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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
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
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).