Use FSL's overlay command to combine background and statistical images
Usage
ni_fsl_overlay(
auto_thresh_bg,
background_image,
bg_thresh,
full_bg_range,
stat_image,
stat_thresh,
args = NULL,
out_file = NULL,
out_type = "float",
show_negative_stats = NULL,
stat_image2 = NULL,
stat_thresh2 = NULL,
transparency = TRUE,
use_checkerboard = NULL,
.cwd = NULL,
.env = NULL,
.engine = NULL,
.profile = NULL,
dry_run = FALSE,
echo = interactive()
)Arguments
- auto_thresh_bg
Logical. automatically threshold the background image Required.
- background_image
Character; file path. image to use as background Required.
- bg_thresh
Character or numeric vector. min and max values for background intensity Required.
- full_bg_range
Logical. use full range of background image Required.
- stat_image
Character; file path. statistical image to overlay in color Required.
- stat_thresh
Character or numeric vector. min and max values for the statistical overlay Required.
- args
Character. Additional parameters to the command
- out_file
Character; file path. combined image volume
- out_type
Character; one of: "float", "int". write output with float or int
- show_negative_stats
Logical. display negative statistics in overlay
- stat_image2
Character; file path. second statistical image to overlay in color
- stat_thresh2
Character or numeric vector. min and max values for second statistical overlay
- transparency
Logical. make overlay colors semi-transparent
- use_checkerboard
Logical. use checkerboard mask for overlay
- .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.