Re: [Freesurfer] Use of PVC PET images (V6) : between versions compatibility and intensity normalisation

2016-01-15 Thread Douglas N Greve 
GTM corrects for all ROIs, including WM and pons. The GTM is always run 
and so pons is always available for normalization. RBV is derived from 
the GTM so is also corrects in WM. MG does not correct in WM.

On 01/15/2016 04:22 AM, Matthieu Vanhoutte wrote:
> Dear Douglas,
>
> If I understand well no PVC corrected pet images from any method 
> (MG,RBV or GTM) have corrected white matter values ?
> Where do you get the pons intensity,that has been PVC'ed, used to 
> normalize ?
>
> Best regards,
> Matthieu
>
> 2016-01-11 21:04 GMT+01:00 Douglas N Greve  >:
>
> Yes with MGPVC the voxel values are rescaled by the MG formula. Note
> that MG (and RBV) use GTM as a preprocessing step. If you average
> the MG
> output over an ROI, then it comes close to the GTM value.
>
> On 01/11/2016 02:39 PM, Matthieu Vanhoutte wrote:
> > Le 11/01/2016 20:33, Douglas N Greve a écrit :
> >> On 01/11/2016 02:14 PM, Matthieu Vanhoutte wrote:
> >>> Dear Douglas,
> >>>
> >>> Sorry if I wasn't clear. With the PVC, voxels intensities are
> modified,
> >>> right ?
> >> Not necessarily. The GTM does not work this way. MG and RBV do.
> For an
> >> ROI analysis, the GTM is by far the preferred method.
> > I suppose I used MG method since I specified --mgx option (I would
> > like to do an entire cortex analysis) ?
> > With MG PVC, voxels intensities are the modified ?
> >
> > Best regards,
> > Matthieu
> >>> So, in the case of anatomical intensity normalization based on
> >>> gray matter of cerebellum, is the mean activity of gray
> cerebellum taken
> >>> from the original PET image or from the PVC'ed PET image ?
> >> Again, not the right question for GTM
> >>> Best regards,
> >>> Matthieu
> >>>
> >>> Le 11/01/2016 18:52, Douglas N Greve a écrit :
>  I'm not sure exactly what you mean. I guess you could set all
> voxels in
>  a given ROI to be the value of that ROI? This is not really a
> voxel-wise
>  correction and probably would not do what you want. You can
> use the mgx
>  data (corrected with muller-gartner method). There is also a
> --rbv
>  (region-based voxel-wise, Thomas 2012) option.
> 
> 
>  On 01/11/2016 12:34 PM, Matthieu Vanhoutte wrote:
> > Dear Douglas,
> >
> > If the pons intensity used to normalize has been PVC'ed,
> couldn't we
> > have an output of mri_gtmpvc with the whole brain PVC'ed ?
> >
> > Because the only files on output of mri_gtmpvc are :
> > mgx.ctxgm.nii.gz - pvc'ed cortex gm only
> > mgx.subctxgm.nii.gz - pvc'ed subcortical gm only
> > mgx.gm.nii.gz - pvc'ed all gm
> >
> > Best regards,
> > Matthieu
> >
> > 2016-01-11 18:20 GMT+01:00 Douglas N Greve
> 
> >  >>:
> >
> >
> >The pons intensity used to normalize has been PVC'ed.
> The file used is
> >the input file.
> >
> >
> >On 01/11/2016 04:04 AM, Matthieu Vanhoutte wrote:
> >> Dear Douglas,
> >>
> >> Just one more question : by default mri_gtmpvc uses
> pons for
> >computing
> >> rSUV, but is this intensity normalization done
> before or after
> >partial
> >> volume correction ? What file is used in input for
> intensity
> >> normalization ?
> >>
> >> Thanks in advance !
> >>
> >> Best regards,
> >> Matthieu
> >>
> >> 2015-12-18 18:26 GMT+01:00 Douglas Greve
> > 
> >
> >>  
> >  >>
> >> You'll see several files that begin with mgx:
> >> mgx.ctxgm.nii.gz - pvc'ed cortex gm only
> >>  mgx.subctxgm.nii.gz - pvc'ed subcortical gm only
> >> mgx.gm.nii.gz - pvc'ed all gm
> >>
> >>
> >> On 12/18/15 6:08 AM, Matthieu Vanhoutte wrote:
> >>> Hello Douglas,
> >>>
> >>> I have run mri_gtmpvc with static PET images
> using the
> >following
> >>> command :

Re: [Freesurfer] Use of PVC PET images (V6) : between versions compatibility and intensity normalisation

2016-01-15 Thread Matthieu Vanhoutte 
Dear Douglas,

If I understand well no PVC corrected pet images from any method (MG,RBV or
GTM) have corrected white matter values ?
Where do you get the pons intensity,that has been PVC'ed, used to normalize
?

