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The purpose of this paper is to present a new method and structure for the automatic configuration of a digital system to unknown delays in synchronous input data channels. The method makes possible to restore synchronism in node-to-node communication. Synchronism may be lost due to different delays introduced by the various communication channels. The proposed method allows differences in the channel delays larger than one clock cycle. The method targets distributed digital systems with high number of node-to-node communication channels that must transmit high data volume at high data rates and maintain data time coherence. The method is used in a medical imaging system, namely in the Data Acquisition (DAQ) module of the Data Acquisition Electronics (DAE) component of a PEM (Positron Emission Mammography) system. The system is implemented in a multiple FPGA platform (9 Xilinx™ xc2v4000-4bf957 FPGA). The method and its architectural solution have been validated in a hardware prototype. Test results are presented.