ravecore (version 0.1.0)

cmd_run_fsl_flirt: Run 'FSL' linear registration

Description

Run 'FSL' linear registration

Usage

cmd_run_fsl_flirt(
  subject,
  mri_path,
  ct_path,
  dof = 6,
  cost = c("mutualinfo", "leastsq", "normcorr", "corratio", "normmi", "labeldiff", "bbr"),
  search = 90,
  searchcost = c("mutualinfo", "leastsq", "normcorr", "corratio", "normmi", "labeldiff",
    "bbr"),
  overwrite = FALSE,
  command_path = NULL,
  dry_run = FALSE,
  verbose = dry_run
)

Value

A command set running the terminal command; a 'coregistration'

folder will be created under the subject imaging directory

Arguments

subject

'RAVE' subject or subject ID

mri_path

path to 'MRI' (fixed image)

ct_path

path to 'CT' (moving image)

dof

degrees of freedom; default is 6 (rigid-body); set to 12 ('affine')

cost, searchcost

cost function name

search

search degrees; default is 90 to save time, set to 180 for full search

overwrite

overwrite existing files

command_path

path to 'FSLDIR' environment variable

dry_run

whether to dry-run

verbose

whether to print out command