| -Autocorrelate | Auto-correlate, output auto-correlation map. |
| -Crosscorrelate file.mrc | Cross-correlate with reference file.mrc, output shifted image. |
| -Validate file.mrc | Cross-correlate and cross-validate with reference file.mrc, output shifted image. |
| -halfshift | Shift correlation map by half the size to put the origin in the middle. |
| -verbose 7 | Verbosity of output. |
| -datatype u | Force writing of a new data type. |
| -resolution 4.5,130 | Resolution range for correlation (default 0 - 1e6 angstrom). |
| -origin 0,-10,30 | Set origin, used with -size option (default 0,0,0). |
| -size 22,33,14 | Size for extraction or hkl input (voxels, default from data). |
| -sampling 2,3.5,1 | Sampling (angstrom/voxel, a single value sets all three). |
| -limit 25 | Shift search limit in cross-correlation map (voxels, default: quarter of x-dimension). |
| -Mask mask.tif | Mask file to use for cross-correlation. |
| -Map ccmap.tif | Cross-correlation map. |