| -inverse | Backward transform (default forward). |
| -powerspectrum | Calculate powerspectrum estimate (can be used with the -tile option). |
| -logarithm | Calculate the logarithm of the power spectrum. |
| -color 1.5 | Generate a phase-coloured power spectrum: amplitude scaling. |
| -weigh | Weigh reflections with FOM. |
| -cutoff 0.2 | Remove reflections with FOM < cutoff threshold. |
| -zeroorigin | Zero the transform origin. |
| -halfshift | Shift correlation map by half the size to put the origin in the middle. |
| -cone 45 | Remove missing cone. |
| -test 2,75,278 | Test FFT execution time: dimensions,size min and max. |
| -verbose 7 | Verbosity of output. |
| -datatype u | Force writing of a new data type. |
| -resolution 4.5,130 | Resolution (default 0 - 10000 angstrom). |
| -free 15 | % flagged for R-free calculations (default 10). |
| -origin 0,-10,30 | Set origin, used with -size option (default 0,0,0). |
| -size 22,33,14 | Size for transform or hkl input (voxels, default from data). |
| -sampling 2,3.5,1 | Sampling (angstrom/voxel, a single value sets all three). |
| -unitcell | 100,100,100,90,90,90 Unit cell parameters. |
| -symmetry 1 | Space group. |
| -tile 1024,1024,1 | Size of tiles for calculating a power spectrum. |