Plot volume slices into scalable vector graphics SVG images

Display slices, or interleave with image overlays. Require installing package htmltools.

Usage

plot_volume_slices(
  x,
  overlay = NULL,
  depths = seq(-100, 100, by = 18),
  which = c("coronal", "axial", "sagittal"),
  nc = NA,
  col = c("black", "white"),
  overlay_col = col,
  overlay_alpha = NA,
  interleave = is.na(overlay_alpha),
  interleave_period = 4,
  interleave_transition = c("ease-in-out", "linear"),
  pixel_width = 0.5,
  underlay_range = NULL,
  overlay_range = NULL,
  ...
)

Arguments

x

underlay, objects that can be converted to as_ieegio_volume; for example, 'NIfTI' or 'FreeSurfer' volume file path, array, loaded volume instances

overlay

same type as x, but optional; served as overlay

depths

depth position in millimeters, along the normal to the which plane

which

which plane to visualize; can be "coronal", "axial", "sagittal"

nc

number of columns; default is to be determined by total number of images

col, overlay_col

underlay and overlay color keys, must have at least two colors to construct color palettes

overlay_alpha

overlay transparency

interleave

whether to interleave overlay; default is true when overlay_alpha is unspecified

interleave_period

interleave animation duration per period, only used when overlay is specified; default is 4 seconds

interleave_transition

interleave animation transition, only used when overlay is specified; choices are 'ease-in-out' (default) and 'linear'

pixel_width

pixel width resolution; default is 0.5 millimeters

underlay_range, overlay_range

numeric vectors of two, value ranges of underlay and overlay

...

passed to internal method

Value

A 'SVG' tag object that can be embedded in shiny applications or plotted directly.

Examples

# toy-example:

shape <- c(10, 10, 10)
vox2ras <- matrix(
  c(10, 17.32, 0, -136,
    -17.32, 10, 20, -63,
    0, -20, 0, 100,
    0, 0, 0, 1),
  nrow = 4, byrow = TRUE
)

# continuous
x <- abs(array(sin(seq_len(100) / 10), shape))

underlay <- ieegio::as_ieegio_volume(x, vox2ras = vox2ras)
overlay <- ieegio::as_ieegio_volume(x > 0.2, vox2ras = vox2ras)

if(interactive()) {

  plot_volume_slices(
    underlay, overlay = overlay,
    depths = seq(0, 150, length.out = 4), pixel_width = 5,
    overlay_col = c("#00000000", "#FF000044", "#FF0000FF")
  )

}

# Require `install_subject("yael_demo_001")`
if(has_rave_subject("YAEL/yael_demo_001")) {

subject <- ravecore::as_rave_subject("YAEL/yael_demo_001",
                                     strict = FALSE)


t1 <- file.path(subject$imaging_path, "coregistration",
                "MRI_reference.nii.gz")

ct <- file.path(subject$imaging_path, "coregistration",
                "CT_RAW.nii.gz")
transform <- read.table(
  file.path(subject$imaging_path, "coregistration",
            "CT_IJK_to_MR_RAS.txt")
)

ct_image_original <- ieegio::read_volume(ct)
ct_image_aligned <- ieegio::as_ieegio_volume(
  ct_image_original[], vox2ras = as.matrix(transform)
)

if(interactive()) {
  plot_volume_slices(
    t1, overlay = ct_image_aligned,
    overlay_col = c("#00000000", "#FF000044", "#FF0000FF"),
    nc = 6
  )
}

}