Interface for FSL topup, a tool for estimating and correcting
Usage
ni_fsl_apply_topup(
encoding_file,
in_files,
args = NULL,
datatype = NULL,
in_index = NULL,
in_topup_fieldcoef = NULL,
interp = NULL,
method = NULL,
out_corrected = NULL,
.cwd = NULL,
.env = NULL,
.engine = NULL,
.profile = NULL,
dry_run = FALSE,
echo = interactive()
)Arguments
- encoding_file
Character; file path. name of text file with PE directions/times Required.
- in_files
Character or numeric vector. name of file with images Required.
- args
Character. Additional parameters to the command
- datatype
Character; one of: "char", "short", "int", "float", "double". force output data type
- in_index
Character or numeric vector. comma separated list of indices corresponding to –datain
- in_topup_fieldcoef
Character; file path. topup file containing the field coefficients
- interp
Character; one of: "trilinear", "spline". interpolation method
- method
Character; one of: "jac", "lsr". use jacobian modulation (jac) or least-squares resampling (lsr)
- out_corrected
Character; file path. output (warped) image
- .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.