Plot '3D' volume in anatomical slices

Usage

# S3 method for class 'ieegio_volume'
plot(
  x,
  position = c(0, 0, 0),
  center_position = FALSE,
  which = c("coronal", "axial", "sagittal"),
  slice_index = 1L,
  transform = "vox2ras",
  zoom = 1,
  pixel_width = max(zoom/2, 1),
  col = c("black", "white"),
  alpha = NA,
  crosshair_gap = 4,
  crosshair_lty = 2,
  crosshair_col = "#00FF00A0",
  label_col = crosshair_col,
  continuous = TRUE,
  vlim = NULL,
  add = FALSE,
  main = "",
  axes = FALSE,
  background = col[[1]],
  foreground = col[[length(col)]],
  ...,
  .xdata = x$data
)

Arguments

x: 'ieegio_volume' object; see read_volume
position: position in 'RAS' (right-anterior-superior) coordinate system on which cross-hair should focus
center_position: whether to center canvas at position, default is FALSE
which: which slice to plot; choices are "coronal", "axial", and "sagittal"
slice_index: length of 1: if x has fourth dimension (e.g. 'fMRI'), then which slice index to draw
transform: which transform to apply, can be a 4-by-4 matrix, an integer or name indicating the matrix in x$transforms; this needs to be the transform matrix from voxel index to 'RAS' (right-anterior-superior coordinate system), often called 'xform', 'sform', 'qform' in 'NIfTI' terms, or 'Norig' in 'FreeSurfer'
zoom: zoom-in level
pixel_width: pixel size, ranging from 0.05 to 50; default is the half of zoom or 1, whichever is greater; the unit of pixel_width divided by zoom is milliliter
col: color palette for continuous x values
alpha: opacity value if the image is to be displayed with transparency
crosshair_gap: the cross-hair gap in milliliter
crosshair_lty: the cross-hair line type
crosshair_col: the cross-hair color; set to NA to hide
label_col: the color of anatomical axis labels (i.e. "R" for right, "A" for anterior, and "S" for superior); default is the same as crosshair_col
continuous: reserved
vlim: the range limit of the data; default is computed from range of x$data; data values exceeding the range will be trimmed
add: whether to add the plot to existing underlay; default is FALSE
main, ...: passed to image
axes: whether to draw axes; default is FALSE
background, foreground: background and foreground colors; default is the first and last elements of col
.xdata: default is x$data, used to speed up the calculation when multiple different angles are to be plotted

Examples


library(ieegio)

nifti_file <- "nifti/rnifti_example.nii.gz"
nifti_rgbfile <- "nifti/rnifti_example_rgb.nii.gz"

# Use
#   `ieegio_sample_data(nifti_file)`
# and
#   `ieegio_sample_data(nifti_rgbfile)`
# to download sample data


if(
  ieegio_sample_data(nifti_file, test = TRUE) &&
  ieegio_sample_data(nifti_rgbfile, test = TRUE)
) {

# ---- NIfTI examples ---------------------------------------------

underlay_path <- ieegio_sample_data(nifti_file)
overlay_path <- ieegio_sample_data(nifti_rgbfile)

# basic read
underlay <- read_volume(underlay_path)
overlay <- read_volume(overlay_path)

par(mfrow = c(1, 3), mar = c(0, 0, 3.1, 0))

ras_position <- c(50, -10, 15)

ras_str <- paste(sprintf("%.0f", ras_position), collapse = ",")

for(which in c("coronal", "axial", "sagittal")) {
  plot(x = underlay, position = ras_position, crosshair_gap = 10,
       crosshair_lty = 2, zoom = 3, which = which,
       main = sprintf("%s T1RAS=[%s]", which, ras_str))
  plot(x = overlay, position = ras_position,
       crosshair_gap = 10, label_col = NA,
       add = TRUE, alpha = 0.9, zoom = 5, which = which)
}


}