Function reference • nat.templatebrains

Package Help Provides an overview of key functions and classes
`nat.templatebrains-package` `nat.templatebrains`	NeuroAnatomy Toolbox add-on package for handling template brains
Template Brains Functions that handle defining template brain spaces and setting the space for objects.
`templatebrain()`	Construct templatebrain object for an image registration template
`is.templatebrain()` `as.character(<templatebrain>)` `print(<templatebrain>)` `as.im3d(<templatebrain>)` `origin(<templatebrain>)` `dim(<templatebrain>)` `voxdims(<templatebrain>)` `boundingbox(<templatebrain>)`	Template brain methods
`regtemplate()` `regtemplate<-`()	Get or set the registration template space in which an object lives
`as.templatebrain()`	Use image file or other object to initialise template brain
`plot3d(<templatebrain>)`	Plot 3D surface of a template brain
`display_slice()`	Display an image slice in 3D
Transformations Functions that handle transformations of objects between different template brain spaces
`xform_brain()`	Transform 3D object between template brains
`mirror_brain()`	Mirror 3D object around a given axis, optionally using a warping registration
`fit_xform()`	Fit affine or thin plate spline transform to arbitrary transformation
`fit_xform_brain()`	Fit a single transform to a bridging registration between brains
Registration Sequences Functions that list available registrations or return registration sequences between different template brains (used by xform_brain and friends but may be useful in their own right).
`bridging_sequence()`	Find sequence of one or more bridging registrations
`bridging_graph()` `shortest_bridging_seq()`	Make or query connected graph of bridging registrations
`allreg_dataframe()`	Make data.frame with details of all registrations
Finding Template Brains Functions that help you find available template brain objects
`all_templatebrains()` `guess_templatebrain()`	Find all template brains or those matching a given image volume
Managing Registrations Functions that inform the package of available bridging registrations or download / update registrations from remote sources.
`add_reg_folders()` `extra_reg_folders()`	Set or list local folders containing registrations for nat.templatebrains
`add_reglist()`	Add reglist object describing a bridging/mirroring registration
`download_reg_repo()`	Download and register git repository containing registrations
`update_reg_repos()`	Update local copy of git repository containing registrations
`local_reg_dir_for_url()`	Standard local checkout location for extra registration directories
Sample data Sample template brain (see nat.flybrains package for more examples)
`FCWB.demo`	Sample template brain: FlyCircuit Whole Brain

Reference

Package Help

Template Brains

Transformations

Registration Sequences

Finding Template Brains

Managing Registrations

Sample data