Introduced a working version of the new ANTS interfaces (specifically for antsRegistration and antsApplyWarps, removing deprecated antsIntroduction.sh and WarpImageMultiTransform), introduced a range of GUI bug fixes and improvements, merged in some of the additions from the 0.3.4a hotfix, introduced major re-organization, documentation and clean-up of cpac_pipeline.py.
Added file containing the "change_transform_type" function for updating func->anat bbreg affines post-conversion to ITK format.