VertexWiseR (version 1.4.0)

DTSERIESvextract: DTSERIESvextract

Description

Extracts vertex-wise surface-based CIFTI dense time-series data from an individual dtseries .nii file from HCP, fMRIprep or XCP-D preprocessed directories, and stores it as a single .RDS file.

Usage

DTSERIESvextract(dtseries, wb_path, filename, silent = FALSE)

Value

A .RDSfile containing a surface data matrix object, with N time-point x M vertices dimensions and can be readily used by VertexWiseR statistical analysis functions. Each row corresponds to a time point in order and contains the left to right hemispheres' vertex-wise values.

Arguments

dtseries

A string object containing the full path to the dtseries files to extract from.

wb_path

The filepath to the workbench folder that you have previously downloaded and unzipped

filename

A string object containing the desired name of the output RDS file. Default is 'fslr32k.rds' in the R temporary directory (tempdir()).

silent

A logical object to determine whether messages will be silenced. Set to 'FALSE' by default

Details

The function extracts the data from the dtseries.nii file provided, and organizes the left and right hemisphere vertex data for each subject as rows in a N x 64984 data matrix within a .rds object.

Examples

#demo cifti dtseries from openneuro
#(ds005012, sub-18_ses-1_task-mid, run-01, 
#reduced to 50 time points)
download.file(paste0("https://github.com/CogBrainHealthLab",
"/VertexWiseR/blob/main/inst/demo_data/",
"demo_91k_bold.dtseries.nii?raw=TRUE"),
destfile=paste0(tempdir(),
"/demo_91k_bold.dtseries.nii"), 
mode = "wb")
             
sub_dtseries=DTSERIESvextract(
dtseries=paste0(tempdir(),
             "/demo_91k_bold.dtseries.nii"), 
wb_path="/path/to/workbench",
filename="demo_91k_bold.dtseries.rds", 
silent=FALSE)

##visualizing e.g. the first 4 frames of the fMRI volume
#plot_surf(sub_dtseries[c(1,10,20,40),], 
#            file="4frames.png")