vol.merge: Merge background volume and overlay to new colors.

In fsbrain: Managing and Visualizing Brain Surface Data

Merge background volume and overlay to new colors.

Description

Merge background volume and overlay to new colors.

Usage

vol.merge(
  volume,
  overlay_colors,
  bbox_threshold = 0L,
  forced_overlay_color = NULL
)

Arguments

volume	3D array, can be numeric (gray-scale intensity values) or color strings. If numeric, the intensity values must be in range ⁠[0, 1]⁠.
overlay_colors	3D array of color strings, values which are not part of the overlay (and should display background in the result) must have NA instead of a color string. Must have same dimensions as the volume.
bbox_threshold	numerical, the threshold intensity used to separate background and foreground. All voxels with intensity values greater than this value in the background volume will be considered foreground voxels. Background-only slices at the borders of the volume will be discarded (in the merged, final image). Pass NULL to use the full image without applying any bounding box.
forced_overlay_color	NULL or an rgb color string, like '#FF0000' for red. If NULL, the activation colors will be used as foreground colors. Otherwise, the given color will be for all foreground vertices.

Value

3D array of color strings, the merged colors

See Also

Other volume utility: vol.boundary.box(), vol.imagestack(), vol.overlay.colors.from.activation(), vol.planes(), vol.slice()

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