We have been doing contrast correction using mri_nu_correct.mni (e.g., mri_nu_correct.mni --i FS090620ll/mri/orig/001.mgz --o FS090620ll/mri/orig/nu2.mgz --n 2).

My question is, after subsequent corrections (control points, white matter) do we need to specify nu2.mgz as the target file for secondary recon steps in the command line (e.g., recon-all -autorecon2-cp -autorecon3 -s FS090620ll -i FS090620ll/mri/orig/nu2.mgz -force)

thanks

ilana