stack_greedy: Paul's histology stack to MRI registration implementation
Usage:
  stack_greedy splat [cmd_options] <project_dir>
Required Command Options:
  -o <filename>          : Destination filename 
  -i <stage_spec> [iter] : Stage of project from which to splat (raw/recon/volmatch/voliter)
                           For voliter, iteration may be specified as second argument
  -rf <filename>         : Reference image for output volume (if -z not specified)
  -z <z0> <z_step> <z1>  : Range of z-positions for the output volume (if -rf not specified)
  -S <mode>              : Splatting mode. Currently supported modes are:
                             exact   : a slide is splatted if it's z matches target (up to ztol)
Additional Command Options:
  -ztol <value>          : Tolerance for the exact splatting mode
  -M <file>              : Alternative manifest file. Can be used to specify the list of ids to
                           include in the splatting (column 1) and the alternative sources for the
                           images (optional column 2). The can be used to splat derived data.
  -H                     : When providing alternative sources with -M, ignore the header of the
                           source images, stretching them to occupy the same physical space as the
                           images in the main manifest. Useful when you have data covering the same
                           slide extents but with headers that don't match.
  -si <sigma>            : Apply in-plane Gaussian smoothing with given standard deviation (voxel
                           units) to images before splatting
  -xy <value>            : Set custom x/y spacing for the output image (in mm units)
  -hm <pts>              : Perform histogram matching to root slide using the given
                           number of histogram remapping points. The inv parameter specifies
                           whether the image should be inverted before running the filter.
  -hm-invert             : Whether to invert the histogram for matching. Do this if the slide
                           background is brighter than the foreground.
Options Shared with Greedy (see Greedy docs for more info):
  -rb <value>            : Background value for 2D/3D interpolation
  -ri <mode> [sigma]     : Interpolation mode (for 2D interpolation)


