality]));
         maskFilter->SetMaskImage(cbica::ReadImage< TImageType >(finalBrainMask));
         try
         {
-          maskFilter->Update();
+            maskFilter->Update();
         }
         catch (const std::exception& e)
         {
-          std::cerr << "Something went wrong when applying the brain mask to modality '"
-            << modality << "': " << e.what();
-          return EXIT_FAILURE;
+            std::cerr << "Something went wrong when applying the brain mask to modality '"
+                << modality << "': " << e.what();
+            return EXIT_FAILURE;
         }
         cbica::WriteImage< ImageType >(maskFilter->GetOutput(), it->second); // write the masked image 
-      }
+    }
+  }
+
+  if (brainTumor)
+  {
+    /// [6] Brain Tumor Segmentation
+    auto brainTumorMaskFile = outputDir + "/dmOut_tumor/tumors_SRI.nii.gz";
+
+    if (!cbica::exists(brainTumorMaskFile))
+    {
       fullCommand = " -md " + captkDataDir + "/deepMedic/saved_models/brainTumorSegmentation/ " +
         "-i " + outputRegisteredMaskedImages["T1"] + "," +
         outputRegisteredMaskedImages["T1CE"] + "," +