construct an unbiased robust template for longitudinal volumes
Usage
ni_freesurfer_robust_template(
auto_detect_sensitivity,
in_files,
out_file,
outlier_sensitivity,
args = NULL,
average_metric = NULL,
fixed_timepoint = NULL,
in_intensity_scales = NULL,
initial_timepoint = NULL,
initial_transforms = NULL,
intensity_scaling = NULL,
no_iteration = NULL,
scaled_intensity_outputs = NULL,
subsample_threshold = NULL,
transform_outputs = NULL,
.cwd = NULL,
.env = NULL,
.engine = NULL,
.profile = NULL,
dry_run = FALSE,
echo = interactive()
)Arguments
- auto_detect_sensitivity
Logical. auto-detect good sensitivity (recommended for head or full brain scans) Required.
- in_files
Character or numeric vector. input movable volumes to be aligned to common mean/median template Required.
- out_file
Character; file path. output template volume (final mean/median image) Required.
- outlier_sensitivity
Numeric. set outlier sensitivity manually (e.g. "–sat 4.685" ). Higher values mean less sensitivity. Required.
- args
Character. Additional parameters to the command
- average_metric
Character; one of: "median", "mean". construct template from: 0 Mean, 1 Median (default)
- fixed_timepoint
Logical. map everything to init TP# (init TP is not resampled)
- in_intensity_scales
Character or numeric vector. use initial intensity scales
- initial_timepoint
Integer. use TP# for special init (default random), 0: no init
- initial_transforms
Character or numeric vector. use initial transforms (lta) on source
- intensity_scaling
Logical. allow also intensity scaling (default off)
- no_iteration
Logical. do not iterate, just create first template
- scaled_intensity_outputs
Character or numeric vector. final intensity scales (will activate –iscale)
- subsample_threshold
Integer. subsample if dim > # on all axes (default no subs.)
- transform_outputs
Character or numeric vector. output xforms to template (for each input)
- .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.