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.
Combining individual files: concat_bvars
Outcome: a single file that contains all studies' files, for a given structure.
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 and contrast files
Outcome: a group of files than are used to run statistical analyses; these are not specific to a structure (and so can be copied across structures to repeat the same analysis).
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 need to be created. Furthermore, the file format is different in SPM and FSL: in FSL, there is a custom design matrix, and t-contrast and f-contrast files are created at the same time as the design matrix. This is different to SPM where the design is specified, then any t or f contrast can be created from that design.
(An older version of these instructions is here.)
Follow these steps:
Glm from FSL GUI
Type "fsl" to start the FSL GUI, click "Misc " then "GLM Setup".
