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
Link 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:
Create this file and save it in the same directory as everything else.
You can also set up this design matrix using FSL. 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."
