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Many CLIs are essentially ITK programs. Porting to ITKv4 usually just involves recompilation.
ITKv4 is the result of an effort to retool ITK after 10 years of continuous development. Preserving APIs was concern. But there were circumstances where the APIs changed or were eliminated. Porting CLIs that utilized these components will require a bit more work. The ITKv4 Migration Guide is a valuable reference to track known issues and the suggested remediations.
Getting started with ITKv4 - has general information on ITKv4
ITKv4 Migration Guide - has a migration guide that explains API changes.
Known issues in porting CLIs
My filter doesn't run.
The API to ThreadedGenerateData() changed in ITKv4.
ITKv3 version of ThreadedGenerateData()
virtual void ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, int threadId );
ITKv4 version of ThreadedGenerateData()
virtual void ThreadedGenerateData(const OutputImageRegionType & outputRegionForThread, ThreadIdType threadId);
Note the use of ThreadIdType.
If you have written a mulit-threaded filter, you need to update the signature of the method. Your ITKv3 version of the method may be 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. Specifically, if your filter is a subclass of a filter that does implement ThreadedGenerateData(), then ITKv4's attempt to inform of the issue is circumvented.
If your filter is not executing in ITKv4, check the declaration of ThreadedGenerateData().
ITKv4 updated the version of GDM used to version 2. GDCM version 2 has many API changes from version 1. If your CLI used GDCM directly, you will need to port your CLI to ITKv4. If you used ITK abstractions to access DICOM, then the changes to GDCM will not affect your CLI.