Create a brain-only mask of the image using AFNI 3dAutomask command
Usage
ni_afni_automask(
in_file,
args = NULL,
brain_file = NULL,
clfrac = NULL,
dilate = NULL,
erode = NULL,
out_file = NULL,
.cwd = NULL,
.env = NULL,
.engine = NULL,
.profile = NULL,
dry_run = FALSE,
echo = interactive()
)Arguments
- in_file
Character; file path. input file to 3dAutomask Required.
- args
Character. Additional parameters to the command
- brain_file
Character; file path. output file from 3dAutomask
- clfrac
Numeric. sets the clip level fraction (must be 0.1-0.9). A small value will tend to make the mask larger [default = 0.5].
- dilate
Integer. dilate the mask outwards
- erode
Integer. erode the mask inwards
- out_file
Character; file path. output image file name
- .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.