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 <fis...@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 > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail.
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