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In brain surgery, placing a microelectrode from the outer brain to the specific target becomes a new medical resource-reduced technology to alleviate Parkinson's disease. During the operation, the brain atlas is an important and auxiliary tool that cannot completely describe the real brain structure of the patient. Thus, a neurosurgeon usually conjectures the surgical target through experience under the condition that no individual brain atlas is available. Hence, the danger of the surgical operation is high and the automation of the whole process is hard to achieve. In this article, we utilize the patient's computed tomography (CT) data, Schaltenbrand-Wahren (SW) brain atlas, and image processing techniques to develop a novel stereotactic surgical planning system, named Brain Deep Tracer. This system can help a neurosurgeon perform minimally invasive brain surgery (e.g., functional stereotaxy) and diagnose brain disease such as Parkinson's. Generally speaking, this system includes versatile functions such as three-dimensional (3-D) reconstruction of the brain atlas, 3-D localization of the patient's brain CT data, registration of the brain atlas and CT data, fusion of the brain atlas and CT data, and surgical trajectory planning. More importantly, this system can correct the distortion due to the tilt of the head frame and make the localization result more accurate than other systems.