knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
The AAL atlas is labeled in MNI space. In order to overlay on an image, we will read in the MNI template. Note, we need the 2mm image as the AAL is in that dimensions.
library(aal) library(neurobase) library(MNITemplate) img = MNITemplate::readMNI(res = '2mm')
Here we will show how to use the borders of the ROIs with the
mask = img * 0 labs = aal_get_labels(version = "4") labs$color = aal_colors[1:nrow(labs)] tri = aal_get_border(version = "4") tri_labs = tri$BORDER.V tri_labs = data.frame( index = tri_labs, order = 1:length(tri_labs)) tri_labs = merge(tri_labs, labs, by = "index", all.x = TRUE, all.y = FALSE, sort = FALSE) tri_labs = tri_labs[ order(tri_labs$order),] tri_labs$order = NULL tri_labs$relabel = factor(tri_labs$index, levels = unique(tri_labs$index)) # save this for later relabeled_fac = tri_labs$relabel tri_labs$relabel = as.numeric(tri_labs$relabel) tri = tri$BORDER.XYZ cols = tri_labs$color cols = unique(cols) mask[tri] = tri_labs$relabel neurobase::ortho2(img, mask, col.y = cols)
Here we will read in the full atlas and plot it:
atlas = aal_image(version = 4) neurobase::ortho2(img, atlas, col.y = cols)
In order to try to keep the colors consistent as with the borders, we will have to refactor the values of the image:
relabeled_atlas = atlas[ atlas > 0 ] relabeled_atlas = as.numeric(factor(relabeled_atlas, levels = levels(relabeled_fac))) relabeled_atlas = remake_img(relabeled_atlas, img = atlas, mask = atlas > 0) neurobase::ortho2(img, relabeled_atlas, col.y = cols)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.