Hi Bruce, 

Thank you for your reply. I am looking at differences in WM intensity, but am concerned that the intensity normalization will reduce tissue differences in addition to addressing inhomogeneity from the MRI. The WM is normalized to an average of 110, but is there any way to keep the variable intensity values for the WM? 

Thanks
Sabrina


On Jun 29, 2016, at 2:51 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

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
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