Best regards,
Matthieu

2016-01-11 21:04 GMT+01:00 Douglas N Greve :

> Yes with MGPVC the voxel values are rescaled by the MG formula. Note
> that MG (and RBV) use GTM as a preprocessing step. If you average the MG
> output over an ROI, then it comes close to the GTM value.
>
> On 01/11/2016 02:39 PM, Matthieu Vanhoutte wrote:
> > Le 11/01/2016 20:33, Douglas N Greve a écrit :
> >> On 01/11/2016 02:14 PM, Matthieu Vanhoutte wrote:
> >>> Dear Douglas,
> >>>
> >>> Sorry if I wasn't clear. With the PVC, voxels intensities are modified,
> >>> right ?
> >> Not necessarily. The GTM does not work this way. MG and RBV do. For an
> >> ROI analysis, the GTM is by far the preferred method.
> > I suppose I used MG method since I specified  --mgx option (I would
> > like to do an entire cortex analysis) ?
> > With MG PVC, voxels intensities are the modified ?
> >
> > Best regards,
> > Matthieu
> >>> So, in the case of anatomical intensity normalization based on
> >>> gray matter of cerebellum, is the mean activity of gray cerebellum
> taken
> >>> from the original PET image or from the PVC'ed PET image ?
> >> Again, not the right question for GTM
> >>> Best regards,
> >>> Matthieu
> >>>
> >>> Le 11/01/2016 18:52, Douglas N Greve a écrit :
>  I'm not sure exactly what you mean. I guess you could set all voxels
> in
>  a given ROI to be the value of that ROI? This is not really a
> voxel-wise
>  correction and probably would not do what you want. You can use the
> mgx
>  data (corrected with muller-gartner method). There is also a --rbv
>  (region-based voxel-wise, Thomas 2012) option.
> 
> 
>  On 01/11/2016 12:34 PM, Matthieu Vanhoutte wrote:
> > Dear Douglas,
> >
> > If the pons intensity used to normalize has been PVC'ed, couldn't we
> > have an output of mri_gtmpvc with the whole brain PVC'ed ?
> >
> > Because the only files on output of mri_gtmpvc are :
> > mgx.ctxgm.nii.gz - pvc'ed cortex gm only
> > mgx.subctxgm.nii.gz - pvc'ed subcortical gm only
> > mgx.gm.nii.gz - pvc'ed all gm
> >
> > Best regards,
> > Matthieu
> >
> > 2016-01-11 18:20 GMT+01:00 Douglas N Greve <
> gr...@nmr.mgh.harvard.edu
> > >:
> >
> >
> >The pons intensity used to normalize has been PVC'ed. The
> file used is
> >the input file.
> >
> >
> >On 01/11/2016 04:04 AM, Matthieu Vanhoutte wrote:
> >> Dear Douglas,
> >>
> >> Just one more question : by default mri_gtmpvc uses pons for
> >computing
> >> rSUV, but is this intensity normalization done before or
> after
> >partial
> >> volume correction ? What file is used in input for intensity
> >> normalization ?
> >>
> >> Thanks in advance !
> >>
> >> Best regards,
> >> Matthieu
> >>
> >> 2015-12-18 18:26 GMT+01:00 Douglas Greve
> > >
> >>  >>>:
> >>
> >> You'll see several files that begin with mgx:
> >> mgx.ctxgm.nii.gz - pvc'ed cortex gm only
> >> mgx.subctxgm.nii.gz - pvc'ed subcortical gm only
> >> mgx.gm.nii.gz - pvc'ed all gm
> >>
> >>
> >> On 12/18/15 6:08 AM, Matthieu Vanhoutte wrote:
> >>> Hello Douglas,
> >>>
> >>> I have run mri_gtmpvc with static PET images using the
> >following
> >>> command :
> >>> mri_gtmpvc --i PET.nii.gz --psf 6 --auto-mask 8 0.01
> --seg
> >>> gtmseg.mgz --reg register.dof6.lta --default-seg-merge
> >--mgx 0.01
> >>> --o gtmpvc.output
> >>>
> >>> In the output directory "gtmpvc.output" where is the
> partial
> >>> volume corrected PET image ?
> >>>
> >>> Thanks !
> >>>
> >>> Best regards,
> >>> Matthieu
> >>>
> >>> 2015-12-15 21:07 GMT+01:00 Douglas N Greve
> >>>  >
> > >>>:
> >>>
> >>> Not necessarily. It needs a good segmentation, so,
> to the
> >>> extent that v6
> >>> has

Re: [Freesurfer] Use of PVC PET images (V6) : between versions compatibility and intensity normalisation

2016-01-11 Thread Matthieu Vanhoutte 
Dear Douglas,

Just one more question : by default mri_gtmpvc uses pons for computing rSUV,
but is this intensity normalization done before or after partial volume
correction ? What file is used in input for intensity normalization ?

