External Email - Use Caution Hello experts,
Anyone would have an advice on my previous questions ? Best, Matthieu Le mer. 30 janv. 2019 à 14:49, Matthieu Vanhoutte < matthieuvanhou...@gmail.com> a écrit : > Hi Douglas, > > In order to apply intensity normalization to non-PVC PET images based on > mean intensity from reference region in gtmseg.mgz, is it better to realign > & reslice PET image onto gtmseg space or the reverse way ? How is it done > when dealing with PVC images using gtmpvc command ? > > I would like to avoid too many reslicing operations before volume to > surface projection, how would you deal with it ? > > Best, > Matthieu > > Le 28 janv. 2019 à 17:41, Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu> > a écrit : > > If you intend to use one of the aseg structures, then they are the same. > > On 1/28/19 10:14 AM, Matthieu Vanhoutte wrote: > > External Email - Use Caution > Hi Douglas, > > > Le 25 janv. 2019 à 18:01, Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu> > a écrit : > > > > On 1/25/19 7:57 AM, Matthieu Vanhoutte wrote: > > External Email - Use Caution > Dear Douglas, > > Could you precise me: > 1) Is the intensity rescaling of PET image included in the mri_gtmpvc > command based on reference region in gtmseg.mgz file rather than aseg.mgz ? > > It depends. If you are using pons, then that is not part of the aseg and > is generated as part of the creation of gtmseg. But most of the rest of > gtmseg is derived from the aseg and surfaces. > > > Is it better to use gtmseg.mgz or aseg.mgz to extract reference region’s > mean intensity ? > > > 2) Is this rescaling applied before PVE correction or after (i.e. based on > PVE corrected reference region’s mean intensity) ? > > After > > > Many thanks in advance for helping. > > Best, > Matthieu > > Le 7 janv. 2019 à 17:26, Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu> > a écrit : > > > > On 1/7/19 11:18 AM, Matthieu Vanhoutte wrote: > > External Email - Use Caution > > I used the following command to obtain only rescaled voxel-wise PET image > (with no PVC): > *mri_gtmpvc --i PET.nii.gz --reg Pet2T1.register.dof6.lta --psf 0 --no-tfe > --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --rbv --o nopvc* > > If I omitted *--rbv *or* --mgx* option I didn't get the rescaled > voxel-wise PET image (without PVC). Could I obtain the rescaled voxel-wise > PET image (without PVC) just by dividing each voxel of the native PET image > by the mean of the reference region ? > > Yes > > > Best, > Matt > > Le lun. 7 janv. 2019 à 16:01, Greve, Douglas N.,Ph.D. < > dgr...@mgh.harvard.edu> a écrit : > >> I'm not sure what you mean. If you are turning off PVC, why are you >> computing RBV and MGX? What is your command line? What do you mean that >> these options don't seem to work? >> >> On 12/21/18 2:22 PM, Matthieu Vanhoutte wrote: >> >> External Email - Use Caution >> Hi Douglas, >> >> Thanks for helping. >> >> To have an only rescaled voxel-wise PET image, these options seem to work >> only when -rbv method is used and not -mgx. >> >> Do you know why ? >> >> Best, >> Matthieu >> >> >> Le mar. 18 déc. 2018 à 17:58, Greve, Douglas N.,Ph.D. < >> dgr...@mgh.harvard.edu> a écrit : >> >>> You will need to set --psf 0 and --no-tfe to fully turn off PVC. >>> >>> On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote: >>> >>> External Email - Use Caution >>> Hi Douglas, >>> >>> Could you help me on this point ? >>> >>> Best, >>> Matthieu >>> >>> >>> Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte < >>> matthieuvanhou...@gmail.com> a écrit : >>> >>>> Dear Douglas, >>>> >>>> Is it possible to use mri_gtmpvc command in order to intensity >>>> normalize PET images without applying PVE correction by setting --psf to 0 >>>> ? >>>> >>>> Best, >>>> Matthieu >>>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing >>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >
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