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PAGE UNDER CONSTRUCTION! DO NOT USE THIS FOR GROUP ANALYSIS!

Please continue to use our old [wiki:FsTutorial/GroupAnalysis tutorial] while we develop this!

FreeSurfer Tutorial: Group Analysis with QDEC

*To follow this exercise exactly be sure you've downloaded the [wiki:FsTutorial/Data 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.

In this tutorial, you will learn how to perform statistical analysis of group surface-based data, including:BR

Assuming that all surface reconstruction has been completed for all subjects in the study, FreeSurfer's mri_glmfit command can be used to perform inter-subject/group averaging and inference on the cortical surface. Mri_glmfit models the data as a linear combination of effects related to variables of interest, confounds and errors, and permits statistical inferences to be made about effects of interest in relation to error variance. It also allows for certain permutation testing and other means for correcting for mutliple comparisons. For group analysis, this technique fits a general linear model (GLM) at each surface vertex to explain the data from all subjects in the study. In this section, a brief overview of linear modeling is presented and mri_glmfit is described for estimating a linear model and testing hypotheses. The modeling overview can be skipped if this material is already familiar. Other software packages have similar types of programs (e.g., FSL's GFEAT).

1.0 Preparing for Group Analysis

For group analysis, you can create an average subject from all the participants in the study. This average will be used as the target subject upon which the results of your group analysis can be output and viewed. To create this average, use make_average_subject. One has already been created for the later exercise, so there is no need to execute this sample command: 

make_average_subject --subjects <subj1> <subj2> ...

The default behavior of this script is to create a subject in the $SUBJECTS_DIR named 'average' using each subjects talairach.xfm transform. This behavior can be modified on the command line. You can specify --out your_named_average to change the name of the average subject and --xform talairach.lta (or talairach.m3z) to specify the use of one of the other transforms.

The average subject is created using the processed volumes and surfaces from the set of subjects you specify following the --subjects flag. The make_average_subject command executes both the make_average_volume and make_average_surface subscripts for you.

The distributed example of an average subject can be found in $FREESURFER_HOME/subjects/buckner_data/tutorial_subjs/group_analysis_tutorial called fsaverage

This average subject was created using the volumes and surfaces of subjects in:

$FREESURFER_HOME/subjects/buckner_data/group_study

(Note: the data in the group_study directory is not required to complete the tutorial. However, [wiki:FsTutorial/Data it is available for download] if you wish to pursue your own group analysis.)

https://surfer.nmr.mgh.harvard.edu/fswiki/make_5faverage_5fsubject