External Email - Use Caution Hi Douglas,
Thanks for these clarifications. I have however one misunderstanding. When sampling PVC corrected PET image onto surface: - I use bbpet2anat.lta when MGX was used as specified un tutorial - I use rbv2anat.lta when RBV was used But why not to use template.reg.lta computed by mri_coreg ? What are the differences between those different files ? Best, Matthieu Le mar. 18 déc. 2018 à 18:13, Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> a écrit : > > > On 12/7/18 9:29 AM, Matthieu Vanhoutte wrote: > > External Email - Use Caution > > > > Hi Douglas, > > > > Thanks for these clarifications. I added some others questions inline > below. > > > > Best, > > Matthieu > > > >> Le 6 déc. 2018 à 17:25, Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu> > a écrit : > >> > >> > >> > >> On 11/30/2018 07:15 AM, Matthieu Vanhoutte wrote: > >>> External Email - Use Caution > >>> > >>> Hi Douglas, > >>> > >>> Thank you for answering. Please find below new questions. > >>> Bien cordialement, > >>> > >>> > >>> Le ven. 30 nov. 2018 à 00:00, Greve, Douglas N.,Ph.D. > >>> <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> a écrit : > >>> > >>> Hi Matthieu, sorry for the delay > >>> > >>> On 11/29/2018 12:50 PM, Matthieu Vanhoutte wrote: > >>>> External Email - Use Caution > >>>> > >>>> Dear Freesurfer's experts, > >>>> > >>>> I tried to use PETSurfer to correct partial volume effect on my > >>> FDG PET images, testing both Muller-Gartner and RBV corrections. > >>>> I ran the commands specified in PETSurfer website and used the > >>> two following commands for both MGX and RBV corrections > respectively: > >>>> mri_gtmpvc --i PET.nii.gz --reg register.dof6.lta --psf-col 5.51 > >>> --psf-row 5.51 --psf-slice 5.9 --seg gtmseg.mgz > >>> --default-seg-merge --auto-mask PSF .01 --mgx .01 --o > ./gtmpvc.output > >>>> mri_gtmpvc --i PET.nii.gz --reg register.dof6.lta --psf-col 5.51 > >>> --psf-row 5.51 --psf-slice 5.9 --seg gtmseg.mgz > >>> --default-seg-merge --auto-mask PSF .01 --rbv --o rbv.output.orig > >>>> 1) However, I found that cortical output mgx.ctxgm.nii.gz of MGX > >>> correction encompass more than just GM and values at the > >>> boundaries of mgx.ctxgm.nii.gz seem to me very high or aberrant. > >>> This is expected. The MG method gives you a value every place that > >>> there > >>> is GM signal *in the PET volume after partial volume effects*. So > >>> basically, if you were to take the cortical ribbon and smooth it > >>> by your > >>> PSF, every non-zero voxel has some GM in it (which is why the > >>> edges are > >>> so high). When you run it with --mgx .01, it will exclude voxels > that > >>> have less than 1% GM after smoothing. If you you are disturbed by > the > >>> wide ribbon, just make the threshold higher. In theory, every point > >>> along the surface normal gives you a valid answer, but the further > >>> from > >>> the center of the ribbon, the noisier it is going to be, so we > >>> generally > >>> only sample it at the center (--projfrac 0.5 to mri_vol2surf). > >>> > >>> > >>> Basically, please find below the mgx.ctxgm with threshold set at 0.01: > >>> image.png > >>> > >>> Then threshold set at 0.1: > >>> image.png > >>> > >>> Values at some parts of the cortex (olfactory, visual) are not the > >>> same between the two thresholds. In the first one in these parts of > >>> the brain, values are higher than the second and seem kind of > >>> aberrant. Is there no reason to prefer a threshold at 0.1 than 0.01 ? > >>> For example, in (Douglas et al., 2016, NeuroImage) a threshold of 0.3 > >>> has been found to be optimal: how determine visually or quantitatively > >>> this optimal threshold ? > >> So when you click on the same voxel in both images, you get different > >> values? Or is it just that the color scale is changing? The threshold > >> should not change the values, just what is in or out of the final mask. > >> The threshold of 0.3 was chosen mainly because it worked for the ROI > >> analysis. In general, you should use GTM instead of MG for ROI analysis. > >> For surface-based analysis, the threshold is not critical because the GM > >> PVF is generally pretty high in cortex. It will make more of a > >> difference in subcortical analysis. > > Yes, thresholding at 0.01 and 0.1 gave me different values in the same > voxel in both images. Whereas when