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.
...
The design matrix is common to FSL statistical routines, and is the same as created in SPM. However, for FIRST there are some differences (see "Create a design matrix" in guide). Specifically, the group should be in one rather than two columns, and F tests should be used. Follow these steps:
1) Open Glm
Either start from the FSL GUI, or from a terminal "cd" to the directory, and type Glm (case sensitive).
2) Enter the total number of subjects, and the number in the first group (if using a two-group design)
...
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 columnssingle column, 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-1 for group 2. A default matrix created by Glm for two groups includes two columns, but this is not what is needed for FIRST. 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".
...