Generates PNG images from 2D brain slices. Can optionally overlay statistical images or overlay an outline of a brain image. This is a wrapper around FSL's overlay, slicer, and pngappend commands.
-h, --help show this help message and exit
input Input 3D brain image
output Output 2D PNG image
--edge-overlay FILE An outline of a brain image is overlaid on the input
(useful for checking registration). Note: the overlay
options don't apply to this input.
--overlay file min max
image to overlay on input
--overlay2 file min max
2nd image to overlay on input
--show-negative Will take the 1st overlay and threshold it to have a
negative range (this would be useful if you wanted to
display positive & negative thresholded maps). Note:
you can't specify both the --overlay2 and this option.
Note: these only apply to --overlay and --overlay2
-t, --transparency make overlay colors semi-transparent
--checkerboard use checkerboard mask for overlay
--background-range min max
setting range of underlay, only used when overlay
option has been given (default: automatic estimation)
Note that the options for --lut are actually not the same as fslview. They are found in $FSLDIR/etc/luts.
--slice-labels
--lut color use a different colour map from that specified in the
header
--scale positive-# relative size of each slice
--intensity min max specify intensity min and max for display range
--no-lr-labels
-s slice_name, --slice slice_name
type of slice; can be: a/axial, c/coronal, or
s/sagittal
-w slices, --width slices
image width in # of slices
-l slices, --height slices
image height in # of slices
-e number, --slice-every number
include every X # of slice
--force overwrite output if it exists
-v, --verbose
--dry-run Won't execute anything but prints what would have been
executed
--version show program's version number and exit