External Email - Use Caution 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 >>> <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 > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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