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= Overview= = Overview =

Index TableOfContents

Overview

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) is plotted in color on the sphere:

{ Sulc on sphere }

  • 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.

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

Synopsis

command argA argB -flag1 arg1 -flag2 arg2 [-flag3 arg3] [-flag4 arg4]

Arguments

Positional Arguments

argA

brief description

detailed description (eg, help file information)

argB

brief description

detailed description (eg, help file information)

Required Flagged Arguments

-flag1 arg1

brief description

detailed description (eg, help file information)

-flag2 arg2

brief description

detailed description (eg, help file information)

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

Description

description

Examples

Example 1

command foo -i f -o out

description

Example 2

command foo -i f -o out -f fvalue

description

Bugs

None

See Also

["othercommand1"], ["othercommand2"]

Links

FreeSurfer, FsFast

Methods Description

description
description

References

["References/Lastname###"]

Reporting Bugs

Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>

Author/s

JaneSmith

TemplateTifImageFiles (last edited 2009-02-02 20:29:28 by GrahamWideman)