Thanks in advance !

Best regards,
Matthieu

2015-12-18 18:26 GMT+01:00 Douglas Greve :

> You'll see several files that begin with mgx:
> mgx.ctxgm.nii.gz - pvc'ed cortex gm only
> mgx.subctxgm.nii.gz - pvc'ed subcortical gm only
> mgx.gm.nii.gz - pvc'ed all gm
>
>
> On 12/18/15 6:08 AM, Matthieu Vanhoutte wrote:
>
> Hello Douglas,
>
> I have run mri_gtmpvc with static PET images using the following command :
> mri_gtmpvc --i PET.nii.gz --psf 6 --auto-mask 8 0.01 --seg gtmseg.mgz
> --reg register.dof6.lta --default-seg-merge --mgx 0.01 --o gtmpvc.output
>
> In the output directory "gtmpvc.output" where is the partial volume
> corrected PET image ?
>
> Thanks !
>
> Best regards,
> Matthieu
>
> 2015-12-15 21:07 GMT+01:00 Douglas N Greve :
>
>> Not necessarily. It needs a good segmentation, so, to the extent that v6
>> has a better segmentation then v6 is better.
>>
>> On 12/15/2015 02:57 PM, Matthieu Vanhoutte wrote:
>> >
>> > Thanks Douglas for the answer !
>> >
>> > But isn't PVC design for better working in terms of results with
>> > v6_beta than v5.3 ?
>> >
>> > Best regards,
>> >
>> > Matthieu
>> >
>> > Le 15 déc. 2015 19:02, "Douglas N Greve" < 
>> gr...@nmr.mgh.harvard.edu
>> > > a écrit :
>> >
>> > It is not subsegmented in 6.0 either:). When you run gtmseg, it will
>> > create the new segmentation that include pons and a few other things
>> >
>> > On 12/15/2015 12:56 PM, Matthieu Vanhoutte wrote:
>> > > Dear Douglas,
>> > >
>> > > Please see below :
>> > >
>> > > 2015-12-15 18:37 GMT+01:00 Douglas N Greve
>> > 
>> > > > > gr...@nmr.mgh.harvard.edu>>>:
>> > >
>> > >
>> > >
>> > > On 12/15/2015 04:46 AM, Matthieu Vanhoutte wrote:
>> > > > Dear experts,
>> > > >
>> > > > Could anyone answer to my questions below ?
>> > > >
>> > > > Thanks !
>> > > >
>> > > > Best regards,
>> > > > Matthieu
>> > > >
>> > > > 2015-12-10 10:10 GMT+01:00 Matthieu Vanhoutte
>> > > > > > 
>> > > > > >
>> > > > > 
>> > > > > > > > >
>> > > > Dear FS experts,
>> > > >
>> > > > 1) First Is it possible to use the partial volume
>> > correction
>> > > > provided in the v6 beta version of FreeSurfer despite
>> > the fact
>> > > > that recon-all have been done for all subjects with
>> > the v5.3 ?
>> > > >
>> > > Yes
>> > >
>> > >
>> > > Great ! but isn't it a problem for computing rSUV with pons as
>> > > reference structure since brainstem isn't sub-segmented in the
>> > version
>> > > 5.3 of recon-all ?
>> > >
>> > > >
>> > > >
>> > > > 2) Does this method supply an intensity normalisation
>> for
>> > > PET images ?
>> > > >
>> > > What do you mean by intensity normalization? For uptake
>> > analysis,
>> > > people
>> > > usually use SUV (standard uptake values where the whole image
>> is
>> > > scaled
>> > > by a value related to the injection mass and subject weight)
>> > or you
>> > > choose a reference structure to scale by (often called rSUV
>> for
>> > > relative). By default mri_gtmpvc uses pons, but you can
>> > choose any
>> > > structure you want with the --rescale flag
>> > >
>> > > >
>> > > >
>> > > > Best regards,
>> > > > Matthieu
>> > > >
>> > > >
>> > > >
>> > > >
>> > > > ___
>> > > > Freesurfer mailing list
>> > > > Freesurfer@nmr.mgh.harvard.edu
>> > 
>> > > > > 
>> Freesurfer@nmr.mgh.harvard.edu>>
>> > > >
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> > >
>> > > --
>> > >
>> > >
>> > > Best regards,
>> > > Matthieu
>> > >
>> > > Douglas N. Greve, Ph.D.
>> > > MGH-NMR Center
>> > > gr...@nmr.mgh.harvard.edu 
>> >

Re: [Freesurfer] Use of PVC PET images (V6) : between versions compatibility and intensity normalisation

2016-01-11 Thread Matthieu Vanhoutte 
Dear Douglas,

If the pons intensity used to normalize has been PVC'ed, couldn't we have
an output of mri_gtmpvc with the whole brain PVC'ed ?

