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FreeSurfer Tutorial: Overlay of Functional Brain Activation Maps (20 minutes of exercises)

Overlaying a color-coded volumetric map of brain activations onto a high resolution anatomical scan permits these activations to be studied in an anatomical context. In FreeSurfer, an activation volume may be overlayed onto an anatomical volume, or an activation volume can be resampled onto a surface derived from the anatomical volume and then overlayed onto that surface for viewing. Both of these ways of visualizing activation data are described below.

1.0 Overlaying the parametric map onto the FreeSurfer anatomical volume

Assuming all fMRI preprocessing and analysis has been completed and a parametric map of brain activations for a given subject has been generated, this activation volume can be visualized as an overlay, with variable transparency, onto the FreeSurfer anatomical volume. By convention, a "heat" colormap is used to represent levels of activation; negative values are indicated in cooler colors with the lowest values in blue, and positive values are drawn in warmer colors with yellow indicating the highest. Displaying the parametric map this way allows the color-coded statistics to be visually associated with anatomical regions in the brain.

2.0 Resampling the parametric map of brain activations onto a surface

In many instances, it is useful to view the brain activation data as projected onto the subject's inflated cortical surface. This type of visualization can be particularly useful for locating activations that occur within the sulci which often require the scrolling through slice planes to see in a volumetric representation. In the following exercise, the activation volume is sampled onto the inflated cortical surface.

3.0 Visualizing and navigating results

Once the parametric map has been resampled onto the inflated cortical surface, it can be visualized in tksurfer. The following exercise shows how to load the surface and newly generated overlay in tksurfer, how to simultaneously view the volumetric representation in tkmedit, and how to mark spatially corresponding points in the two different visualizations.


2010-02-06 17:59