FSL Tutorials 4-5: Group-Level Analysis

It has well been said that analyzing an fMRI dataset is like using a roll of toilet paper; the closer you get to the end, the faster it goes. Now that you know how to analyze a single run, applying this concept to the rest of the dataset is straightforward; simply apply the same steps to each run, and then use the "Higher-Level Analysis" option within FEAT to select your output directories. You might want to label them for ease of reference, with the run number appended to each directory (e.g., output_run01, output_run02, etc).

Also uploaded is a walkthrough for how to locate and look at your results. The main directory of interest is the stats folder, which contains z-maps for each contrast; simply open up fslview and underlay an anatomical image (or a standard template, such as the MNI 152 brain, if it is a higher-level analysis that has been normalized), and then overlay a z-map to visualize your results. The sliders at the top of fslview allow you to set the threshold for the lower and upper bounds of your z-scores, so that, for example, you only see z-scores with a value of 3.0 or greater.

After that, the same logic applies to collapsing parameter estimates across subjects, except that in this case, instead of feeding in single-run FEAT directories into your analysis, you use the GFEAT directories output from collapsing across runs for a single subject. With the use of shell scripting to automate your FEAT analyses, as we will discuss in the next tutorial, you can carry out any analysis quickly and uniformly; not only is scripting an excellent way to reduce the amount of drudge work, but it also ensures that human error is out of the equation once you hit the go button.

Make sure to stay tuned for how to use this amazing feature, therewith achieving the coveted title of Nerd Baller and Creator of the Universe.