The "Vertex Analysis: requires you to prepare two files: the individual segmented structures combined into one file, and a design matrix to indicate which file belongs to which group.
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Create this file in the same directory as everything else. Either start from the FSL GUI, or "cd" to the directory, and type Glm (case sensitive), select "Higher-level / non-timeseries design" from the pull-down menu, enter the number of subjects (# inputs), click Wizard, select "two groups, unpaired", enter the number of subjects in group 1, click Process, then Save. When saving, navigate to something like \mnt\hgfs\LinuxShare\temp, and choose a file name like design_2group.mat."
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The design matrix is a text file with header information and numbers in columns. By tradition, the file is saved with a name like "design.mat". 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:
Glm from FSL GUI
Type "fsl" to start the FSL GUI, click "Misc " then "GLM Setup".
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