FSL describes the shape analysis as "Vertex Analysis," which is a section in the User Guide. There is a simple preparation step, and then there is running the model, which is a single step but with several options.
Combining individual files: concat_bvars
In a terminal, navigate to the directory with all the bvars files, e.g., [user@localhost temp]$ cd /mnt/hgfs/LinuxShare/temp
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.
The files will be ordered alphabetically; knowing the order is required for the later steps (specifically, creating the design matrix).
Design Matrix
The design matrix is a text file with numbers in columns. 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 single column with +1 for one group and -1 for another.