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
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