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| This document provides an overview of four related topics: | This page provides an overview of two related topics: |
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| * How the !FreeSurfer pipeline compares a subject's surface data to an '''atlas''' to automatically derive an '''annotation''' file marking anatomical cortical regions for that subject. * The process for creating one's own '''atlas''', perhaps to define a different set of regions. |
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| = Label = | You might also be interested in how surface label atlases are created and used: SurfaceLabelAtlas |
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| Xxxx | = The FreeSurfer pipeline surface registration process = |
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| == Label file == Xxxx |
(In the following "?h." refers to either of "lh." or "rh.".) |
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| The registration process includes several key steps: | |
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| === 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'''. || attachment:fsbert_sulc_sphere.jpg || === Registration of a subject's surface === 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'''. === Registation output === ||<^>The output from registation is yet another version of the subject's surface mesh, typically named '''?h.sphere.reg''', 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".|| attachment:fsbert_sulc_spherereg.jpg || == 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". == Registration process diagram == attachment:gw_sphere_reg.gif = Creating a registration template = attachment:gw_make_template.gif |
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. |
attachment:fsbert_sulc_sphere.jpg |
Registration of a subject's surface
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.
Registation output
The output from registation is yet another version of the subject's surface mesh, typically named ?h.sphere.reg, 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". |
attachment:fsbert_sulc_spherereg.jpg |
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".
Registration process diagram
attachment:gw_sphere_reg.gif
Creating a registration template
attachment:gw_make_template.gif