[Freesurfer] -normalization all black

Hi Everyone, I would like to normalize some images. But even when I test the -normalize option with recon-all -s burt/ -normalization which from what I can see changes /burt/mri/nu.mgz (which came with the freesurfer download) to /burt/mri/T1.mgz, T1.mgz is entirely black. Is there a way to fi

[Freesurfer] Skull-Stripping Atlas Usage

Hi Everyone, I am trying to skullstrip an mri image without using an atlas. Does the following command use an atlas at any point? If so, is there a way to run the skullstripping algorithm without using information from an atlas? recon-all -s bert/ -clean-bm -skullstrip Thanks. Teo Gelles