Customize 3D Viewer Color Palette

This post contains interactive components (experimental) that allows you to execute RAVE code from the web browsers. If you would like to try this feature and customize/play with the code, please be patient. It might take a while for the browser to finish setting up (depending on your network speed). Once the script is ready, you will see “WEBR STATUS: 🟢 Ready!” in the above banner.

Prerequisites

This post assumes that you have already imported subject’s imaging data to RAVE and finished the electrode localization. If you haven’t done so, please im.

1. Simple 3D viewer

Library raveio provides simple high-level function rave_brain to load 3D brain object.

Use brain$plot(<your arguments...>) to show the viewer:

Preview of the result. See below if you want to play with the 3D viewer interactively

2. Render electrodes with values

brain$set_electrode_values(table_or_path) allows users to load a data table and render electrodes with colors. Users can create a csv table using Excel or their favorite programming languages, as long as the table follows the following format:

Subject	Electrode	varname*
DemoSubject	1	0.25
DemoSubject	14	-0.4
…	…	…

Here is the explanation of the columns (case-sensitive):

• Subject is the subject code
• Electrode is the electrode channel number (integer)
• varname* can be almost anything (give it a meaningful name, for e.g., Power, Cluster, …) that you would like to show, and the values can be either numeric or categorical
  • The variable name is recommended to only contain letters and digits. For example, BetaBandPower seems to be a good idea, while names like 75-150 Hz should be avoided
  • The variable values must not be numerical if the intent is categorical. For example cluster values such as 1, 2, 3, … should be avoided and users should use Cluster 1, Cluster 2, Cluster 3, …, or A, B, C, … instead

Here’s an example data table

Left: continuous values with symmetric value range. The color palette transition from blue to white to red (default); Right: Categorical data with default color palette

3. Render options

brain$plot allows users to provide render options to change the following components:

• Color palette
• Default value ranges (for continuous data)
• Control panels

Here’s a full example:

Key Documentations

Function raveio::rave_brain

Load ‘FreeSurfer’ or ‘AFNI/SUMA’ brain from ‘RAVE’

rave_brain

Description

Create 3D visualization of the brain and visualize with modern web browsers

Usage

rave_brain(
  subject,
  surfaces = "pial",
  use_141 = TRUE,
  recache = FALSE,
  clean_before_cache = FALSE,
  compute_template = FALSE,
  usetemplateifmissing = FALSE,
  include_electrodes = TRUE
)

Arguments

subject	character, list, or RAVESubject instance; for list or other objects, make sure subject$subject_id is a valid ‘RAVE’ subject ‘ID’
surfaces	one or more brain surface types from “pial”, “white”, “smoothwm”, “pial-outer-smoothed”, etc.; check freesurfer_brain2
use_141	whether to use ‘AFNI/SUMA’ standard 141 brain
recache	whether to re-calculate cache; only should be used when the original ‘FreeSurfer’ or ‘AFNI/SUMA’ files are changed; such as new files are added
clean_before_cache	whether to clean the original cache before recache; only set it to be true if original cached files are corrupted
compute_template	whether to compute template mappings; useful when template mapping with multiple subjects are needed
usetemplateifmissing	whether to use template brain when the subject brain files are missing. If set to true, then a template (usually ‘N27’) brain will be displayed as an alternative solution, and electrodes will be rendered according to their ‘MNI305’ coordinates, or ‘VertexNumber’ if given.
include_electrodes	whether to include electrode in the model; default is true

Value

A ‘threeBrain’ instance if brain is found or usetemplateifmissing is set to true; otherwise returns NULL

Examples

# Please make sure DemoSubject is correctly installed
# The subject is ~1GB from Github

if(interactive()){
  brain <- rave_brain("demo/DemoSubject")

  if( !is.null(brain) ) { brain$plot() }

}