R: Construct templatebrain object for an image registration...
templatebrain
R Documentation
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, 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.
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 availavle 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.