Perform intramodal linear registration (translation and rotation) using
Usage
ni_freesurfer_robust_register(
auto_sens,
outlier_sens,
source_file,
target_file,
args = NULL,
est_int_scale = NULL,
force_double = NULL,
force_float = NULL,
half_source = NULL,
half_source_xfm = NULL,
half_targ = NULL,
half_targ_xfm = NULL,
half_weights = NULL,
high_iterations = NULL,
in_xfm_file = NULL,
init_orient = NULL,
iteration_thresh = NULL,
least_squares = NULL,
mask_source = NULL,
mask_target = NULL,
max_iterations = NULL,
no_init = NULL,
no_multi = NULL,
out_reg_file = TRUE,
outlier_limit = NULL,
registered_file = NULL,
subsample_thresh = NULL,
trans_only = NULL,
weights_file = NULL,
write_vo2vox = NULL,
.cwd = NULL,
.env = NULL,
.engine = NULL,
.profile = NULL,
dry_run = FALSE,
echo = interactive()
)Arguments
- auto_sens
Logical. auto-detect good sensitivity Required.
- outlier_sens
Numeric. set outlier sensitivity explicitly Required.
- source_file
Character; file path. volume to be registered Required.
- target_file
Character; file path. target volume for the registration Required.
- args
Character. Additional parameters to the command
- est_int_scale
Logical. estimate intensity scale (recommended for unnormalized images)
- force_double
Logical. use double-precision intensities
- force_float
Logical. use float intensities
- half_source
Character or numeric vector. write source volume mapped to halfway space
- half_source_xfm
Character or numeric vector. write transform from source to halfway space
- half_targ
Character or numeric vector. write target volume mapped to halfway space
- half_targ_xfm
Character or numeric vector. write transform from target to halfway space
- half_weights
Character or numeric vector. write weights volume mapped to halfway space
- high_iterations
Integer. max # of times on highest resolution
- in_xfm_file
Character; file path. use initial transform on source
- init_orient
Logical. use moments for initial orient (recommended for stripped brains)
- iteration_thresh
Numeric. stop iterations when below threshold
- least_squares
Logical. use least squares instead of robust estimator
- mask_source
Character; file path. image to mask source volume with
- mask_target
Character; file path. image to mask target volume with
- max_iterations
Integer. maximum # of times on each resolution
- no_init
Logical. skip transform init
- no_multi
Logical. work on highest resolution
- out_reg_file
Character or numeric vector. registration file; either True or filename
- outlier_limit
Numeric. set maximal outlier limit in satit
- registered_file
Character or numeric vector. registered image; either True or filename
- subsample_thresh
Integer. subsample if dimension is above threshold size
- trans_only
Logical. find 3 parameter translation only
- weights_file
Character or numeric vector. weights image to write; either True or filename
- write_vo2vox
Logical. output vox2vox matrix (default is RAS2RAS)
- .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.