Thanks responding Doug! I am interested us using centrum semiovale as reference region. Is there a way I can save the unsegmented white matter [5001& 5002] during the gtmseg step or what would be its equivalent label in the gtm_pvc results table?
Thanks, Pradeep On Thu, Jul 7, 2016 at 11:20 AM Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > > > On 06/20/2016 08:25 PM, Pradeep wrote: > > Hello Freesrufer Team, > > > > I am trying to use the Partial volume correction procedure implemented > > in the freesurfer 6 beta version and have a few questions. > > > > In your recent Neuroimaging paper, the left and right hemispheres were > > combined by taking the average of the two as they did not show any > > age-by-hemisphere interaction. > > > > I might have interpreted the Supplementary figure 1 incorrectly, but > > the Geometric transfer matrix seem to show around 52 ROI's, So were > > the L and R ROIs combined for the PVC results you reported in that > > paper? Or were the same 52 used for the general PVC in the FS pipeline? > They were combined only after the PVC calculation. For the figure, I > changed the GTM to show the combined GTM. > > > > Do you have any concrete results to examine the effects of the size > > variation over the ROIs used for PVC? > Not sure what you mean here. You can get the variance reduction factor > for each ROI in the gtm.stats.dat file. This indicates how much noise > reduction you can expect (assuming gaussian noise, etc) in each ROI > given the size and anatomical distribution of the ROIs and PSF. > > Should a threshold be set for the sizes of these ROIs? > What do you mean? > > > > How were the white matter hypo-intensities dealt with while generating > > the ROI masks? > I merged them with WM. I tried it with and without, and it did not make > much of a difference. > doug > > > > > > Thanks, > > Pradeep > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > 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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