Index TableOfContents

Context: The surface registration process

This page relates to the "template" file type used in the FreeSurfer pipeline as part of the process of coregistering the surfaces of individual subjects. Several concepts are needed to understand this area. (In the following "?h." refers to either of "lh." or "rh.".)

What is to be discussed below relates to the content and format of the template file just mentioned.

Disambiguation: template vs atlas

In many places, especially within the FreeSurfer source code, the word "atlas" is often used interchangeably with "template". I am reserving the term atlas for the GCA files used in labeling regions.

Template data

Template data grid

As might be guessed, a template contains curvature-related data as an array of data items that correspond to a grid of points on the sphere -- but which grid? Is it a specific surface mesh supplied with FreeSurfer? A standard "icosahedron"? As it turns out, it's a grid defined in spherical coordinates:BR

... the two parameters of the so-called "surface parameterization" (elsewhere known as u and v).

So, for any single data item, we can expect an array(256 * 512) of numbers.

Template data items

The various programs involved have some flexibility in what size and shape of template to work with, but here I will describe the standard ?h.average.curvature.filled.buckner40.tif.

The registration process does not simply attempt to match a subject and template based on a single variable. Instead it works with several variables, and statistics about those variables.

Here's what I think is in the standard template:




inflated ("football")




sulc (ie: convexity)