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 the single file with this command: concat_bvars output_name.bvars [list of ".bvars" files]. You most likely will use a wildcard "*" rather than typing each filename. For example, to combine all the left hippocampus files in the directory: [user@localhost temp]$ concat_bvars L_Hipp_all.bvars con*_-L_Hipp_first.bvars dis*_-L_Hipp_first.bvars
This command will combine ALL individuals' L_Hipp files. Therefore, if you want to exclude a subject, you need to move the files out of the folder, and re-run concat_bvars. You may want to name the output file with the number of subjects, e.g., "L_Hipp_all_N35.bvars" for 35 subjects.
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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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