Because the only files on output of mri_gtmpvc are :
mgx.ctxgm.nii.gz - pvc'ed cortex gm only
mgx.subctxgm.nii.gz - pvc'ed subcortical gm only
mgx.gm.nii.gz - pvc'ed all gm

Best regards,
Matthieu

2016-01-11 18:20 GMT+01:00 Douglas N Greve :

>
> The pons intensity used to normalize has been PVC'ed. The file used is
> the input file.
>
>
> On 01/11/2016 04:04 AM, Matthieu Vanhoutte wrote:
> > Dear Douglas,
> >
> > Just one more question : by default mri_gtmpvc uses pons for computing
> > rSUV, but is this intensity normalization done before or after partial
> > volume correction ? What file is used in input for intensity
> > normalization ?
> >
> > Thanks in advance !
> >
> > Best regards,
> > Matthieu
> >
> > 2015-12-18 18:26 GMT+01:00 Douglas Greve  > >:
> >
> > You'll see several files that begin with mgx:
> > mgx.ctxgm.nii.gz - pvc'ed cortex gm only
> > mgx.subctxgm.nii.gz - pvc'ed subcortical gm only
> > mgx.gm.nii.gz - pvc'ed all gm
> >
> >
> > On 12/18/15 6:08 AM, Matthieu Vanhoutte wrote:
> >> Hello Douglas,
> >>
> >> I have run mri_gtmpvc with static PET images using the following
> >> command :
> >> mri_gtmpvc --i PET.nii.gz --psf 6 --auto-mask 8 0.01 --seg
> >> gtmseg.mgz --reg register.dof6.lta --default-seg-merge --mgx 0.01
> >> --o gtmpvc.output
> >>
> >> In the output directory "gtmpvc.output" where is the partial
> >> volume corrected PET image ?
> >>
> >> Thanks !
> >>
> >> Best regards,
> >> Matthieu
> >>
> >> 2015-12-15 21:07 GMT+01:00 Douglas N Greve
> >> >:
> >>
> >> Not necessarily. It needs a good segmentation, so, to the
> >> extent that v6
> >> has a better segmentation then v6 is better.
> >>
> >> On 12/15/2015 02:57 PM, Matthieu Vanhoutte wrote:
> >> >
> >> > Thanks Douglas for the answer !
> >> >
> >> > But isn't PVC design for better working in terms of results
> >> with
> >> > v6_beta than v5.3 ?
> >> >
> >> > Best regards,
> >> >
> >> > Matthieu
> >> >
> >> > Le 15 déc. 2015 19:02, "Douglas N Greve"
> >> 
> >> >  >> >> a écrit :
> >> >
> >> > It is not subsegmented in 6.0 either:). When you run
> >> gtmseg, it will
> >> > create the new segmentation that include pons and a few
> >> other things
> >> >
> >> > On 12/15/2015 12:56 PM, Matthieu Vanhoutte wrote:
> >> > > Dear Douglas,
> >> > >
> >> > > Please see below :
> >> > >
> >> > > 2015-12-15 18:37 GMT+01:00 Douglas N Greve
> >> >  >> 
> >>  >> >
> >> > >  >> 
> >> >  >>  >> > >
> >> > >
> >> > >
> >> > > On 12/15/2015 04:46 AM, Matthieu Vanhoutte wrote:
> >> > > > Dear experts,
> >> > > >
> >> > > > Could anyone answer to my questions below ?
> >> > > >
> >> > > > Thanks !
> >> > > >
> >> > > > Best regards,
> >> > > > Matthieu
> >> > > >
> >> > > > 2015-12-10 10:10 GMT+01:00 Matthieu Vanhoutte
> >> > > >  >> 
> >> >  >> >
> >> > >  >> 
> >> >  >> >>
> >> > >  >> 
> >> >  >> >
> >> > >  >> 
> >> >  >> :
> >> > > >
> >> > > > Dear

Re: [Freesurfer] Use of PVC PET images (V6) : between versions compatibility and intensity normalisation

2016-01-11 Thread Douglas N Greve 

The pons intensity used to normalize has been PVC'ed. The file used is 
the input file.


