run_first_all {fslr}

Run FIRST All

Description

Wrapper for run_first_all from FSL for FIRST analysis segmentation of subcortical structures

Usage

run_first_all(
  img,
  oprefix = tempfile(),
  brain_extracted = FALSE,
  structures = NULL,
  affine = NULL,
  opts = "",
  verbose = TRUE
)

Arguments

img

specifies the input image (T1-weighted)

oprefix

specifies the output image basename (extensions will be added to this)

brain_extracted

specifies that the input image has been brain extracted

structures

a restricted set of structures to be segmented

affine

specifies the affine registration matrix to standard space (optional)

opts

(character) operations to be passed to run_first_all

verbose

(logical) print out command before running

Value

List of results, including result of system and some output files