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== 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. |
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= Synopsis = command argA argB -flag1 arg1 -flag2 arg2 [-flag3 arg3] [-flag4 arg4] |
= 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]] * theta (0..2*pi in 512 steps) * phi (0..pi in 256 steps)[[BR]] ... the two parameters of the so-called "surface parameterization" (elsewhere known as u and v). |
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= Arguments = == Positional Arguments == || argA || brief description || detailed description (eg, help file information) || || argB || brief description || detailed description (eg, help file information) || |
So, for any single data item, we can expect an array(256 * 512) of numbers. |
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== Required Flagged Arguments == || -flag1 arg1 || brief description || detailed description (eg, help file information) || || -flag2 arg2 || brief description || detailed description (eg, help file information) || |
== 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. |
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== Optional Flagged Arguments == || -flag3 arg3 || brief description ||detailed description (eg, help file information) || || -flag4 arg4 || brief description ||detailed description (eg, help file information) || = Outputs = || volume1 || description || || volume2 || description || |
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. |
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= Description = description |
Here's what I think is in the standard template: |
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= Examples = == Example 1 == command foo -i f -o out |
||<#D0D0D0>Surface||<#D0D0D0>Measure||<#D0D0D0>Variable/Statistics|| ||inflated ("football")||inflated.H ||mean[[BR]]variance[[BR]]Degrees-of-freedom || ||smoothwm ||sulc (ie: convexity)||mean[[BR]]variance[[BR]]Degrees-of-freedom|| ||smoothwm ||curv? ||mean[[BR]]variance[[BR]]Degrees-of-freedom|| |
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| description | |
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== Example 2 == command foo -i f -o out -f fvalue |
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= Bugs = None |
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= See Also = ["othercommand1"], ["othercommand2"] |
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= Links = FreeSurfer, FsFast |
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= Methods Description = {{{ description description }}} |
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= References = ["References/Lastname###"] |
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= Reporting Bugs = Report bugs to <analysis-bugs@nmr.mgh.harvard.edu> |
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= Author/s = JaneSmith |
= Author(s) = GrahamWideman |
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.".)
Inflated Spherical "version" of a subject's surface mesh: As the pipeline progresses, the initial white surface mesh is "inflated" (with constraints to minimize distortion) 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 appearance, 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 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
- theta (0..2*pi in 512 steps)
phi (0..pi in 256 steps)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:
Surface |
Measure |
Variable/Statistics |
inflated ("football") |
inflated.H |
|
smoothwm |
sulc (ie: convexity) |
|
smoothwm |
curv? |