registration2: Console user interface built on top of 'registration()'...

In mjin1812/SMART: SMART (Semi-manual alignment to reference template): a pipeline for whole brain mapping projects

Description

Allows you to alter correspondance points with user interface with the console This uses the original registration() function from wholebrain and retains the same arguments.

Usage

registration2(
  input,
  coordinate = NULL,
  plane = "coronal",
  right.hemisphere = NULL,
  interpolation = "tps",
  intrp.param = NULL,
  brain.threshold = 200,
  blurring = c(4, 15),
  pixel.resolution = 0.64,
  resize = (1/8)/4,
  correspondance = NULL,
  resolutionLevel = c(4, 2),
  num.nested.objects = 0,
  plateimage = FALSE,
  forward.warp = FALSE,
  filter = NULL,
  output.folder = "../",
  batch.mode = FALSE,
  channel = 0,
  verbose = TRUE,
  closewindow = TRUE,
  width = 18,
  height = 10.2
)

Arguments

input	(required) A character vector consisting of the full path name to 16-bit raw tif image files.
coordinate	(default = NULL) Matching coordinates in the main plane to be registered to (in millimeters).
plane	(default = "coronal") The main plane to register to: "coronal", "sagittal".
right.hemisphere	(default = NULL)
interpolation	(default = "tps")
intrp.param	(default = NULL)
brain.threshold	(default = 200) An integer value, which determinesthe segmentation of the brain slice.
blurring	(default = c(4, 15))
pixel.resolution	(default = 0.64)
resize	(default = (1/8)/4)
correspondance	(default = NULL)
resolutionLevel	(default = c(4, 2))
num.nested.objects	(default = 0)
plateimage	(default = FALSE)
forward.warp	(default = FALSE)
filter	(default = NULL)
output.folder	(default = "../")
batch.mode	(default = FALSE)
channel	(default = 0)
verbose	(default = TRUE) If TRUE diagnostic output is written to the R console. Default is true.
closewindow	(default = TRUE) If TRUE, windows will close after every correspondance point alteration.
width	(default = 18) Plotting window width in inches.
height	(default = 10.2 ) Plotting window height in inches.

Value

returns regi, a vector list of registration information for each registration slice.

See Also

See also wholebrain::registration() for the original registration function from wholebrain.

mjin1812/SMART documentation built on Oct. 30, 2021, 7:25 p.m.