Usage:alignlinear.exe standard_file reslice_file air_out -m model_menu_number [options] Model Menu: 3-D models: 6. rigid body 6 parameter model 7. global rescale 7 parameter model 9. traditional 9 parameter model (std must be on AC-PC line) 12. affine 12 parameter model 15. perspective 15 parameter model 2-D models (constrained to in-plane, no interpolation): 23. 2-D rigid body 3 parameter model 24. 2-D global rescale 4 parameter model 25. 2-D affine/fixed determinant 5 parameter model 26. 2-D affine 6 parameter model 28. 2-D perspective 8 parameter model options: (defaults in parentheses) [-b1 FWHM_x(0.000000e+000) FWHM_y(0.000000e+000) FWHM_z(0.000000e+000)] (standard file) [-b2 FWHM_x(0.000000e+000) FWHM_y(0.000000e+000) FWHM_z(0.000000e+000)] (reslice file) [-c convergence_threshold(0.000010)] [-d] use static partitioning (like AIR3.0 and earlier) [-e1 standard_file_mask] [-e2 reslice_file_mask] [-f initialization_file] [-fs scaling_initialization_file] [-g termination_file [overwrite?(y/n)]] [-gs scaling_termination_file [overwrite?(y/n)] [-h halt_after_(5)_iterations_without_improvement] [-j] use non-positive definite Hessian matrices (not validated, use at your own risk) [-p1 segment_standard_file_into_(1)_partitions] [-p2 segment_reslice_file_into_(1)_partitions] [-q] assume non-interaction of spatial parameter derivatives [-r repeated_iterations(25)] [-s initial_sampling(81) final_sampling(1) sampling_decrement_ratio(3)] [-t1 threshold_standard_file(7000)] [-t2 threshold_reslice_file(7000)] [-v] verbose reporting of interim results [-x cost_function(1)] 1. standard deviation of ratio image 2. least squares 3. least squares with intensity rescaling [-z] (no additional argument; turns on pre-alignment interpolation)

Last updated 2014-10-22 12:53:47