volume and surface brain plotting knitr tutorial

Here is the second of my pair of posts introducing my updated knitr brain plotting tutorials. The first tutorial describes setting up RStudio for knitr compilation, with base R graphics examples - start there. This post adds a pair of brain plotting tutorials, one for volumetric images and the other for surfaces. The source (knitrIntro_NIfTI.rnw, knitrIntro_gifti.rnw) and image files needed for compilation can be downloaded from the blog osf site, "knitr tutorials" section. The compiled pdfs are included as well, at knitrIntro_NIfTI.pdf and knitrIntro_gifti.pdf.

The surface and volume examples are roughly parallel, covering plotting both continuous statistical overlays and parcellations. The example code includes assigning values to parcels (e.g., to show the results of an analysis), adjusting the plot appearance, and doing math with the images in R. Please read both the text in the pdf and the code comments.

The brain images in the knitrs (a few of which are above) are added with a pair of functions I wrote: plot.volume() and plot.surface(). These are updated versions of the functions in previous posts on this blog, with changes to improve the appearance of the surface images and make the color scaling parameters for volumes more similar to those for surfaces.

My intention is that the plotting functions and usage examples in these knitrs will enable beginners to quickly start making useful (and attractive!) knitr documents to summarize, explore, and describe their own analyses. Please let me know if you encounter any bugs, have a suggestion for an improvement, or have a new feature suggestion.

UPDATE 31 March 2023: I uploaded corrected versions of niftiPlottingFunctions.R and knitrIntro_NIfTI.pdf to osf and the volumetric screenshot above. The correction was needed because of a bug in my plot.volume() function causing the negative colors to be reversed: instead of values near zero being dark blue, they were cyan. Major thanks to Tan Nguyen for spotting the unexpected coloring! If you downloaded a copy of niftiPlottingFunctions.R before 30 March 2023, please replace it with this version.

UPDATE 29 June 2021: Changed the volumetric screenshot to show the new (diverging) cool colors (and a legend); niftiPlottingFunctions.R and giftiPlottingFunctions.R now use the same color scales.