
| <fixed input> | Reference image |
| <input> | Images to be aligned |
| <output> | Output filename |
| [fixn=<n>] | Image number to use in fixed input stack |
| [noflip] | Rotational/translational alignment without flips |
| [precen] | No translational alignment |
| [seqali] | Align 1st image to ref, 2nd to 1st, 3rd to 2nd, etc. |
| [eulali] | Align each image to images with similar Eulers, referring to the 1st image in the file. |
| [pgm] | Output in pgm format, note there should only be one input in this case |
| [log] | Logs rotations/translations to align.log |
| [edgenorm] | Perform an edgenormalization of both images before alignment |
| [keepeulers] | Indicates that the input images have accurate Eulers which need to be preserved. |
align2d proj.hed cls000.hed tst.hed
Pretty self explanatory. If the input is a stack, the first image is used.