They tend to under-sample the underlying volumetric data and do not produce optimal visualizations. Furthermore, current packages use standard computer graphics libraries that are not optimized for accurate visualization of volume projections. However, most of these tools produce static views of the data so it is often difficult to interpret the relationship between cortical anatomy and inflated and flattened surfaces. More sophisticated tools use 3D reconstructions of the cortical surface to create inflated or flattened cortical surfaces ( Cox, 1996 Goebel, 1997 Dale et al., 1999 Van Essen et al., 2001). Volumetric views that show single slices or maximum intensity projections (Figure 1) reveal only a small portion of the available data. However, tools for visualization of fMRI data remain relatively primitive. This allows complex fMRI surface maps to be distributed broadly online without requiring installation of complex software.įunctional magnetic resonance imaging (fMRI) experiments produce rich data revealing the patterns of hemodynamic activity throughout the brain ( Huettel et al., 2009). The output of pycortex can be viewed using WebGL, a technology compatible with modern web browsers. The surface can be inflated and flattened interactively, aiding interpretation of the correspondence between the anatomical surface and the flattened cortical sheet. Anatomical and functional information can be projected onto the cortical surface. Pycortex exploits the power of modern graphics cards to sample volumetric data on a per-pixel basis, allowing dense and accurate mapping of the voxel grid across the surface. To address these problems we have developed pycortex, a Python toolbox for interactive surface mapping and visualization.

Furthermore, it is difficult to understand the relationship between flattened cortical surfaces and the underlying 3D anatomy using tools available currently.

However, surface visualizations are difficult to generate and most common visualization techniques rely on unnecessary interpolation which limits the fidelity of the resulting maps. Surface visualizations of fMRI provide a comprehensive view of cortical activity.

3Department of Psychology, University of California, Berkeley, Berkeley, CA, USA.

2Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA.

1Vision Science Program, University of California, Berkeley, Berkeley, CA, USA.

2d to 3d conversion in cortex