ciftiTools

Tools for reading and visualizing CIFTI brain imaging files. CIFTI files contain brain imaging data in “gray-ordinates”, which includes all the gray matter of the brain. The gray matter is divided into cortical surface (left and right) and subcortical (cerebellum, basal ganglia, and other deep gray matter). ciftiTools uses the Connectome Workbench to separate CIFTI files into two GIFTI files representing the cortical surface data and one NIFTI file representing the subcortical data, and reads the data into R. It also provides visualization tools for the surface and subcortical data. ciftiTools also includes processing functions to apply common preprocessing steps to the CIFTI data (e.g. smoothing, resampling).

Installation

You can install the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("mandymejia/ciftiTools")

Example

Visualizing CIFTI data with ciftiTools:

library(ciftiTools)

# Tell ciftiTools where to find the Connectome Workbench folder/executable.
ciftiTools.setOption('wb_path', 'Desktop/workbench')

# Read in the CIFTI file, and resample it to 8000 vertices per hemisphere.
cifti <- read_cifti(
  cifti_fname='Desktop/data/my_CIFTI_file.dtseries.nii', 
  surfL_fname='Desktop/data/32k_inflated_left.gii', 
  surfR_fname='Desktop/data/32k_inflated_right.gii', 
  resamp_res=8000, 
  # The spheres are only required for resampling.
  sphereL_fname='Desktop/data/32k_left_sphere.gii', 
  sphereR_fname='Desktop/data/32k_right_sphere.gii'
)

# Visualize the surface.
plot(cifti)

Wishlist

• static images in view_cifti()
• slider in view_cifti() to change column/time
• write_cifti()
• unflatten_cifti()
• tests
• CRAN
• Neuroconductor