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.
templatebrain(
name,
regName = name,
type = NULL,
sex = NULL,
dims = NULL,
BoundingBox = NULL,
voxdims = NULL,
origin = NULL,
units = NULL,
description = NULL,
doi = NULL,
...
)A list with class templatebrain.
the full name of the template.
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).
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.
the sex of the template brain. For templates with
type=='average', the possibility of sex='intersex' exists.
dimensions of the image (number of voxels).
physical dimensions of the image (see
boundingbox).
physical spacing between voxels.
the physical location of the first voxel
units of physical measurements (e.g. microns).
details of the template.
a DOI for the original template brain image.
additional named arguments that will be added as fields to the
templatebrain object.
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.
as.templatebrain, templatebrain-meths,
xform_brain, mirror_brain.