which "native" space? the pet native? the anatomical native? On 08/09/2016 05:46 PM, Pradeep wrote: > Hello Doug, > > The aux/seg.nii image which has all the ROI's defined does not seem to > be in the subject's native space or the CVS template space. > > How do I bring it to the subjects native space? > > Thanks, > Pradeep > > Screenshot from 2016-08-09 14:42:10.png > > On Tue, Jul 19, 2016 at 5:03 PM Pradeep <tprad...@gmail.com > <mailto:tprad...@gmail.com>> wrote: > > 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 <mailto: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 > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://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 > <mailto: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. >
-- 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
