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 ? 2) Is this rescaling applied before PVE correction or after (i.e. based on PVE corrected reference region’s mean intensity) ? 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 <mailto: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 <mailto: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 <mailto: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 list >>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
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