Before this final message, the prompt showed me some warnings, but was ignored aparently.
Starting rigid registration of input images...
Reading input data...
Setting/generating masks...
Matching centroids (approx. align)...
Matching resolution of the images...
Normalizing intensity of images...
Performing affine registration with 6 degrees of freedom...
Search-based initialization...
Scale 1 of 6 running...
Scale 2 of 6 running...
Scale 3 of 6 running...
Scale 4 of 6 running...
Scale 5 of 6 running...
Scale 6 of 6 running...
Refine: Scale 1 of 2 running...
Refine: Scale 2 of 2 running...Warning: check this case.
> In register_volumes_affine>my_normalized_mutual_information (line 611)
In register_volumes_affine>error_affine_reg (line 501)
In register_volumes_affine>error_grad_affine_reg (line 470)
In register_volumes_affine>@(x)error_grad_affine_reg(x,scale,Imoving_small,Istatic_small,mask_moving_small,mask_static_small,reg_options) (line 409)
In gradient_descent_backtrack (line 45)
In register_volumes_affine (line 408)
In register_files_affine (line 451)
In EPI_correct_files_registration_INVERSION (line 109)
In coregister_diffusion_mprage_pipeline (line 219)
In BrainSuite_Diffusion_pipeline (line 26)
Warning: The KEYBOARD function cannot be used in compiled applications.
> In keyboard (line 4)
In register_volumes_affine>my_normalized_mutual_information (line 612)
In register_volumes_affine>error_affine_reg (line 501)
In register_volumes_affine>error_grad_affine_reg (line 470)
In register_volumes_affine>@(x)error_grad_affine_reg(x,scale,Imoving_small,Istatic_small,mask_moving_small,mask_static_small,reg_options) (line 409)
In gradient_descent_backtrack (line 45)
In register_volumes_affine (line 408)
In register_files_affine (line 451)
In EPI_correct_files_registration_INVERSION (line 109)
In coregister_diffusion_mprage_pipeline (line 219)
In BrainSuite_Diffusion_pipeline (line 26)
Warning: check this case.
*This repeated a lot of time over the prompt before saying: “Rigid registration done”*