Documentation/4.2/Developers/Tutorials/PortingCLIToITKv4

1. "My filter doesn't run". The API to ThreadedGenerateData() changed in ITKv4 (use of a defined type ThreadIdType). This can result in your implementation of ThreadedGenerateData() defining a new function instead of overriding the version called by the pipeline. ITKv4 attempts to emit a run-time exception but there are circumstances where the exception cannot be thrown (for instance, if the superclass already provided a valid version of ThreadedGenerateData()). If your filter is not executing in ITKv4, check the declaration of ThreadedGenerateData().
2. DICOM/GDCM. If your CLI used GDCM directly, you will need to port your CLI to ITKv4. ITKv4 uses GDCM 2 which has many API changes from GDCM 1.