FSL MCFLIRT wrapper for within-modality motion correction
Usage
ni_fsl_mcflirt(
in_file,
args = NULL,
bins = NULL,
cost = NULL,
dof = NULL,
init = NULL,
interpolation = NULL,
mean_vol = NULL,
out_file = NULL,
ref_file = NULL,
ref_vol = NULL,
rotation = NULL,
save_mats = NULL,
save_plots = NULL,
save_rms = NULL,
scaling = NULL,
smooth = NULL,
stages = NULL,
stats_imgs = NULL,
use_contour = NULL,
use_gradient = NULL,
.cwd = NULL,
.env = NULL,
.engine = NULL,
.profile = NULL,
dry_run = FALSE,
echo = interactive()
)Arguments
- in_file
Character; file path. timeseries to motion-correct Required.
- args
Character. Additional parameters to the command
- bins
Integer. number of histogram bins
- cost
Character; one of: "mutualinfo", "woods", "corratio", "normcorr", "normmi", "leastsquares". cost function to optimize
- dof
Integer. degrees of freedom for the transformation
- init
Character; file path. initial transformation matrix
- interpolation
Character; one of: "spline", "nn", "sinc". interpolation method for transformation
- mean_vol
Logical. register to mean volume
- out_file
Character; file path. file to write
- ref_file
Character; file path. target image for motion correction
- ref_vol
Integer. volume to align frames to
- rotation
Integer. scaling factor for rotation tolerances
- save_mats
Logical. save transformation matrices
- save_plots
Logical. save transformation parameters
- save_rms
Logical. save rms displacement parameters
- scaling
Numeric. scaling factor to use
- smooth
Numeric. smoothing factor for the cost function
- stages
Integer. stages (if 4, perform final search with sinc interpolation
- stats_imgs
Logical. produce variance and std. dev. images
- use_contour
Logical. run search on contour images
- use_gradient
Logical. run search on gradient images
- .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.