While each subject's data has already been (spatially) warped to the common template space, and subject fixels have been reoriented accordingly, there is still no specification of which fixels match (across subjects, and between the subject and template fixels).  This step establishes exactly that, by matching the fixels of each individual subject to the single common set of template fixels (which then inherently also defines how they match across subjects). This is achieved by, for each fixel in the template fixel mask, identifying the corresponding fixel in the matching voxel of the subject image and assigning the FD value of this corresponding subject fixel to that fixel in template space. If no fixel exists or can be found in a subject that corresponds to a given template fixel then it is assigned a value of zero (as the absence of a subject fixel at this stage is most likely due to a very low, or even zero, FD). This step is performed as follows::

    foreach * : fixelcorrespondence IN/fixel_in_template_space/fd.mif ../template/fixel_mask ../template/fd PRE.mif

Note that the output fixel directory :code:`../template/fd` is the same for all subjects. This makes sense, since after this operation, there is only a single remaining set of fixels (i.e. the template fixels), with corresponding FD values as obtained from each subject. This resulting directory :code:`../template/fd` now stores these data as individual fixel data files: one for each subject, and all with respect to a single set of corresponding template fixels. This way of storing the entire population's FD data is then ready for input to :code:`fixelcfestats` later on.

