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
)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