QDEC Group Analysis

This post will take you through all of the steps needed to be able to run surface-based group analysis using the Query, Design, Execute, Contrast (QDEC) interface.

1. Create a qdec directory within the directory where all of your subject files are stored.

e.g.

% mkdir qdec

4. For display purposes you will need to have an average subject in your subjects_dir. There is an fsaverage already stored in freesurfer which has been made in MNI space.

e.g. cd $SUBJECTS_DIR
     if (! -e fsaverage) ln -s $FREESURFER_HOME/subjects/fsaverage

3. Create a text file containing all of the subject/demographic information that is required to carry out the analysis (e.g. subject ID, Group membership, age, gender etc). It is important to keep in mind that QDEC can normally handle two additional covariates, so try not to include unnecessary information in this text file.
It is likely that you will need to de-mean the ages, depending on whether you use DODS or DOSS.
You should name this file ending in .table.dat :

e.g.

% nedit mydata.table.dat

SubjectID  Group  Age  Gender
Subject1    HC       50     Female 
Subject2    Patient 48     Male
etc..

Remember:

• Ensure that all subjects are named with the exact same ID as the original image folders.
• There should be no empty lines between subjects.
• keep the information stored in this file to a minimum/only include necessary information that will be used in the analysis.
• If you have more than one table.dat file, containing different categorical information (e.g. controls and patients/ controls and recovered patients) be sure to change the categories in the Group.levels file when running qdec.

4. Any categorical factors (i.e. Group, Gender) will need a separate text file containing the different levels:

e.g.

% nedit Group.levels

HC
Patient

Continuous factors do not need a separate file to define them.

5. If the FreeSurfer environment has been set up properly (as described in previous blog post) you should be able to type in 'qdec' to the terminal and the qdec interface will start to load.

6. When the qdec interface opens up, you can select the table.data file that you have created.

e.g.

File- Load data table

You will also need to go into the 'Design' tab and give the design a name, this will create a directory within your qdec directory, containing all of the output from the analysis you are about to run.

See http://freesurfer.net/fswiki/FsTutorial/QdecGroupAnalysis_freeview for more qdec information.