DTSERIESvextract

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)

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

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.

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)
#> The path to the workbench directory could be not found in the set wb_path.

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