| -invert | Invert density in the image before other operations. |
| -rescale -0.1,5.2 | Rescale data to average and standard deviation before other operations. |
| -smooth 0.8 | Smooth using a gaussian kernel with the given width. |
| -type srm | Type of segmentation (simple, srm). |
| -minimum 2300 | Join segments smaller than this size. |
| -voxel 23,241,193,1 | Select the segment containing this voxel with an optional inversion flag. |
| -colorize | Generate random segment colors. |
| -verbose 7 | Verbose output. |
| -datatype u | Force writing of a new data type. |
| -origin 0.8,-10,15.7 | Set the origin (default from input image). |
| -connectivity | Flag to use full neighbor connectivity (default 2*dimension). |
| -complexity 1.6 | Segmentation complexity: larger value gives more regions (default 1). |
| -Mask mask.tif | Mask to limit segmentation. |