On 2/14/19 1:14 PM, Matthieu Vanhoutte wrote:
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Le jeu. 14 févr. 2019 à 18:31, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@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 interpolationShould 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 <matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@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
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