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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