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.
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 ?
3) What are the advantages/inconveniences of RBV vs GMX ?
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 ?
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
Hi Matthieu, sorry for the delay
On 11/29/2018 12:50 PM, Matthieu Vanhoutte wrote:
External Email - Use CautionDear 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
- 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).
- 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.
- 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.
- 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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. < DGREVE@mgh.harvard.edu> a écrit :
Hi Matthieu, sorry for the delay
On 11/29/2018 12:50 PM, Matthieu Vanhoutte wrote:
External Email - Use CautionDear 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
- 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: image.png]
Then threshold set at 0.1: [image: 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 ?
- 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.
- 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 ?
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 ?
- 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 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
External Email - Use Caution
Hi Douglas,
Did you have time to look at my new questions ?
Best, Matthieu
Le ven. 30 nov. 2018 à 12:15, Matthieu Vanhoutte < matthieuvanhoutte@gmail.com> a écrit :
Hi Douglas,
Thank you for answering. Please find below new questions.
Le ven. 30 nov. 2018 à 00:00, Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> a écrit :
Hi Matthieu, sorry for the delay
On 11/29/2018 12:50 PM, Matthieu Vanhoutte wrote:
External Email - Use CautionDear 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
- 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: image.png]
Then threshold set at 0.1: [image: 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 ?
- 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.
- 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 ?
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 ?
- 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 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
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. <DGREVE@mgh.harvard.edu mailto:DGREVE@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.
> > 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.
> > 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.
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.
> > 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
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. DGREVE@mgh.harvard.edu a écrit :
On 11/30/2018 07:15 AM, Matthieu Vanhoutte wrote:
External Email - Use CautionHi 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. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> a écrit :
Hi Matthieu, sorry for the delay
On 11/29/2018 12:50 PM, Matthieu Vanhoutte wrote:
External Email - Use CautionDear 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
- 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 ?
- 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 ?
- 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 ?
- 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
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 matthieuvanhoutte@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. DGREVE@mgh.harvard.edu
a écrit :
On 11/30/2018 07:15 AM, Matthieu Vanhoutte wrote:
External Email - Use CautionHi 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. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> a écrit :
Hi Matthieu, sorry for the delay
On 11/29/2018 12:50 PM, Matthieu Vanhoutte wrote:
External Email - Use CautionDear 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
- 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 ?
- 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 ?
- 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 ?
- 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
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 < matthieuvanhoutte@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. DGREVE@mgh.harvard.edu
a écrit :
On 11/30/2018 07:15 AM, Matthieu Vanhoutte wrote:
External Email - Use CautionHi 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. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> a écrit :
Hi Matthieu, sorry for the delay
On 11/29/2018 12:50 PM, Matthieu Vanhoutte wrote:
External Email - Use CautionDear 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
- 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 ?
- 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 ?
- 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 ?
- 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
On 12/7/18 9:29 AM, Matthieu Vanhoutte wrote:
External Email - Use CautionHi 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. DGREVE@mgh.harvard.edu a écrit :
On 11/30/2018 07:15 AM, Matthieu Vanhoutte wrote:
External Email - Use CautionHi 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. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> a écrit :
Hi Matthieu, sorry for the delay On 11/29/2018 12:50 PM, Matthieu Vanhoutte wrote:External Email - Use CautionDear 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.outputmri_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
- 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.
- 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
- 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.
- 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
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. < DGREVE@mgh.harvard.edu> a écrit :
On 12/7/18 9:29 AM, Matthieu Vanhoutte wrote:
External Email - Use CautionHi 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. DGREVE@mgh.harvard.edu
a écrit :
On 11/30/2018 07:15 AM, Matthieu Vanhoutte wrote:
External Email - Use CautionHi 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. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> a écrit :
Hi Matthieu, sorry for the delay On 11/29/2018 12:50 PM, Matthieu Vanhoutte wrote:External Email - Use CautionDear 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 correctionsrespectively:
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
- 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 voxelsthat
have less than 1% GM after smoothing. If you you are disturbed bythe
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.
- 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
- What are the advantages/inconveniences of RBV vs GMX ?
Not entirely sure. RBV may be more precise since it at least hasthe
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.
- 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
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Hi Douglas,
Could you answer to my previous request ?
Best, Matt
Le 21 déc. 2018 à 20:29, Matthieu Vanhoutte matthieuvanhoutte@gmail.com a écrit :
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. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> a écrit :
On 12/7/18 9:29 AM, Matthieu Vanhoutte wrote:
External Email - Use CautionHi 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. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> a écrit :
On 11/30/2018 07:15 AM, Matthieu Vanhoutte wrote:
External Email - Use CautionHi 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. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu>> a écrit :
Hi Matthieu, sorry for the delay On 11/29/2018 12:50 PM, Matthieu Vanhoutte wrote:External Email - Use CautionDear 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.outputmri_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
- 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.
- 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 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 https://www.ncbi.nlm.nih.gov/pubmed/21336694
- 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.
- 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
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For MGX, the field of view is reduced to reduce computation and space usage; this requires a new registration matrix. For RBV, the voxel size is changed in addition. In both cases, a new registration is computed from the input registration
On 12/21/18 2:29 PM, Matthieu Vanhoutte wrote:
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. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> a écrit :
On 12/7/18 9:29 AM, Matthieu Vanhoutte wrote:
External Email - Use CautionHi 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. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> a écrit :
On 11/30/2018 07:15 AM, Matthieu Vanhoutte wrote:
External Email - Use CautionHi 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. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu>> a écrit :
Hi Matthieu, sorry for the delay On 11/29/2018 12:50 PM, Matthieu Vanhoutte wrote:External Email - Use CautionDear 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.outputmri_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
- 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.
- 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
- 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.
- 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.edumailto:Freesurfer@nmr.mgh.harvard.edu
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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. DGREVE@mgh.harvard.edu a écrit :
On 11/30/2018 07:15 AM, Matthieu Vanhoutte wrote:
External Email - Use CautionHi 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. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> a écrit :
Hi Matthieu, sorry for the delay
On 11/29/2018 12:50 PM, Matthieu Vanhoutte wrote:
External Email - Use CautionDear 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
- 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 ?
- 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 ?
- 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 ?
- 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
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Greve, Douglas N.,Ph.D. -
Matthieu Vanhoutte