Great that you were able to get this installed.
To run the cortical thickness analysis, look at slide 27. It shows the 3 steps needed to load the data, execute the model, and save the statistical outputs.
For the first step, you will need 2 things.
i. Location of the subject directory (subjdir variable in load_bss_data)
ii. A demographics csv file (csv variable in load_bss_data, which contains columns such as age, sex, and group. Your group will be HC or HP (for now set it as 1 or 0).
Step 1. Then call the command given in Step 1 by setting the appropriate variables. For e.g. hemi="left" for left hemisphere. If you haven’t smoothed your data, don’t pass the smooth variable.
Step 2. Call the command in Step 2 as bss_model <- bss_anova(main_effect = "group", covariates = "age", bss_data = bss_data)
Step 3. Call save_bss_out(bss_data, bss_model, outdir="/path/to/some/output directory")
To compare volumes, I’d suggest running the TBM analysis. See slide 34 for the steps. The functions are same as above. The options change.
To compare surface areas, I’d suggest running the ROI analysis. (Slide 43).