Merge pull request #362 from rijobro/fix-sirf_registration

fix sirf_registration

src/Synergistic/sirf_registration.cpp

@@ -49,7 +49,7 @@ static std::shared_ptr<const ImageData> image_as_sptr(const std::string &filenam
         return sptr_img;
     }
     else
-        throw std::runtime_error("Synergistic_aladin: unknown engine - " + engine + ".\n");
+        throw std::runtime_error("Synergistic_aladin: unknown image engine - " + engine + ".\n");
 }
 
 static std::shared_ptr<Registration<float> > algo_as_sptr(const std::string &algorithm)
@@ -135,11 +135,23 @@ int main(int argc, char* argv[])
         // Get images
         int flag_ref = find_flag(unused_flags,argv,"-ref",true);
         int flag_eng_ref = find_flag(unused_flags,argv,"-eng_ref");
-        std::shared_ptr<const ImageData> ref = image_as_sptr(argv[flag_ref+1],argv[flag_eng_ref+1]);
+        std::shared_ptr<const ImageData> ref;
+        if (flag_eng_ref==-1) {
+            std::cout << "\nNo engine supplied for reference image, assuming Nifti.\n";
+            ref = image_as_sptr(argv[flag_ref+1]);
+        }
+        else
+            ref = image_as_sptr(argv[flag_ref+1],argv[flag_eng_ref+1]);
 
         int flag_flo = find_flag(unused_flags,argv,"-flo",true);
         int flag_eng_flo = find_flag(unused_flags,argv,"-eng_flo");
-        std::shared_ptr<const ImageData> flo = image_as_sptr(argv[flag_flo+1],argv[flag_eng_flo+1]);
+        std::shared_ptr<const ImageData> flo;
+        if (flag_eng_flo==-1) {
+            std::cout << "\nNo engine supplied for floating image, assuming Nifti.\n";
+            flo = image_as_sptr(argv[flag_flo+1]);
+        }
+        else
+            flo = image_as_sptr(argv[flag_flo+1],argv[flag_eng_flo+1]);
 
         // Set images
         reg->set_reference_image(ref);