Introduction
This tutorial is designed to introduce you to the "command-line" group analysis stream in FreeSurfer (as opposed to QDEC which is GUI-driven), including correction for multiple comparisons. While this tutorial shows you how to perform a surface-based thickness study, it is important to realize that most of the concepts learned here apply to any group analysis in FreeSurfer, surface or volume, thickness or fMRI.
QDEC Tutorial
FSGD Format
FSGD Examples
DODS vs DOSS
This Data Set
The data used for this tutorial is 40 subjects from Randy Buckner's lab. It consists of males and females ages 18 to 93. You can see the demograhics here. You will perform an analysis looking for the effect of age on cortical thickness accounting for the effects of gender in the analysis. This is the same data set used in the [[FsTutorial/QdecGroupAnalysis | QDEC Tutorial]], and you will get the same result.
General Linear Model (GLM) Setup
For this example, we will model the thickness as a straight line. A line has two parameters: intercept (or offset) and a slope.
- The slope is the change of thickness with age
- The intercept is interpreted as the thickness at age=0.
To account for effects of gender, we will model each sex with its own line, meaning that there will be four linear parameters (also called "betas"):
- Intercept for Females
- Intercept for Males
- Slope for Females
- Slope for Males
In FreeSurfer, this type of design is called DODS (for Different-Offset, Different-Slope).
As a matrix equation, the GLM is set up as y=X*b. y is the vector of thickness values at one vertex. There are 40 subjects, so y will have 40 rows. b (beta) is the vector of parameters (intercepts and slopes above). There are 4, so b has 4 elements. X is the design matrix and is constrained to be 40x4. Each row represents a subject. Each column represents a parameter. The demographics page has an example of this design DODS matrix.