A cardiac functional analysis system reconstructs a 3D anatomical image volume using image frames acquired at predetermined cardiac phases over multiple cardiac cycles in response to a trigger derived from hemodynamic signals. A medical imaging system generates 3D anatomical imaging volume datasets from acquired 2D anatomical images. The system includes an image acquisition device for acquiring 2D anatomical images of a portion of patient anatomy in selectable angularly variable imaging planes in response to a synchronization signal derived from a patient blood flow related parameter. A synchronization processor provides the synchronization signal derived from the patient blood flow related parameter. An image processor processes 2D images acquired by the image acquisition device of the portion of patient anatomy in multiple different imaging planes having relative angular separation, to provide a 3D image reconstruction of the portion of patient anatomy.