Source template brain (e.g. IS2) that data is currently in.
reference
Target template brain (e.g. IS2) that data should be
transformed into.
via
optional intermediate brain to use when there is no direct
bridging registration.
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.listbridging_sequence produces output like
list(JFRC2 = structure(
"/GD/dev/R/nat.flybrains/inst/extdata/bridgingregistrations/JFRC2_IS2.list",
swapped = 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".