>>But in the case where --psf 0 --no-tfe are specified, isn't the high resolution of gtmseg lost when rescaling intensities to mean reference region ? Yes
On 2/14/19 5:25 PM, Matthieu Vanhoutte wrote: > > External Email - Use Caution > > > > Le jeu. 14 févr. 2019 à 21:36, Greve, Douglas N.,Ph.D. > <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> a écrit : > > > > 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 <mailto: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> > <mailto: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. > > > But in the case where --psf 0 --no-tfe are specified, isn't the high > resolution of gtmseg lost when rescaling intensities to mean reference > region ? > > > > >>> 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> > <mailto: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> > >>> <mailto: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> > >>> <mailto: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> > >>> <mailto: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> > >>> <mailto: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> > >>> <mailto: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> > <mailto: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
