External Email - Use Caution
> > Hi Douglas, > > Could you help me about my previous mail with questions ? > > Thanks, > Matthieu > > > Le ven. 7 déc. 2018 à 14:31, Matthieu Vanhoutte < > matthieuvanhou...@gmail.com> a écrit : > >> 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 ? >> >> GTM is always computed in the *.stat file whatever the method specified >> in mri_gtmpvc command ? >> >> 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 ? >> >> >> >> >> >> >>> >> >>> 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 ? >> >> Would you have the article from which RBV correction is based on ? >> >> >> >> >>> >> >>> 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 ? >> >> >> >> >> 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 ? >> >> >> >> >>> >> >>> 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 >> >>
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