Transcranial magnetic stimulation (TMS) is a well-known technique to study brain function. Location of TMS points can be visualized on the subject’s Magnetic Resonance Image (MRI). However inter-subject comparison is possible only after a normalization i.e. a transformation of the stimulation points to a reference atlas image. Here, we propose a generic and automatic image processing pipe-line for normalizing a collection of subjects’ MRI and TMS points. The normalization uses a loop of rigid-transform followed by Basis-Splines registration. The used reference atlas is the common Montreal National Institute (MNI) brain atlas. We show preliminary results from 10 subjects. Those normalized points were compared to the SPM normalization and validated by TMS experts.