epongpipat / r-for-brain-network

Analyze brain surface/volume (gifti, cifti, nifti) in R and extract networks

R for brain network

• Documentation of how to
  • Manipulate gifti (surface), nifti (volume), cifti (surf+vol) in R to generate network matrices
  • Calculate network metrics/measures
  • Analyze data
  • Visualize results.

Prerequisites

• The gifti package is required to read in gifti files.

• A forked version of the r package cifti is used for loading in cifti files from MSC data. The cifti files from MSC (at least the .dtseries storing functional time series) are in non-standard arrangement. Standard cifti would have rows x dense (vertex), whereas MSC's ciftis have dense (vertex) x column. Using the original cifti package would arrange the cifti from MSC incorrectly (as of 2/7/2019).

• gridExtra & ggplotify for arranging the plots. pals for color pallete.

• A forked version of the r package superheat is used for most of the visualization. Example:

Acknowledgments

• The superheat package was super convenient for my work. Check out the original author's vignette for examples.
• The gifti and cifti packages from John Muschelli are obviously critical for interacting with these data format.