The current reproducibility study evaluates 140 children treated for medulloblastoma and 92 age-similar controls using TBSS analysis of FA and dosimetry accounting for age. Treatment included surgery, post-operative standard or high dose craniospinal irradiation and adjuvant chemotherapy. FA measures at baseline after surgery but prior to therapy demonstrated an immediate decrease due to tumor and surgery, which was then accentuated by irradiation. A partial recovery of FA followed, which was attenuated in patients receiving higher doses. These longitudinal profiles need to be considered when conducting cross-sectional studies of patients at time points during or after therapy.