templatebrain: Construct templatebrain object for an image registration...

In nat.templatebrains: NeuroAnatomy Toolbox ('nat') Extension for Handling Template Brains

Construct templatebrain object for an image registration template

Description

templatebrain objects encapsulate key information for the reference brain in an image registration. Usually this will be a standard template brain used for many registrations. It will normally be much more convenient to use as.templatebrain methods to convert an image file or an im3d object into a templatebrain.

Usage

templatebrain(
  name,
  regName = name,
  type = NULL,
  sex = NULL,
  dims = NULL,
  BoundingBox = NULL,
  voxdims = NULL,
  origin = NULL,
  units = NULL,
  description = NULL,
  doi = NULL,
  ...
)

Arguments

name	the full name of the template.
regName	the short name. This will be the stem used to prefix registrations (e.g. JFRC2_someimage.list) for this template brain and likely also the stem of the template brain image (e.g. JFRC2.nrrd).
type	one of c('single brain', 'average'), indicating whether the template brain has been created from just one image, or is the average of multiple images.
sex	the sex of the template brain. For templates with type=='average', the possibility of sex='intersex' exists.
dims	dimensions of the image (number of voxels).
BoundingBox	physical dimensions of the image (see boundingbox).
voxdims	physical spacing between voxels.
origin	the physical location of the first voxel
units	units of physical measurements (e.g. microns).
description	details of the template.
doi	a DOI for the original template brain image.
...	additional named arguments that will be added as fields to the templatebrain object.

Details

A variety of methods are available to work on templatebrain objects. See templatebrain-meths for basic methods. The two main functions that are available for using template brains are xform_brain and mirror_brain.

templatebrain objects are only useful for transformation processes when the BoundingBox is specified to define the physical extent of the volume. We use the definition of the Amira 3D visualisation and analysis software. This corresponds to the node centers option in the NRRD format. The bounding box can be obtained from NRRD or AmiraMesh format files. See boundingbox for details.

Value

A list with class templatebrain.

See Also

as.templatebrain, templatebrain-meths, xform_brain, mirror_brain.

nat.templatebrains documentation built on July 9, 2023, 6:18 p.m.