The brain MR imaging-based clinical research and analysis system were specifically built and the development for a large-scale data was targeted. We used the general clinical data available for building large-scale data. Registration period for the selection of the lesion ROI and the region growing algorithm was used and the Mesh-warp algorithm for matching was implemented. The accuracy of the matching errors was modified individually. Also, the large ROI research data can accumulate by our developed compression method. In this way, the correctly decision criteria to the research result was suggested. The experimental groups were age, sex, MR type, patient ID and smoking which can easily be queries. The result data was visualized of the overlapped images by a color table. Its data was calculated by the statistical package. The evaluation for the utilization of this system in the chronic ischemic damage in the area has done from patients with the acute cerebral infarction. This is the cause of neurologic disability index location in the center portion of the lateral ventricle facing. The corona radiate was found in the position. Finally, the system reliability was measured both inter-user and intra-user registering correlation.