On 2/14/19 2:25 PM, Matthieu Vanhoutte wrote: > External Email - Use Caution > >> Le 14 févr. 2019 à 19:37, Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu> a >> écrit : >> >> >> >> On 2/14/19 1:14 PM, Matthieu Vanhoutte wrote: >>> External Email - Use Caution >>> >>> >>> >>> Le jeu. 14 févr. 2019 à 18:31, Greve, Douglas N.,Ph.D. >>> <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> a écrit : >>> >>> >>> >>> On 2/14/19 12:16 PM, Matthieu VANHOUTTE wrote: >>>> External Email - Use Caution >>>> >>>> Hi Douglas, >>>> >>>> So to register PET to gtmseg space mri_gtmpvc command use nearest >>>> neighbor, interpolation right ? >>> It does not map the PET to the gtmseg space. It maps the gtmseg to >>> the >>> PET space. Since this is a segmentation, it uses nearest neighbor. >>> But >>> the algorithm is much more complicated; see the paper. >>> >>> >>> Thank you I will look into the paper, I was wondering how not to loose >>> the gtmseg resolution ? >> I thought you wanted to turn off all PVC? If you want to correct for the >> tissue fraction effect, then don't use --no-tfe > Oh, I had to miss something. I didn’t know PVC had several components, whose > one is tissue fraction effect… What are the different corrections applied > during PVC ? Tissue fraction effect and correction for blur induced by the low res nature of pet. See the paper. > When papers mention no PVC they principally don’t correct for tissue fraction > effect ? I don't know. Generally, people don't give many details on their method. > > I wanted to know what is the interest of computing a high resolution > segmentation (gtmseg) if it goes to PET space and resliced to its lower > resolution ? As I said before, this is not what happens. PETsurfer takes the TFE into account. Please see the paper for how it is done. > >>> Concerning RBV PVC in which order and what type of interpolation are >>> used since PVE corrected output is on gtmseg_space ? >> This question does not make sense in the context of RBV. Each ROI gets a >> value, and this value is then assigned to all the voxels in that ROI in >> gtmseg prior to apply the RBV algorithm. > Ok thank you, so in RBV case native PET is interpolated (trilinear?) first to > gtmseg space ? > >>>> And what about the interpolation method to use when projecting PVE >>>> corrected PET on surface ? >>> I usually use nearest neighbor to avoid interpolation >>> >>> >>> Should you precise this on PETSurfer wiki since on the mri_vol2surf >>> command trilinear interpolation is used by default ? >> By default, mri_vol2surf uses nearest neighbor. mri_vol2vol uses trilin >> by default. An unfortunate inconsistency I made about 15 years ago and >> have been too afraid to change it:) > Thank you I didn’t know this one and supposed the trilinear as default as it > is done in moi_vol2vol. Good to know it :) > >>> Best. >>> >>>> Thanks, >>>> >>>> Matthieu >>>> >>>> On 14/02/2019 17:44, Greve, Douglas N.,Ph.D. wrote: >>>>> The GTM operates on regions, so you can't do trilin interp. The >>>>> operations that you describe below are not used in mri_gtmpvc. >>> If you >>>>> are trying to get something close to what the GTM does, then >>> use nearest >>>>> neighbor >>>>> >>>>> On 2/14/19 3:43 AM, Matthieu Vanhoutte wrote: >>>>>> External Email - Use Caution >>>>>> >>>>>> Hi Douglas, >>>>>> >>>>>> Could you help me concerning my previous questions ? >>>>>> >>>>>> Thanks, >>>>>> Matthieu >>>>>> >>>>>>> Le 11 févr. 2019 à 17:37, Matthieu VANHOUTTE >>> <matthieuvanhou...@gmail.com <mailto:matthieuvanhou...@gmail.com>> >>> a écrit : >>>>>>> Hi Douglas, >>>>>>> >>>>>>> Thanks for clarification. Why use "nearest neighbor" instead >>> of classical "trilinear" interpolation ? >>>>>>> Should it be done as well when projecting from volume to >>> surface with mri_vol2surf ? >>>>>>> Best, >>>>>>> >>>>>>> Matthieu >>>>>>> >>>>>>> On 11/02/2019 17:32, Greve, Douglas N.,Ph.D. wrote: >>>>>>>> It will not used trilinear interp. Try it with nearest neighbor >>>>>>>> >>>>>>>> On 2/10/19 11:55 AM, Matthieu Vanhoutte wrote: >>>>>>>>> External Email - Use Caution >>>>>>>>> >>>>>>>>> Dear Douglas, >>>>>>>>> >>>>>>>>> Before using "mri_gtmpvc --psf 0 --no-tfe -- rbv" according >>> your advice to obtain voxel-wise output rescaled without PVC >>> correction, I have done sequentially the different steps to obtain >>> this output. However, when comparing voxel-wise rescaled output >>> (rbv.nii.gz) between the two methods, final values at each voxel >>> are not the same… >>>>>>>>> To obtain first rescaled voxel-wise output I have used >>> sequentially these steps: >>>>>>>>> 1. Concatenate transforms from PET space to gtmseg.mgz >>>>>>>>> 2. Register native PET into gtmseg space (trilin. >>> interpolation) >>>>>>>>> 3. Compute mean PET inside reference regions (with >>> regions masks from gtmseg.mgz) >>>>>>>>> 4. Compute intensity normalized PET images in gtmseg >>> space >>>>>>>>> Doesn’t the "mri_gtmpvc --psf 0 --no-tfe -- rdv" command >>> use these same steps ? >>>>>>>>> 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 >>>>>>>> _______________________________________________ >>>>>>>> Freesurfer mailing list >>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>> 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 >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>> 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 >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> 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 >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> 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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