External Email - Use Caution Hi Douglas,
Could you answer to my previous question ? Best, Matthieu > Le 30 janv. 2019 à 14:48, 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 >> <mailto: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 >>>> <mailto: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> >>> >>> >>> _______________________________________________ >>> 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 >
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