Re: [Freesurfer] No intensity command

Hi Sabrina

what are you trying to accomplish? This is unlikely to work well (if at all), as we depend on the normalization

cheers Bruce On Wed, 29 Jun 2016, Sabrina Yu wrote:

Hello,

I have a question about taking out the intensity normalization commands in recon-all. I want to eliminate all normalization steps so that the WM will not be set at an average of 110. Using the ReconAllDevTable (https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable), I took out all command flags related to intensity normalization. Are these commands correct?

1. I copied orig.mgz to generate nu.mgz, T1.mgz, norm.mgz.
2. recon-all -i <.nii file> -motioncor -talairach -skullstrip -s SUBJECT
3. recon-all -skullstrip -s SUBJECT
4. recon-all -gcareg -careg -calabel -maskbfs -segmentation -fill

-tessellate -smooth1 -inflate1 -qsphere -fix -white -smooth2 -inflate2 -s SUBJECT 5) recon-all -autorecon3 -s SUBJECT

I hope that my question makes sense. Thank you in advance for your time.

Sabrina