civet.getAllFilenames: civet.getAllFilenames

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

civet.getAllFilenames

Description

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

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.

Value

gf is returned with CIVET filenames

See Also

civet.readAllCivetFiles

Examples

## Not run: 
getRMINCTestData() 
gf = read.csv("/tmp/rminctestdata/CIVET_TEST.csv")
gf = civet.getAllFilenames(gf,"ID","TEST","/tmp/rminctestdata/CIVET","TRUE","1.1.12")

## End(Not run)

Mouse-Imaging-Centre/RMINC documentation built on Nov. 12, 2022, 1:50 p.m.