Tract-based spatial statistics (TBSS) has been used to assess the integrity of the visual pathway in glaucoma patients. TBSS uses the subjects' FA data to create a mean FA skeleton of white matter tracts before running voxel-wise cross-subject statistics. We compared four different approaches of registration of FA maps to create the skeleton and evaluated alignment and subsequently the impact of the chosen registration on voxel-wise statistics. Our study comprised 69 subjects, i.e. 46 patients with primary open angle glaucoma (POAG) and a healthy, age-matched control group of 23 subjects. Mean FA skeletons were created using the following registration approaches: registration to a standard template (T), registration to the group mean (GM), registration to a group-wise atlas (GW) and registration to the most typical subject (N). Subsequently, maps of standard deviation of the 4D images were created to assess the alignment. Voxel-wise statistics for each registration approach were performed. We found distinct differences in voxel-wise statistics depending on the chosen registration approach. Best alignment results were achieved by registration to a study specific template, i.e. to the group mean (GM) or to a group-wise atlas (GW). Overall alignment did not differ between these two approaches. However, voxel-wise statistics showed clusters of significantly decreased FA values in the T and GM approach, which were not significant after GW registration. These voxels of significantly decreased FA values after T and GM registration did not represent white matter tracts and correlated with higher standard deviation in FA maps across subjects, thus implying registration errors, especially in the optic radiation. Registration to a study-specific template, i.e. to the group mean or a group-wise atlas seems to be the method of choice in TBSS-analysis of glaucoma patients as it shows better alignment of the optic radiation and helps to rule out registration errors due to misalignment.