imageListToMatrix: Read Images into a Matrix

In stnava/ANTsR: ANTs in R: Quantification Tools for Biomedical Images

Read Images into a Matrix

Description

Read images into rows of a matrix.

Usage

imageListToMatrix(
  imageList,
  mask,
  sigma = NA,
  epsilon = 0,
  asymmetryTx = NULL,
  asymmetryMask = NULL
)

Arguments

imageList	A character vector containing a list of image files to read, in order - these are image objects, not file names. these are assumed to be in a normalized space i.e. they are all in registration.
mask	An antsImage containing a binary mask, voxels in the mask are placed in the matrix. If not provided, estimated from first image in list. If the mask is a different size than the image, the images will be downsampled and smoothed to the size of the mask.
sigma	smoothing operation in physical space. See smoothImage.
epsilon	threshold value determining what is included in the mask
asymmetryTx	a reflection transform
asymmetryMask	a mask defining left and right side of the image. this should be defined in the space of the images within the imageList.

Value

A matrix containing the masked data, the result of calling as.numeric(image, mask) on each input image.

Author(s)

Cook PA, Avants B, Kandel BM

See Also

matrixToImages, getMask

Examples

img <- ri(1) %>% resampleImage(c(32, 32))
imglist <- list()
nsubj <- 3
for (ii in 1:nsubj) {
  imglist[[ii]] <- img
}
mask <- getMask(img)
imgmat <- imageListToMatrix(imglist, mask)

stnava/ANTsR documentation built on April 13, 2025, 4:10 a.m.