thresholding between 0.1 and 0.3 gave me > same values. What could it be due to ? > I don't know. Are the differences widespread or just a voxel near the edge? > > > > GTM is always computed in the *.stat file whatever the method specified > in mri_gtmpvc command ? > Yes, the GTM is the basis for all the methods. > > > > If threshold is not critical for cortical surface, how to determine the > best threshold for subcortical analysis ? Is it better to have more in the > final mask ? > In general, I don't think it is critical since the cortical surface > should be sampled in a location where there is a lot of GM. > > > >>> > >>>> 2) Concerning RBV correction, output rbv.nii.gz seems to me > >>> following more precisely the GM ribbon. However contrary to what > >>> is said in PETSurfer website, rbv.nii.gz seems to be in the > >>> anatomical space (not in native PET) at the resolution of > >>> gtmseg.mgz. How then map rbv.nii.gz to the anatomical space when > >>> mapping the volume to the surface ? > >>> Where does it say this? It should be in the anatomical space in the > >>> sense that it shares an RAS space with the conformed volume (aseg > >>> does > >>> gtmseg.mgz). This means that you can use --regheader with > >>> mri_vol2surf > >>> or mri_vol2vol when mapping into another space. > >>> > >>> > >>> In https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer it says that > >>> "mgx.ctxgm is in same resolution of the input PET", which is the case > >>> since resolution and orientation are identical to native PET. The > >>> PETsurfer tutorial then explains that "bbpet2anat.lta. is a > >>> registration file that can be used to map the output PET volume (in > >>> the mask bounding box) to the anatomical space". > >>> > >>> However, when I open rbv.nii file it is not in native PET resolution > >>> and orientation but those of gtmseg.mgz (anatomical space but with > >>> resolution of 0.5x0.5x05 mm). Why these differences between these two > >>> methods of PVC and which registration file then to use when mapping > >>> rbv.nii to the surface (rbv2anat.lta ?) ? I think I can't use directly > >>> --regheader since resolution of rbv.nii is 0.5 mm3 whereas anatomical > >>> space is of 1 mm3. > >> Yes, the rbv is in a higher resolution because the rbv does not have > >> separate maps for each tissue type, so you need smaller voxels to avoid > >> re-introducing PVEs. > > Ok. Which file should I use then to map rbv.nii to anatomical space: > bbpet2anat.lta ? > there should be a file there called aux/rbv2anat.lta > > > > Would you have the article from which RBV correction is based on ? > https://www.ncbi.nlm.nih.gov/pubmed/21336694 > > > >>>> 3) What are the advantages/inconveniences of RBV vs GMX ? > >>> Not entirely sure. RBV may be more precise since it at least has > the > >>> ability to correct for the PVE across the bank of a sulcus, but > >>> the two > >>> banks have to be in different ROIs. The bad news is that the RBV > >>> correction depends on the ROIs that you use. > >>> > >>> > >>> MGX doesn't correct PVE across the bank of a sulcus ? > >> Correct. > > Is it a big problem to deal with when using MGX correction ? > Not sure what you mean. Do you mean to implement it into MGX? That is a > big deal. > > > >>> By saying that "RBV correction depends on the ROIs that you use", do > >>> you mean the parcellation (aparc or aparc.a2009s) you give to the > >>> gtmseg command ? If this is the case is there a better compromise ? > >> It depends on the aparc (and aseg). There is not a better compromise. > > If not a better compromise, would there be some cases when aparc.a2009 > is better to use ? > I don't know. It is much more detailed, meaning smaller ROIs, meaning > that the PVC will cause more noise. > > > >>>> 4) Would it be beneficial to upsample native PET to the > >>> anatomical resolution before launching gtmpvc in order to preserve > >>> the high resolution of the anatomical tissues during partial > >>> volume correction ? > >>> No, this is all taken care of in mri_gtmpvc. > >>> > >>>> Could you have a look at and give me back your opinion on these > >>> questions ? I could send the associated files if needed. > >>>> Thank you. > >>>> > >>>> 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 > >>> 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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