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civet.getAllFilenames

Source: R/civet.R
civet.getAllFilenames.Rd

Generates list of filenames output by CIVET

Usage

civet.getAllFilenames(
  gf,
  idvar,
  prefix,
  basedir,
  append = TRUE,
  civetVersion = "1.1.9",
  cnf = NULL
)

Arguments

gf

Data Frame with subject information

idvar

column name in gf with subject IDs

prefix

Prefix specified when CIVET was run

basedir

directory where all CIVET output was stored

append

Whether to append the results to the input gf

civetVersion

Version of CIVET

cnf

A list of configuration information used to parse CIVET files produced by CBRAIN. Unnecessary for CIVETs < 2. Should be read from CBRAIN yaml config file, but can be input manually as a list containing thickness_method (tlink or laplacian), thickness_kernel (in mm), and atlas as either AAL or DKT

Value

gf is returned with CIVET filenames

Details

Prior to running, read.csv may be called to generate the input argument gf. The results will be stored under the column name CIVETFILES either in the input gf (if append = TRUE) or in a new gf. Currently only CIVET versions 1.1.9 and 1.1.12 are supported.

See also

civet.readAllCivetFiles

Examples

if (FALSE) { # \dontrun{
getRMINCTestData()
gf = read.csv("/tmp/rminctestdata/CIVET_TEST.csv")
gf = civet.getAllFilenames(gf,"ID","TEST","/tmp/rminctestdata/CIVET","TRUE","1.1.12")
} # }