On 01/11/2016 04:04 AM, Matthieu Vanhoutte wrote:
> Dear Douglas,
>
> Just one more question : by default mri_gtmpvc uses pons for computing 
> rSUV, but is this intensity normalization done before or after partial 
> volume correction ? What file is used in input for intensity 
> normalization ?
>
> Thanks in advance !
>
> Best regards,
> Matthieu
>
> 2015-12-18 18:26 GMT+01:00 Douglas Greve  >:
>
> You'll see several files that begin with mgx:
> mgx.ctxgm.nii.gz - pvc'ed cortex gm only
> mgx.subctxgm.nii.gz - pvc'ed subcortical gm only
> mgx.gm.nii.gz - pvc'ed all gm
>
>
> On 12/18/15 6:08 AM, Matthieu Vanhoutte wrote:
>> Hello Douglas,
>>
>> I have run mri_gtmpvc with static PET images using the following
>> command :
>> mri_gtmpvc --i PET.nii.gz --psf 6 --auto-mask 8 0.01 --seg
>> gtmseg.mgz --reg register.dof6.lta --default-seg-merge --mgx 0.01
>> --o gtmpvc.output
>>
>> In the output directory "gtmpvc.output" where is the partial
>> volume corrected PET image ?
>>
>> Thanks !
>>
>> Best regards,
>> Matthieu
>>
>> 2015-12-15 21:07 GMT+01:00 Douglas N Greve
>> >:
>>
>> Not necessarily. It needs a good segmentation, so, to the
>> extent that v6
>> has a better segmentation then v6 is better.
>>
>> On 12/15/2015 02:57 PM, Matthieu Vanhoutte wrote:
>> >
>> > Thanks Douglas for the answer !
>> >
>> > But isn't PVC design for better working in terms of results
>> with
>> > v6_beta than v5.3 ?
>> >
>> > Best regards,
>> >
>> > Matthieu
>> >
>> > Le 15 déc. 2015 19:02, "Douglas N Greve"
>> 
>> > > >> a écrit :
>> >
>> > It is not subsegmented in 6.0 either:). When you run
>> gtmseg, it will
>> > create the new segmentation that include pons and a few
>> other things
>> >
>> > On 12/15/2015 12:56 PM, Matthieu Vanhoutte wrote:
>> > > Dear Douglas,
>> > >
>> > > Please see below :
>> > >
>> > > 2015-12-15 18:37 GMT+01:00 Douglas N Greve
>> > > 
>> > >
>> > > > 
>> > > > > >
>> > >
>> > >
>> > > On 12/15/2015 04:46 AM, Matthieu Vanhoutte wrote:
>> > > > Dear experts,
>> > > >
>> > > > Could anyone answer to my questions below ?
>> > > >
>> > > > Thanks !
>> > > >
>> > > > Best regards,
>> > > > Matthieu
>> > > >
>> > > > 2015-12-10 10:10 GMT+01:00 Matthieu Vanhoutte
>> > > > > 
>> > > >
>> > > > 
>> > > >>
>> > > > 
>> > > >
>> > > > 
>> > > :
>> > > >
>> > > > Dear FS experts,
>> > > >
>> > > > 1) First Is it possible to use the partial
>> volume
>> > correction
>> > > > provided in the v6 beta version of
>> FreeSurfer despite
>> > the fact
>> > > > that recon-all have been done for all
>> subjects with
>> > the v5.3 ?
>> > > >
>> > > Yes
>> > >
>> > >
>> > > Great ! but isn't it a problem for computing rSUV
>> with pons as
>> > > reference structure since brainstem isn't
>>

Re: [Freesurfer] Use of PVC PET images (V6) : between versions compatibility and intensity normalisation

2016-01-11 Thread Douglas N Greve 
I'm not sure exactly what you mean. I guess you could set all voxels in 
a given ROI to be the value of that ROI? This is not really a voxel-wise 
correction and probably would not do what you want. You can use the mgx 
data (corrected with muller-gartner method). There is also a --rbv 
(region-based voxel-wise, Thomas 2012) option.


