<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.