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• To follow this exercise exactly be sure you've downloaded the tutorial data set before you begin. If you choose not to download the data set you can follow these instructions on your own data, but you will have to substitute your own specific paths and subject names.

Specify contrast vectors to test hypotheses

Contrast vectors are given to mri_glmfit to specify the comparison you want to look at. They will be used in conjunction with the design matrix that was generated from your FSGD file. For instance, a contrast vector such as [1 0 0 0 ...] is used to examine the strength of the observed effect from the EV in the first design matrix column. Another contrast vector, [1 -1 0 0 ...], is used to compare the effects between the first two EVs in the design matrix. You can specify your contrast vector as a separate file, which will be read in by mri_glmfit, and used to test your hypotheses. For the example described here there were two classes (male, female) and one variable (age). The 3 regressors in the design matrix, when using DOSS, will be:

1. Intercept of Male
2. Intercept of Female
3. Age Slope

Your contrast vector can be set up, using these regressors, to make any comparisons you'd want. If you wanted to compare the thickness differences between Males and Females, while regressing out age you could use a contrast vector [1 -1 0]. If you wanted to make a direct comparison between thickness and age, regardless of gender, you could use the contrast vector [0 0 1].

If you are using DODS there will be 4 regressors in the design matrix:

1. Intercept of Male
2. Intercept of Female
3. Age Slope (male)
4. Age Slope (female)

Your contrast vector can be set up, using these regressors, to make any comparisons you'd want. If you wanted to compare the thickness differences between Males and Females, while regressing out age you could use a contrast vector [1 -1 0 0]. If you wanted to make a direct comparison between thickness and age between class, you could use the contrast vector [0 0 1 -1].