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| === 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". |
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| = The FreeSurfer pipeline surface registration process = | |
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| = Label = | (In the following "?h." refers to either of "lh." or "rh.".) |
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| Xxxx | The registration process includes several key steps: |
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| == Label file == Xxxx |
== 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. |
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| == Vertex-wise data is applicable to all versions of the surface == | |
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| ||<^>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 registration 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 || == Registration process diagram == The diagram below summarizes the registration process. Program mris_register inputs a specific subject's ?h.sphere.reg file and associated sulc and curv data from the inflated and smoothwm surfaces. The program compares these to the template file input. The registration sphere, ?h.sphere.reg is output. attachment:gw_sphere_reg.gif = Creating a registration template = The process of creating a template involves calculating an "average" pattern of curvature-related values, along with the variance of these variables. This task is performed by program mris_make_template. However, mris_make_template expects the input subjects to be already aligned (ie: already have ?h.sphere.reg files). This of course will not be the case if you are about to create a template! Consequently, the process proceeds iteratively, starting by creating a template from a single subject. Then two or more iterations are carried out where all the reference subjects are aligned to the latest template using mris_register, then a new template is created based on the latest alignments. This is diagrammed below. attachment:gw_make_template.gif The blue box contains one iteration of the process, which can be repeated until the process converges sufficiently. === Notes === 1. As of this date (2008-01-24), I have not verified that this process is entirely correct -- these are assembled from email exchanges with MGH staff, and from reading source code. 2. The above diagram assumes that the subjects have all been processed once by !FreeSurfer's recon-all pipeline or similar to produce all the required files needed for the template-creation process. Recon-all will also have produced ?h.sphere.reg aligned to the standard reference template (?h.average.curvature.filled.buckner40.tif), and corresponding annotation files. For purposes here, these can be ignored. Indeed, once a satisfactory new template has been created, the recon-all script can be modified to swap in the new template, and the subjects can be re-run to create new improved annotations. 3. For technical details on the template file contents and format, see: TemplateTifImageFiles. = References = The registration process is a main topic in: High-resolution inter-subject averaging and a coordinate system for the cortical surface, Fischl, B., Sereno, M.I., Tootell, R.B.H., and Dale, A.M., (1999). Human Brain Mapping, 8:272-284(1999). See ArticlesSlidesAndPosters |
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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
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 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 registration 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 |
Registration process diagram
The diagram below summarizes the registration process. Program mris_register inputs a specific subject's ?h.sphere.reg file and associated sulc and curv data from the inflated and smoothwm surfaces. The program compares these to the template file input. The registration sphere, ?h.sphere.reg is output.
attachment:gw_sphere_reg.gif
Creating a registration template
The process of creating a template involves calculating an "average" pattern of curvature-related values, along with the variance of these variables. This task is performed by program mris_make_template. However, mris_make_template expects the input subjects to be already aligned (ie: already have ?h.sphere.reg files). This of course will not be the case if you are about to create a template!
Consequently, the process proceeds iteratively, starting by creating a template from a single subject. Then two or more iterations are carried out where all the reference subjects are aligned to the latest template using mris_register, then a new template is created based on the latest alignments. This is diagrammed below.
attachment:gw_make_template.gif
The blue box contains one iteration of the process, which can be repeated until the process converges sufficiently.
Notes
1. As of this date (2008-01-24), I have not verified that this process is entirely correct -- these are assembled from email exchanges with MGH staff, and from reading source code.
2. The above diagram assumes that the subjects have all been processed once by FreeSurfer's recon-all pipeline or similar to produce all the required files needed for the template-creation process. Recon-all will also have produced ?h.sphere.reg aligned to the standard reference template (?h.average.curvature.filled.buckner40.tif), and corresponding annotation files. For purposes here, these can be ignored. Indeed, once a satisfactory new template has been created, the recon-all script can be modified to swap in the new template, and the subjects can be re-run to create new improved annotations.
3. For technical details on the template file contents and format, see: TemplateTifImageFiles.
References
The registration process is a main topic in: High-resolution inter-subject averaging and a coordinate system for the cortical surface, Fischl, B., Sereno, M.I., Tootell, R.B.H., and Dale, A.M., (1999). Human Brain Mapping, 8:272-284(1999). See ArticlesSlidesAndPosters