Archive - old design matrix and contrast files

These are the old steps.

1) Open Glm

Either start from the FSL GUI, or from a terminal "cd" to the directory, and type Glm (case sensitive).

2) Enter the total number of subjects, and the number in the first group (if using a two-group design)

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.

3) Adjust the design to have one column for group

Go the to General Linear Model window, and set to 1 EV; the Group B column will disappear.

4) Change the second group EV value from 0 to "-1"

Scroll down to the second group (where values change from 1 to 0 in EV1 column); change all the "0"'s to "-1" (tedious).

5) Set one T contrast and one F contrast

From the top of the General Linear Model window select the "Contrasts & F-tests" tab, and set to one Contrast, one F-test, and select the C1 contrast for the F1 (click on the small square).

6) Save the file

Under the GLM Setup window click Save, navigate to the directory with the files, and choose a descriptive name ("des_2sample" for example). You can ignore the warning.

This will save a number of files, as in the example below (where "des" was chosen as the name). These files are used as input to several of the following procedures.

Other designs (covariate, more groups)

Covariates are added as extra columns (add an "EV"), as explained in the Glm user guide.Note that these examples do not have the group variable set up as above, so you will need to change from a column per group to a single column with different values for each. (For example see the Two-Group Difference Adjusted for Covariate in the user guide.)

Moving the files to a separate folder

Because the stats only needs the design matrix and combined all.bvars files, these can be copied to subfolders for the next stages; this helps keep everything organized. Since you will likely be doing multiple models and statistical analyses, you can create as many well-named folders as you like, and copy the same set of design matrix & all.bvars files.

Background on design matrix

The design matrix is a text file with header information and numbers in columns. By tradition, the file is saved with a name like "design.mat". 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 single column, with +1 for group 1 and -1 for group 2. A default matrix created by Glm for two groups includes two columns, but this is not what is needed for FIRST. 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: