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 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