civet.readCBRAIN: Read a CBRAIN project in R

In Mouse-Imaging-Centre/RMINC: Statistical Tools for Medical Imaging NetCDF (MINC) Files

Read a CBRAIN project in R

Description

Simplified file input for CBRAIN projects. Attempts to use as much information as possible from the directory structure and internal CBRAIN config files to find and read the correct CIVET results for CIVET 2.0.0 and 2.1.0

Usage

civet.readCBRAIN(
  path,
  prefix,
  subjects = NULL,
  atlas = "AAL",
  civetVersion = "2.1.0",
  readFiles = TRUE,
  readQC = TRUE,
  flatten = TRUE,
  QCDir = "QC",
  columnsToKeep = "subject",
  confFile = Sys.glob(paste0(path, "/*/*.yml"))[1]
)

Arguments

path	Path to the civet project
prefix	The prefix used to create the subject names
subjects	A character vector specifying which subjects to read in. If not specified, All files within path that don't match QC, scripts, stats, or analysis will be read in.
atlas	Either AAL (default), DKT, or a path to the specific atlas used
civetVersion	the version of CIVET used, either 2.1.0 (default) or 2.0.0
readFiles	logical whether or not to read the files into R or just generate the file names
readQC	logical whether to read and merge the QC results (must be used with flatten)
flatten	logical whether to convert the CIVET results into a dplyr compatible data frame or leave it in the legacy format
QCDir	The directory, or vector of directories of where to find QC tables
columnsToKeep	Additional columns from civet.readAllCivetFiles to include in the output
confFile	A configuration file produced by CBRAIN, defaults to the first .yml file amongst the subjects.

Value

A data.frame in the format of civet.getAllFilenames if readFiles is FALSE. A data.frame in the format of civet.readAllCivetFiles if readFiles is TRUE and flatten is FALSE. And a data.frame in the format of civet.flattenForDplyr if readQC, readFiles, and flatten are all TRUE (default)

See Also

civet.getAllFilenames civet.readAllCivetFiles civet.flattenForDplyr

Mouse-Imaging-Centre/RMINC documentation built on Feb. 24, 2025, 1:22 a.m.