Hi Teo, You might just need to adjust the contrast/brightness settings when viewing the volume in freeview. If you move your mouse around do any non-zero values appear in the bottom right voxel info panel?
The T1.mgz for bert should be 4.6mb, so you can see if what you have matches that.
Otherwise, could you send us the log file or terminal output from when you ran the normalization step? -Louis
On Wed, 2 Jul 2014, Teo Gelles wrote:
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 fix this issue?
Thanks. Teo