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The files will be ordered alphabetically; knowing the order is required for the later steps (specifically, creating the design matrix).
Design Matrix
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Click to example of two-group, 96 subject design matrix file.
The design matrix is a text file with header information and numbers in columns. by traditional, the file is saved with a name like "design.mat" but you could also use "design.txt." Each row represents a subject, in the order stored in the concatenated bvars file. The simplest design matrix (for a two group dataset) is a two columns, with the first +1 for rows in group 1 and 0 otherwise, and similarly +1 in the second column for rows in the second group. There is also header information which includes the number of columns (I think), the number of subjects, and the maximum value of each column. For example, here is a two-group, 5 subjects/group design matrix:
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