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 >>> <mailto: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> >> >> >> _______________________________________________ >> 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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