External Email - Use Caution Hi Douglas,
Please find comments inline below. best, Matthieu > 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. >> 2) Is this rescaling applied before PVE correction or after (i.e. based on >> PVE corrected reference region’s mean intensity) ? > After Thank you for this clarification. But do you use mean PET signal inside the reference region after the PVE correction, since in the particular case of pons there is no PVE correction applied to white matter ? Do you see any objection whether intensity normalization was done before PVE correction based on the mean PET signal inside the reference region ? >> >> 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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