On 01/11/2016 12:34 PM, Matthieu Vanhoutte wrote:
> Dear Douglas,
>
> If the pons intensity used to normalize has been PVC'ed, couldn't we 
> have an output of mri_gtmpvc with the whole brain PVC'ed ?
>
> Because the only files on output of mri_gtmpvc are :
> mgx.ctxgm.nii.gz - pvc'ed cortex gm only
> mgx.subctxgm.nii.gz - pvc'ed subcortical gm only
> mgx.gm.nii.gz - pvc'ed all gm
>
> Best regards,
> Matthieu
>
> 2016-01-11 18:20 GMT+01:00 Douglas N Greve  >:
>
>
> The pons intensity used to normalize has been PVC'ed. The file used is
> the input file.
>
>
> On 01/11/2016 04:04 AM, Matthieu Vanhoutte wrote:
> > Dear Douglas,
> >
> > Just one more question : by default mri_gtmpvc uses pons for
> computing
> > rSUV, but is this intensity normalization done before or after
> partial
> > volume correction ? What file is used in input for intensity
> > normalization ?
> >
> > Thanks in advance !
> >
> > Best regards,
> > Matthieu
> >
> > 2015-12-18 18:26 GMT+01:00 Douglas Greve
> 
> >  >>:
> >
> > You'll see several files that begin with mgx:
> > mgx.ctxgm.nii.gz - pvc'ed cortex gm only
> > mgx.subctxgm.nii.gz - pvc'ed subcortical gm only
> > mgx.gm.nii.gz - pvc'ed all gm
> >
> >
> > On 12/18/15 6:08 AM, Matthieu Vanhoutte wrote:
> >> Hello Douglas,
> >>
> >> I have run mri_gtmpvc with static PET images using the
> following
> >> command :
> >> mri_gtmpvc --i PET.nii.gz --psf 6 --auto-mask 8 0.01 --seg
> >> gtmseg.mgz --reg register.dof6.lta --default-seg-merge
> --mgx 0.01
> >> --o gtmpvc.output
> >>
> >> In the output directory "gtmpvc.output" where is the partial
> >> volume corrected PET image ?
> >>
> >> Thanks !
> >>
> >> Best regards,
> >> Matthieu
> >>
> >> 2015-12-15 21:07 GMT+01:00 Douglas N Greve
> >>  
>  >>:
> >>
> >> Not necessarily. It needs a good segmentation, so, to the
> >> extent that v6
> >> has a better segmentation then v6 is better.
> >>
> >> On 12/15/2015 02:57 PM, Matthieu Vanhoutte wrote:
> >> >
> >> > Thanks Douglas for the answer !
> >> >
> >> > But isn't PVC design for better working in terms of
> results
> >> with
> >> > v6_beta than v5.3 ?
> >> >
> >> > Best regards,
> >> >
> >> > Matthieu
> >> >
> >> > Le 15 déc. 2015 19:02, "Douglas N Greve"
> >>  
> >
> >> >  
> >>   >> >
> >> > It is not subsegmented in 6.0 either:). When you run
> >> gtmseg, it will
> >> > create the new segmentation that include pons and
> a few
> >> other things
> >> >
> >> > On 12/15/2015 12:56 PM, Matthieu Vanhoutte wrote:
> >> > > Dear Douglas,
> >> > >
> >> > > Please see below :
> >> > >
> >> > > 2015-12-15 18:37 GMT+01:00 Douglas N Greve
> >> >  
> >>  >
> >>  
> >>  >>
> >> > >  
> >>  >
> >> >  
> >>

Re: [Freesurfer] Use of PVC PET images (V6) : between versions compatibility and intensity normalisation

2016-01-11 Thread Douglas N Greve 


On 01/11/2016 02:14 PM, Matthieu Vanhoutte wrote:
> Dear Douglas,
>
> Sorry if I wasn't clear. With the PVC, voxels intensities are modified,
> right ?
Not necessarily. The GTM does not work this way. MG and RBV do. For an 
ROI analysis, the GTM is by far the preferred method.
> So, in the case of anatomical intensity normalization based on
> gray matter of cerebellum, is the mean activity of gray cerebellum taken
> from the original PET image or from the PVC'ed PET image ?
Again, not the right question for GTM
>
> Best regards,
> Matthieu
>
> Le 11/01/2016 18:52, Douglas N Greve a écrit :
>> I'm not sure exactly what you mean. I guess you could set all voxels in
>> a given ROI to be the value of that ROI? This is not really a voxel-wise
>> correction and probably would not do what you want. You can use the mgx
>> data (corrected with muller-gartner method). There is also a --rbv
>> (region-based voxel-wise, Thomas 2012) option.
>>
>>
>> On 01/11/2016 12:34 PM, Matthieu Vanhoutte wrote:
>>> Dear Douglas,
>>>
>>> If the pons intensity used to normalize has been PVC'ed, couldn't we
>>> have an output of mri_gtmpvc with the whole brain PVC'ed ?
>>>
>>> Because the only files on output of mri_gtmpvc are :
>>> mgx.ctxgm.nii.gz - pvc'ed cortex gm only
>>> mgx.subctxgm.nii.gz - pvc'ed subcortical gm only
>>> mgx.gm.nii.gz - pvc'ed all gm
>>>
>>> Best regards,
>>> Matthieu
>>>
>>> 2016-01-11 18:20 GMT+01:00 Douglas N Greve >> >:
>>>
>>>
>>>   The pons intensity used to normalize has been PVC'ed. The file used is
>>>   the input file.
>>>
>>>
>>>   On 01/11/2016 04:04 AM, Matthieu Vanhoutte wrote:
>>>   > Dear Douglas,
>>>   >
>>>   > Just one more question : by default mri_gtmpvc uses pons for
>>>   computing
>>>   > rSUV, but is this intensity normalization done before or after
>>>   partial
>>>   > volume correction ? What file is used in input for intensity
>>>   > normalization ?
>>>   >
>>>   > Thanks in advance !
>>>   >
>>>   > Best regards,
>>>   > Matthieu
>>>   >
>>>   > 2015-12-18 18:26 GMT+01:00 Douglas Greve
>>>   
>>>   > >>   >>:
>>>   >
>>>   > You'll see several files that begin with mgx:
>>>   > mgx.ctxgm.nii.gz - pvc'ed cortex gm only
>>>   > mgx.subctxgm.nii.gz - pvc'ed subcortical gm only
>>>   > mgx.gm.nii.gz - pvc'ed all gm
>>>   >
>>>   >
>>>   > On 12/18/15 6:08 AM, Matthieu Vanhoutte wrote:
>>>   >> Hello Douglas,
>>>   >>
>>>   >> I have run mri_gtmpvc with static PET images using the
>>>   following
>>>   >> command :
>>>   >> mri_gtmpvc --i PET.nii.gz --psf 6 --auto-mask 8 0.01 --seg
>>>   >> gtmseg.mgz --reg register.dof6.lta --default-seg-merge
>>>   --mgx 0.01
>>>   >> --o gtmpvc.output
>>>   >>
>>>   >> In the output directory "gtmpvc.output" where is the partial
>>>   >> volume corrected PET image ?
>>>   >>
>>>   >> Thanks !
>>>   >>
>>>   >> Best regards,
>>>   >> Matthieu
>>>   >>
>>>   >> 2015-12-15 21:07 GMT+01:00 Douglas N Greve
>>>   >> >>   
>>>   >>   >>:
>>>   >>
>>>   >> Not necessarily. It needs a good segmentation, so, to the
>>>   >> extent that v6
>>>   >> has a better segmentation then v6 is better.
>>>   >>
>>>   >> On 12/15/2015 02:57 PM, Matthieu Vanhoutte wrote:
>>>   >> >
>>>   >> > Thanks Douglas for the answer !
>>>   >> >
>>>   >> > But isn't PVC design for better working in terms of
>>>   results
>>>   >> with
>>>   >> > v6_beta than v5.3 ?
>>>   >> >
>>>   >> > Best regards,
>>>   >> >
>>>   >> > Matthieu
>>>   >> >
>>>   >> > Le 15 déc. 2015 19:02, "Douglas N Greve"
>>>   >> >>   
>>>   >
>>>   >> > >>   
>>>   >> >>   >>   >> >
>>>   >> > It is not subsegmented in 6.0 either:). When you run
>>>   >> gtmseg, it will
>>>   >> > create the new segmentation that include pons and
>>>   a few
>>>   >> other things
>>>   >> >
>>>   >> > On

