Plotting brain mesh atlases in plotly • ggseg3d

Introduction

Some times, you want to plot the 3d-surfaces from FreeSurfer. Here, it is easier to use data from FreeSurfer (like annot and colorlut files) to create colours for the vectors. The data is somewhat more complex than the 2d ggplot polygon version ggseg ggseg3d() will create a plotly plot, which is interactive, and provides another type of flexibility to the user. A lot of credit goes to A.M.Winkler and his Brainder work, which supplied us with the first examples of going from .srf to .ply files, and whose scripts massively aided us in making this work.

Basic use

The function ggseg3d(), is based in the plotly, it is recommended to get a little familiarized with with plotly.

Out-of-the-box, ggseg() works without supplying any extra information. It will create a base plot of the aparc (dk) brain segmentations. All [...]_3d atlases have a built in colour column for default colour plotting of the segments.

library(ggseg3d)
library(dplyr)
library(tidyr)

ggseg3d() %>% 
  remove_axes() %>% 
  pan_camera("right medial")