bridging_sequence: Find sequence of one or more bridging registrations

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

Find sequence of one or more bridging registrations

Description

This function is primarily intended for developer use (it is used inside xform_brain) but may be useful for end users.

Usage

bridging_sequence(
  sample,
  reference,
  via = NULL,
  imagedata = FALSE,
  checkboth = !imagedata,
  mustWork = FALSE
)

Arguments

sample	Source template brain (e.g. IS2) that data is currently in. Specified either as character vector or a templatebrain object.
reference	Target template brain (e.g. IS2) that data should be transformed into.
via	(optional) intermediate template brain that the registration sequence must pass through.
imagedata	Whether x should be treated as image data (presently only supported as a file on disk) or 3D object vertices - see details.
checkboth	whether to look for registrations in both directions. The default (checkboth=FALSE) will only return registrations in the forward direction (see details).
mustWork	whether to error out if appropriate registrations are not found.

Details

When checkboth=FALSE, only registrations that can be directly used to map image data from sample to reference are returned. When working with 3D points, use checkboth=TRUE. Note that all possible directories will first be scanned for registrations in the preferred direction and then rescanned for the opposite direction if nothing is found.

Registration direction

When mapping points from JFRC2 -> IS2 -> FCWB (i.e. sample=JFRC2, via=IS2, ref=FCWB) the command line passed to CMTK's streamxform should look like: ⁠streamxform -- JFRC2_IS2.list --inverse FCWB_IS2.list⁠ However when mapping image data the command line for CMTK's reformatx should look like: ⁠reformatx -o out.nrrd --floating JFRC2.nrrd FCWB.nrrd FCWB_IS2.list --inverse JFRC2_IS2.list⁠ bridging_sequence produces output like ⁠ list(JFRC2 = structure( "/GD/dev/R/nat.flybrains/inst/extdata/bridgingregistrations/JFRC2_IS2.list", swap = TRUE), IS2 = "/GD/dev/R/nat.flybrains/inst/extdata/bridgingregistrations/FCWB_IS2.list") ⁠ in these circumstances, which xformpoints.cmtkreg turns into "– JFRC2_IS2.list –inverse FCWB_IS2.list".

Examples

## Not run: 
bridging_sequence(sample=JFRC2, ref=FCWB, checkboth = TRUE)
bridging_sequence(sample=JFRC2, via=IS2, ref=FCWB, checkboth = TRUE)

## End(Not run)

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