Re: [Freesurfer] Use of PVC PET images (V6) : between versions compatibility and intensity normalisation

2016-01-11 Thread Douglas N Greve 
Yes with MGPVC the voxel values are rescaled by the MG formula. Note 
that MG (and RBV) use GTM as a preprocessing step. If you average the MG 
output over an ROI, then it comes close to the GTM value.

On 01/11/2016 02:39 PM, Matthieu Vanhoutte wrote:
> Le 11/01/2016 20:33, Douglas N Greve a écrit :
>> On 01/11/2016 02:14 PM, Matthieu Vanhoutte wrote:
>>> Dear Douglas,
>>>
>>> Sorry if I wasn't clear. With the PVC, voxels intensities are modified,
>>> right ?
>> Not necessarily. The GTM does not work this way. MG and RBV do. For an
>> ROI analysis, the GTM is by far the preferred method.
> I suppose I used MG method since I specified  --mgx option (I would 
> like to do an entire cortex analysis) ?
> With MG PVC, voxels intensities are the modified ?
>
> Best regards,
> Matthieu
>>> So, in the case of anatomical intensity normalization based on
>>> gray matter of cerebellum, is the mean activity of gray cerebellum taken
>>> from the original PET image or from the PVC'ed PET image ?
>> Again, not the right question for GTM
>>> Best regards,
>>> Matthieu
>>>
>>> Le 11/01/2016 18:52, Douglas N Greve a écrit :
 I'm not sure exactly what you mean. I guess you could set all voxels in
 a given ROI to be the value of that ROI? This is not really a voxel-wise
 correction and probably would not do what you want. You can use the mgx
 data (corrected with muller-gartner method). There is also a --rbv
 (region-based voxel-wise, Thomas 2012) option.


