- typedef itk::JoinSeriesImageFilter<SliceType, ImageType> JointSeriesFilterType;
- typename JointSeriesFilterType::Pointer jointFilter = JointSeriesFilterType::New();
- for(int i=0; i<mInputSlices.size(); i++) {
- jointFilter->SetInput(i, mInputSlices[i]);
+
+ // Join the slices
+ m_working_input = clitk::JoinSlices<ImageType>(mInputSlices, input, GetDirection());
+ this->template StopCurrentStep<ImageType>(m_working_input);
+
+ //--------------------------------------------------------------------
+ // Step 7: autocrop
+ if (this->GetAutoCropFlag()) {
+ this->StartNewStep("Final AutoCrop");
+ typedef clitk::AutoCropFilter<ImageType> CropFilterType;
+ typename CropFilterType::Pointer cropFilter = CropFilterType::New();
+ cropFilter->SetInput(m_working_input);
+ cropFilter->ReleaseDataFlagOff();
+ cropFilter->Update();
+ m_working_input = cropFilter->GetOutput();
+ this->template StopCurrentStep<ImageType>(m_working_input);