alignReg {patternize}

Aligns images using niftyreg utilities for automated image registration..

Description

Aligns images using niftyreg utilities for automated image registration..

Usage

alignReg(
  sampleList,
  target,
  resampleFactor = NULL,
  useBlockPercentage = 75,
  crop = c(0, 0, 0, 0),
  removebgR = NULL,
  maskOutline = NULL,
  plotTransformed = FALSE
)

Arguments

sampleList

List of RasterStack objects.

target

Image imported as RasterStack used as target for registration.

resampleFactor

Integer for downsampling used by redRes (default = NULL).

useBlockPercentage

Block percentage as used in niftyreg (default = 75).

crop

Vector c(xmin, xmax, ymin, ymax) that specifies the pixel coordinates to crop the original image.

removebgR

Integer indicating the range RGB treshold to remove from image (e.g. 100 removes pixels with average RGB > 100; default = NULL) for registration analysis. This works only to remove a white background.

maskOutline

When outline is specified, everything outside of the outline will be masked for the color extraction (default = NULL).

plotTransformed

Whether to plot transformed images while processing (default = FALSE).

Value

List of raster objects.