| -create 20,60,30 | Create a new mask of this size in place of input image |
| -threshold -0.55,1.2 | One or more thresholds to generate a mask. |
| -variance 5,1 | Generate mask based on local variance in a kernel of a given size, |
| and flag to generate a background with value -1. | |
| -invert | Invert mask. |
| -dilate 2 | Dilate mask a number of times. |
| -erode 3 | Erode mask a number of times. |
| -open 4 | Open (erode-dilate) mask a number of times. |
| -close 2 | Close (dilate-erode) mask a number of times. |
| -hole 3,56,23 | Fill a hole indicated by the voxel. |
| -plane | 0.3,0.5,-0.1,0,3,25 Mask on one side of a plane with the given normal and origin. |
| -rectangle 40,20,45 | Rectangular mask with given length, width and rotation angle. |
| -radius 10,45 | Generate a mask inside these radii. |
| -asu D3 | Generate an asymmetric unit mask. |
| -color size | Generate a RGBA image (random/size). |
| -size | Convert level mask to region size map. |
| -collapse | Convert a multi-level mask to a binary mask. |
| -select 1,5-7 | Select levels in a multi-level mask. |
| -voxel 23,241,193 | Select the level including this voxel. |
| -level 134 | Convert a mask to multiple levels, with the given voxels per level. |
| -bands 250,-1,150,1,30,0 | Banded mask for reciprocal space (pairs of numbers: angstrom,value). |
| Band with 0: Not used. | |
| Band with 1: Use for orientation determination. | |
| Band with -1: Use for cross-validation. | |
| -apply | Apply the mask to the input image (default output mask). |
| -rescaleapply 0.5,2.3 | Rescale region inside mask and apply the mask to the input image. |
| -verbose 1 | Verbosity of output. |
| -datatype u | Force writing of a new data type. |
| -sampling 1.5,1.5,1.5 | Sampling (A/pixel; a single value can be given). |
| -origin 110,50,44 | Origin for the mask (default from input image). |
| -fill 28.3 | Fill value (default average). |
| -wrap | Flag to wrap around image boundaries (default not). |
| -Mask file.img | Input mask to apply or get difference with main input image. |
| 1. Creating a new mask: | |
| bmask -v 7 -create 100,100,50 -radius 10,20 -origin 50,50,25 mask.mrc | |
| 2. Generating a mask from an image: | |
| bmask -v 7 -threshold 1.5 test.map mask.mrc | |
| 3. Applying a mask to an image: | |
| bmask -v 7 -Mask mask.mrc test.map new.map | |
| 4. Generating and applying a mask to an image: | |
| bmask -v 7 -apply -radius 50,80 -origin 100,100,100 test.map new.map | |