Use Freesurfer's mri_mask to apply a mask to an image.
Usage
ni_freesurfer_apply_mask(
in_file,
mask_file,
args = NULL,
invert_xfm = NULL,
keep_mask_deletion_edits = NULL,
mask_thresh = NULL,
out_file = NULL,
transfer = NULL,
use_abs = NULL,
xfm_file = NULL,
xfm_source = NULL,
xfm_target = NULL,
.cwd = NULL,
.env = NULL,
.engine = NULL,
.profile = NULL,
dry_run = FALSE,
echo = interactive()
)Arguments
- in_file
Character; file path. input image (will be masked) Required.
- mask_file
Character; file path. image defining mask space Required.
- args
Character. Additional parameters to the command
- invert_xfm
Logical. invert transformation
- keep_mask_deletion_edits
Logical. transfer voxel-deletion edits (voxels=1) from mask to out vol
- mask_thresh
Numeric. threshold mask before applying
- out_file
Character; file path. final image to write
- transfer
Integer. transfer only voxel value # from mask to out
- use_abs
Logical. take absolute value of mask before applying
- xfm_file
Character; file path. LTA-format transformation matrix to align mask with input
- xfm_source
Character; file path. image defining transform source space
- xfm_target
Character; file path. image defining transform target space
- .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.