This is a study on autonomic neuroscience. In a previous paper in [1], we studied a subject affected from facioscapulohumeral muscular dystrophy before and after Ken Ware treatment (NPT). Using the non linear methodology of the Generalized Mutual Information (GMI) analysis of Sensory Motor Rhythm, we produced detailed results evidencing that the mentioned NPT treatment involved a net improvement of the patient under his subjective psychological condition, and in particular, under the neurological and sensory motor profile. We quantified with accuracy the improvement that the subject realized during such treatment. Of course, previous studies of several authors have evidenced that muscular dystrophies are strongly linked to a profound ANS disfunction.Therefore, the aim of the present study was to analyze the ANS of the subject before and after the treatment. We performed analysis in time as well as in frequency domain and by using non linear methods. The basic result of the paper was that, according to our analysis, the subjects started with a serious ANS disfunction before the NPT treatment and that a net improvement was obtained after this therapy. All the examined parameters resulted strongly altered before the treatment and all they returned in the normal range after the NPT.