FSL FAST wrapper for segmentation and bias correction
Usage
ni_fsl_fast(
in_files,
args = NULL,
bias_iters = NULL,
bias_lowpass = NULL,
hyper = NULL,
img_type = NULL,
init_seg_smooth = NULL,
init_transform = NULL,
iters_afterbias = NULL,
manual_seg = NULL,
mixel_smooth = NULL,
no_bias = NULL,
no_pve = NULL,
number_classes = NULL,
other_priors = NULL,
out_basename = NULL,
output_biascorrected = NULL,
output_biasfield = NULL,
probability_maps = NULL,
segment_iters = NULL,
segments = NULL,
use_priors = NULL,
verbose = NULL,
.cwd = NULL,
.env = NULL,
.engine = NULL,
.profile = NULL,
dry_run = FALSE,
echo = interactive()
)Arguments
- in_files
Character or numeric vector. image, or multi-channel set of images, to be segmented Required.
- args
Character. Additional parameters to the command
- bias_iters
Character. number of main-loop iterations during bias-field removal
- bias_lowpass
Character. bias field smoothing extent (FWHM) in mm
- hyper
Character. segmentation spatial smoothness
- img_type
Character; one of: "1", "2", "3". int specifying type of image: (1 = T1, 2 = T2, 3 = PD)
- init_seg_smooth
Character. initial segmentation spatial smoothness (during bias field estimation)
- init_transform
Character; file path. <standard2input.mat> initialise using priors
- iters_afterbias
Character. number of main-loop iterations after bias-field removal
- manual_seg
Character; file path. Filename containing intensities
- mixel_smooth
Character. spatial smoothness for mixeltype
- no_bias
Logical. do not remove bias field
- no_pve
Logical. turn off PVE (partial volume estimation)
- number_classes
Character. number of tissue-type classes
- other_priors
Character or numeric vector. alternative prior images
- out_basename
Character; file path. base name of output files
- output_biascorrected
Logical. output restored image (bias-corrected image)
- output_biasfield
Logical. output estimated bias field
- probability_maps
Logical. outputs individual probability maps
- segment_iters
Character. number of segmentation-initialisation iterations
- segments
Logical. outputs a separate binary image for each tissue type
- use_priors
Logical. use priors throughout
- verbose
Logical. switch on diagnostic messages
- .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.