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 > > 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. > > > > > 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:) > > 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
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