compute.surface.contour.slices: Compute surface contour slice images (internal).

In fsbrain: Managing and Visualizing Brain Surface Data

Compute surface contour slice images (internal).

Description

Internal helper that loads a volume and surface meshes, computes the intersection contours of each surface with each slice plane, and draws them onto individual magick slice images. Used by both volvis.lb.with.surface (which grids the results) and volvis.slices.with.surface (which exports them individually).

Usage

compute.surface.contour.slices(
  subjects_dir,
  subject_id,
  volume = "brain",
  surface = "white",
  hemi = "both",
  surface_color = "#FF0000",
  surface_lwd = 1,
  slices = -5,
  axis = 1L,
  silent = TRUE
)

Arguments

subjects_dir	character string, the FreeSurfer SUBJECTS_DIR.
subject_id	character string, the subject identifier.
volume	numeric 3D array or character string. Either a 3D brain volume or the name of a volume file to load from the subject's mri/ directory. Defaults to "brain".
surface	character string or vector of strings, the surface(s) to use for contour extraction.
hemi	character string, one of 'lh', 'rh', or 'both'.
surface_color	character string or vector, color(s) for the contour lines.
surface_lwd	numeric, line width for contours.
slices	passed to volvis.lightbox. A negative integer N means "use every Nth slice". A numeric vector gives explicit slice indices (1-based). Defaults to -5.
axis	integer, the slice axis. 1 = sagittal, 2 = coronal, 3 = axial. Defaults to 1L.
silent	logical, whether to suppress messages.

Value

named list with entries: images (list of magick images, one per slice), slice_indices (integer vector of 1-based slice indices used), has_contour (logical vector, TRUE if at least one contour segment was drawn on the slice). Also includes metadata entries axis, surfaces, hemis, subject_id for downstream use.

fsbrain documentation built on Aug. 23, 2026, 5:06 p.m.