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| = The !FreeSurfer pipeline surface registration process = | |
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| (In the following "?h." refers to either of "lh." or "rh.".) | |
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The registration process includes several key steps: === Inflated Spherical "version" of a subject's surface mesh === As the !FreeSurfer pipeline processes a subject's data, the initial white surface mesh is "inflated" to several other states, one of which is a sphere, typically '''?h.sphere'''. The inflation process is constrainted to minimize the total distortion. === Vertex-wise data is applicable to all versions of the surface === The inflation process does not add or remove any vertices, so any data associated with the white vertices (such as curvature or convexity) is still associated with the same-numbered vertices of the sphere mesh. This is the basis of displays such as the following where a per-vertex variable "convexity" of the white surface (aka 'sulc') is plotted in color on the '''lh.sphere surface''':[[BR]]attachment:fsbert_sulc_sphere.jpg * '''Registration of a subject's surface''' to a reference consists of a 2-D warp of the subject's sphere surface so that the individual's curvature data pattern aligns with a reference '''template''' pattern. The template was previously prepared as the "average" (loosely speaking) pattern from a group of representative subjects. The standard template supplied with !FreeSurfer is in the files '''{fshome}/average/?h.average.curvature.filled.buckner40.tif'''. * '''The result of registation''' is yet another version of the subject's surface mesh, typically named '''?h.sphere.reg''', this time with the x,y,z vertex positions still on a sphere, but warped so that the subject's curvature pattern best aligns with the template data. Here is the same convexity data, now plotted on the '''lh.sphere.reg''' surface. Similar pattern, but "stretched around". [[BR]]attachment:fsbert_sulc_spherereg.jpg. What is to be discussed below relates to the content and format of the template file just mentioned. == Disambiguation: template, atlas, parameterization file == 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. Further, a template file is sometimes referred to as a "parameterization file". |
The Surface Registration Process; Templates
Index TableOfContents
Overview
This page provides an overview of two related topics:
How the FreeSurfer pipeline registers the surfaces of individual subjects to an "average" reference surface, using "template" ("tif") file.
The process of creating one's own template file, perhaps for subject groups or species for which the provided template is not suitable.
You might also be interested in how surface label atlases are created and used: SurfaceLabelAtlas
The !FreeSurfer pipeline surface registration process
(In the following "?h." refers to either of "lh." or "rh.".)
The registration process includes several key steps:
Inflated Spherical "version" of a subject's surface mesh
As the FreeSurfer pipeline processes a subject's data, the initial white surface mesh is "inflated" to several other states, one of which is a sphere, typically ?h.sphere. The inflation process is constrainted to minimize the total distortion.
Vertex-wise data is applicable to all versions of the surface
The inflation process does not add or remove any vertices, so any data associated with the white vertices (such as curvature or convexity) is still associated with the same-numbered vertices of the sphere mesh. This is the basis of displays such as the following where a per-vertex variable "convexity" of the white surface (aka 'sulc') is plotted in color on the lh.sphere surface:BRattachment:fsbert_sulc_sphere.jpg
Registration of a subject's surface to a reference consists of a 2-D warp of the subject's sphere surface so that the individual's curvature data pattern aligns with a reference template pattern. The template was previously prepared as the "average" (loosely speaking) pattern from a group of representative subjects. The standard template supplied with FreeSurfer is in the files {fshome}/average/?h.average.curvature.filled.buckner40.tif.
The result of registation is yet another version of the subject's surface mesh, typically named ?h.sphere.reg, this time with the x,y,z vertex positions still on a sphere, but warped so that the subject's curvature pattern best aligns with the template data. Here is the same convexity data, now plotted on the lh.sphere.reg surface. Similar pattern, but "stretched around". BRattachment:fsbert_sulc_spherereg.jpg.
What is to be discussed below relates to the content and format of the template file just mentioned.
Disambiguation: template, atlas, parameterization file
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. Further, a template file is sometimes referred to as a "parameterization file".
Xxxx
Label file
Xxxx