Re: [Freesurfer] [PETsurfer] Use of MGX and RBV partial volume correction

[Greve, Douglas N.,Ph.D.]

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. 
mailto:dgr...@mgh.harvard.edu>> a écrit :


On 12/7/18 9:29 AM, Matthieu Vanhoutte wrote:
>  External Email - Use Caution
>
> Hi Douglas,
>
> Thanks for these clarifications. I added some others questions inline below.
>
> Best,
> Matthieu
>
>> Le 6 déc. 2018 à 17:25, Greve, Douglas N.,Ph.D. 
>> mailto: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.
>>> 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.

Re: [Freesurfer] [PETsurfer] Use of MGX and RBV partial volume correction

[Matthieu Vanhoutte]

External Email - Use Caution

Hi Douglas,

Could you answer to my previous request ?

Best,
Matt

> Le 21 déc. 2018 à 20:29, Matthieu Vanhoutte  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.  > a écrit :
> 
> 
> On 12/7/18 9:29 AM, Matthieu Vanhoutte wrote:
> >  External Email - Use Caution
> >
> > Hi Douglas,
> >
> > Thanks for these clarifications. I added some others questions inline below.
> >
> > Best,
> > Matthieu
> >
> >> Le 6 déc. 2018 à 17:25, Greve, Douglas N.,Ph.D.  >> > 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.
> >>> 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 
> > 

Re: [Freesurfer] [PETsurfer] Use of MGX and RBV partial volume correction

[Matthieu Vanhoutte]

External Email - Use Caution

Hi Douglas,

Thanks for these clarifications. I have however one misunderstanding.

When sampling PVC corrected PET image onto surface:
- I use bbpet2anat.lta when MGX was used as specified un tutorial
- I use rbv2anat.lta when RBV was used

But why not to use template.reg.lta computed by mri_coreg ? What are the
differences between those different files ?

Best,
Matthieu

Le mar. 18 déc. 2018 à 18:13, Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> a écrit :

>
>
> On 12/7/18 9:29 AM, Matthieu Vanhoutte wrote:
> >  External Email - Use Caution
> >
> > Hi Douglas,
> >
> > Thanks for these clarifications. I added some others questions inline
> below.
> >
> > Best,
> > Matthieu
> >
> >> Le 6 déc. 2018 à 17:25, Greve, Douglas N.,Ph.D. 
> 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.
> >>> 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 

Re: [Freesurfer] [PETsurfer] Use of MGX and RBV partial volume correction

[Matthieu Vanhoutte]

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. 
>> 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.
>> >> 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 

Re: [Freesurfer] [PETsurfer] Use of MGX and RBV partial volume correction

[Matthieu Vanhoutte]

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 
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. 
> 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.
> >> 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 

Re: [Freesurfer] [PETsurfer] Use of MGX and RBV partial volume correction

[Matthieu Vanhoutte]

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.  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. 
>> 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 

Re: [Freesurfer] [PETsurfer] Use of MGX and RBV partial volume correction

[Matthieu Vanhoutte]

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.  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. 
>> 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 
>> 

Re: [Freesurfer] [PETsurfer] Use of MGX and RBV partial volume correction

[Greve, Douglas N.,Ph.D.]

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. 
> 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.
>
>
> >
> > 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 

Re: [Freesurfer] [PETsurfer] Use of MGX and RBV partial volume correction

[Greve, Douglas N.,Ph.D.]

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).
>
> 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.
>
> 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.
>
> 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
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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[Freesurfer] [PETsurfer] Use of MGX and RBV partial volume correction

[Matthieu Vanhoutte]

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

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