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 > >
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
