you can, but why do you need to do it outside of the recon-all stream? On Fri, 10 Mar 2017, shi yao wang wrote:

Dear FS experts, I am wondering the process of MRI intensity normalization.  Before I am running recon -all, can I run following process to normalize our MRI images.

mri_normalize SUBJECT/mri/nu SUBJECT/mri/wm

or any other preprocessing methods to avoid bias.

thanks Lawrence Emory University