FSL FLIRT wrapper for coregistration
Usage
ni_fsl_flirt(
in_file,
reference,
angle_rep = NULL,
apply_isoxfm = NULL,
apply_xfm = NULL,
args = NULL,
bbrslope = NULL,
bbrtype = NULL,
bgvalue = NULL,
bins = NULL,
coarse_search = NULL,
cost = NULL,
cost_func = NULL,
datatype = NULL,
display_init = NULL,
dof = NULL,
echospacing = NULL,
fieldmap = NULL,
fieldmapmask = NULL,
fine_search = NULL,
force_scaling = NULL,
in_matrix_file = NULL,
in_weight = NULL,
interp = NULL,
min_sampling = NULL,
no_clamp = NULL,
no_resample = NULL,
no_resample_blur = NULL,
no_search = NULL,
out_file = NULL,
out_matrix_file = NULL,
padding_size = NULL,
pedir = NULL,
ref_weight = NULL,
rigid2D = NULL,
schedule = NULL,
searchr_x = NULL,
searchr_y = NULL,
searchr_z = NULL,
sinc_width = NULL,
sinc_window = NULL,
uses_qform = NULL,
verbose = NULL,
wm_seg = NULL,
wmcoords = NULL,
wmnorms = NULL,
.cwd = NULL,
.env = NULL,
.engine = NULL,
.profile = NULL,
dry_run = FALSE,
echo = interactive()
)Arguments
- in_file
Character; file path. input file Required.
- reference
Character; file path. reference file Required.
- angle_rep
Character; one of: "quaternion", "euler". representation of rotation angles
- apply_isoxfm
Numeric. as applyxfm but forces isotropic resampling
- apply_xfm
Logical. apply transformation supplied by in_matrix_file or uses_qform to use the affine matrix stored in the reference header
- args
Character. Additional parameters to the command
- bbrslope
Numeric. value of bbr slope
- bbrtype
Character; one of: "signed", "global_abs", "local_abs". type of bbr cost function: signed [default], global_abs, local_abs
- bgvalue
Numeric. use specified background value for points outside FOV
- bins
Integer. number of histogram bins
- coarse_search
Integer. coarse search delta angle
- cost
Character; one of: "mutualinfo", "corratio", "normcorr", "normmi", "leastsq", "labeldiff", "bbr". cost function
- cost_func
Character; one of: "mutualinfo", "corratio", "normcorr", "normmi", "leastsq", "labeldiff", "bbr". cost function
- datatype
Character; one of: "char", "short", "int", "float", "double". force output data type
- display_init
Logical. display initial matrix
- dof
Integer. number of transform degrees of freedom
- echospacing
Numeric. value of EPI echo spacing - units of seconds
- fieldmap
Character; file path. fieldmap image in rads/s - must be already registered to the reference image
- fieldmapmask
Character; file path. mask for fieldmap image
- fine_search
Integer. fine search delta angle
- force_scaling
Logical. force rescaling even for low-res images
- in_matrix_file
Character; file path. input 4x4 affine matrix
- in_weight
Character; file path. File for input weighting volume
- interp
Character; one of: "trilinear", "nearestneighbour", "sinc", "spline". final interpolation method used in reslicing
- min_sampling
Numeric. set minimum voxel dimension for sampling
- no_clamp
Logical. do not use intensity clamping
- no_resample
Logical. do not change input sampling
- no_resample_blur
Logical. do not use blurring on downsampling
- no_search
Logical. set all angular searches to ranges 0 to 0
- out_file
Character; file path. registered output file
- out_matrix_file
Character; file path. output affine matrix in 4x4 asciii format
- padding_size
Integer. for applyxfm: interpolates outside image by size
- pedir
Integer. phase encode direction of EPI - 1/2/3=x/y/z & -1/-2/-3=-x/-y/-z
- ref_weight
Character; file path. File for reference weighting volume
- rigid2D
Logical. use 2D rigid body mode - ignores dof
- schedule
Character; file path. replaces default schedule
- searchr_x
Character or numeric vector. search angles along x-axis, in degrees
- searchr_y
Character or numeric vector. search angles along y-axis, in degrees
- searchr_z
Character or numeric vector. search angles along z-axis, in degrees
- sinc_width
Integer. full-width in voxels
- sinc_window
Character; one of: "rectangular", "hanning", "blackman". sinc window
- uses_qform
Logical. initialize using sform or qform
- verbose
Integer. verbose mode, 0 is least
- wm_seg
Character; file path. white matter segmentation volume needed by BBR cost function
- wmcoords
Character; file path. white matter boundary coordinates for BBR cost function
- wmnorms
Character; file path. white matter boundary normals for BBR cost function
- .cwd
Working directory override.
- .env
Named character vector of environment variables.
- .engine
Execution engine override.
- .profile
Runtime profile override.
- dry_run
Logical; preview command without executing.
- echo
Logical; echo stdout/stderr in real time.