In Mouse-Imaging-Centre/RMINC: Statistical Tools for Medical Imaging NetCDF (MINC) Files

Visualizing 3D Objects with RMINC

As of RMINC 1.3 we've begun to support visualizing 3D volumes with R. This document is designed to showcase a few of these features.

#Load in our libraries
library(RMINC)
library(rgl)

```{R, echo = FALSE} setupKnitr()

Lets pull in a demonstration object file. The file format currently supported by RMINC is the BIC-MNI text obj format, documented [on their github](https://github.com/BIC-MNI/bicpl/Documentation). This file format is used by CIVET, amongst other tools, to store brain surfaces. The figures produced are interactive and can be rotated and magnified with the mouse.

```{R, rgl = TRUE}
mouse_cortex <- 
  read_obj("/axiom2/projects/software/cortical-thickness/MWM/c57bl6_laplacian_grid_full_surface_simplified.obj")

plot(mouse_cortex)

In addition to creating surfaces, it is possible to add thresholdable statistics maps with colour legends

```{R, rgl = TRUE} demo_stats <- #Generate some random uniform vertex data runif(ncol(mouse_cortex$vertex_matrix))

plot(mouse_cortex, demo_stats, colour_range = c(.5,1))

It is also possible to identify vertices from a figure

```{R, eval = FALSE}
selected_vertices <- vertexSelect(multiples = TRUE)

```{R, echo = FALSE} selected_vertices <- matrix(c(1.29478, -1.22361, 3.57911, 1.49924, -1.86518, 3.39112, 1.79532, -2.49190, 3.08894), ncol = 3, byrow = TRUE)

![](RMINC_rgl_data/selected_vertices.png)

To disable the indicator spheres, simply run `vertexSelect` with `indicate = FALSE`. To remove the spheres after you've verified they are correct, run `rgl::pop3d()`, only do this if you have not added elements to the rgl scene after the spheres, otherwise you will need to look up their ids with `rgl::ids()`. See `?vertexSelect` for details.

Once you've identified your vertices of interest, you can find those vertices within the statistic map

```{R}
vertexLookup(mouse_cortex, selected_vertices, demo_stats)

Mouse-Imaging-Centre/RMINC documentation built on Nov. 12, 2022, 1:50 p.m.