Population template creation is one of the most time consuming steps in a fixel-based analysis. If you have a very large number of subjects in your study, you can opt to create the template from a limited subset of 30-40 individuals. Typically, subjects are chosen so the generated template is representative of your population (e.g. similar number of patients and controls, though avoid patients with excessive abnormalities compared to the rest of the population). To build a template, put all FOD images in a single folder and put a set of corresponding mask images (with the same prefix as the FOD images) in another folder (using masks speeds up registration significantly)::

      mkdir -p ../template/fod_input
      mkdir ../template/mask_input

