Monday, October 1, 2012

searchlight shapes: BrainVoyager

Rainer Goebel kindly provided a description and images of the searchlight creation used in BrainVoyager:

"BrainVoyager uses the "sphere" approach (as in our original PNAS paper Kriegeskorte, Goebel, Bandettini 2006), i.e. voxels are considered in a cube neighborhood defined by the radius and in this neighborhood only those voxels are included in the "sphere" that have an Euclidean distance from the center of less than (or equal to) the radius of the sphere. From your blog, I think the resulting shapes in BrainVoyager are the same as for pyMVPA.

Note, however, that in BrainVoyager the radius is a float value (not an integer) and this allows to create "spheres" where the center layer has a single element on each side at cardinal axes (e.g. with radius 1, 2, 3, 4... voxels, see snapshot below) but also "compact" spheres as you seem to have used by setting the radius, e.g. to 1.6, 1.8, 2.6, 2.8, 3.6...). "

At right is an image Rainer generated showing  radius 1.0 and 2.0 searchlights created in BrainVoyager.

I am intrigued by Rainer's comment that using non-integer radii will make more "compact" spheres; non-interger radii underscores the need to be explicit in describing searchlight shape in methods sections. It appears that pyMVPA requires integer radii, but the Princeton MVPA Toolbox does not.

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