 On 01/11/2016 12:34 PM, Matthieu Vanhoutte wrote:
> Dear Douglas,
>
> If the pons intensity used to normalize has been PVC'ed, couldn't we
> have an output of mri_gtmpvc with the whole brain PVC'ed ?
>
> Because the only files on output of mri_gtmpvc are :
> mgx.ctxgm.nii.gz - pvc'ed cortex gm only
> mgx.subctxgm.nii.gz - pvc'ed subcortical gm only
> mgx.gm.nii.gz - pvc'ed all gm
>
> Best regards,
> Matthieu
>
> 2016-01-11 18:20 GMT+01:00 Douglas N Greve  >:
>
>
>The pons intensity used to normalize has been PVC'ed. The file 
> used is
>the input file.
>
>
>On 01/11/2016 04:04 AM, Matthieu Vanhoutte wrote:
>> Dear Douglas,
>>
>> Just one more question : by default mri_gtmpvc uses pons for
>computing
>> rSUV, but is this intensity normalization done before or after
>partial
>> volume correction ? What file is used in input for intensity
>> normalization ?
>>
>> Thanks in advance !
>>
>> Best regards,
>> Matthieu
>>
>> 2015-12-18 18:26 GMT+01:00 Douglas Greve
>
>> >>:
>>
>> You'll see several files that begin with mgx:
>> mgx.ctxgm.nii.gz - pvc'ed cortex gm only
>> mgx.subctxgm.nii.gz - pvc'ed subcortical gm only
>> mgx.gm.nii.gz - pvc'ed all gm
>>
>>
>> On 12/18/15 6:08 AM, Matthieu Vanhoutte wrote:
>>> Hello Douglas,
>>>
>>> I have run mri_gtmpvc with static PET images using the
>following
>>> command :
>>> mri_gtmpvc --i PET.nii.gz --psf 6 --auto-mask 8 0.01 --seg
>>> gtmseg.mgz --reg register.dof6.lta --default-seg-merge
>--mgx 0.01
>>> --o gtmpvc.output
>>>
>>> In the output directory "gtmpvc.output" where is the partial
>>> volume corrected PET image ?
>>>
>>> Thanks !
>>>
>>> Best regards,
>>> Matthieu
>>>
>>> 2015-12-15 21:07 GMT+01:00 Douglas N Greve
>>> 
>>>:
>>>
>>> Not necessarily. It needs a good segmentation, so, to 
> the
>>> extent that v6
>>> has a better segmentation then v6 is better.
>>>
>>> On 12/15/2015 02:57 PM, Matthieu Vanhoutte wrote:
>>> >
>>> > Thanks Douglas for the answer !
>>> >
>>> > But isn't PVC design for better working in terms of
>results
>>> with
>>> > v6_beta than v5.3 ?
>>> >
>>> > Best regards,
>>> >
>>> >

Re: [Freesurfer] Use of PVC PET images (V6) : between versions compatibility and intensity normalisation

2016-01-11 Thread Matthieu Vanhoutte 
Dear Douglas,

Sorry if I wasn't clear. With the PVC, voxels intensities are modified, 
right ? So, in the case of anatomical intensity normalization based on 
gray matter of cerebellum, is the mean activity of gray cerebellum taken 
from the original PET image or from the PVC'ed PET image ?

Best regards,
Matthieu

Le 11/01/2016 18:52, Douglas N Greve a écrit :
> I'm not sure exactly what you mean. I guess you could set all voxels in
> a given ROI to be the value of that ROI? This is not really a voxel-wise
> correction and probably would not do what you want. You can use the mgx
> data (corrected with muller-gartner method). There is also a --rbv
> (region-based voxel-wise, Thomas 2012) option.
>
>
> On 01/11/2016 12:34 PM, Matthieu Vanhoutte wrote:
>> Dear Douglas,
>>
>> If the pons intensity used to normalize has been PVC'ed, couldn't we
>> have an output of mri_gtmpvc with the whole brain PVC'ed ?
>>
>> Because the only files on output of mri_gtmpvc are :
>> mgx.ctxgm.nii.gz - pvc'ed cortex gm only
>> mgx.subctxgm.nii.gz - pvc'ed subcortical gm only
>> mgx.gm.nii.gz - pvc'ed all gm
>>
>> Best regards,
>> Matthieu
>>
>> 2016-01-11 18:20 GMT+01:00 Douglas N Greve > >:
>>
>>
>>  The pons intensity used to normalize has been PVC'ed. The file used is
>>  the input file.
>>
>>
>>  On 01/11/2016 04:04 AM, Matthieu Vanhoutte wrote:
>>  > Dear Douglas,
>>  >
>>  > Just one more question : by default mri_gtmpvc uses pons for
>>  computing
>>  > rSUV, but is this intensity normalization done before or after
>>  partial
>>  > volume correction ? What file is used in input for intensity
>>  > normalization ?
>>  >
>>  > Thanks in advance !
>>  >
>>  > Best regards,
>>  > Matthieu
>>  >
>>  > 2015-12-18 18:26 GMT+01:00 Douglas Greve
>>  
>>  > >  >>:
>>  >
>>  > You'll see several files that begin with mgx:
>>  > mgx.ctxgm.nii.gz - pvc'ed cortex gm only
>>  > mgx.subctxgm.nii.gz - pvc'ed subcortical gm only
>>  > mgx.gm.nii.gz - pvc'ed all gm
>>  >
>>  >
>>  > On 12/18/15 6:08 AM, Matthieu Vanhoutte wrote:
>>  >> Hello Douglas,
>>  >>
>>  >> I have run mri_gtmpvc with static PET images using the
>>  following
>>  >> command :
>>  >> mri_gtmpvc --i PET.nii.gz --psf 6 --auto-mask 8 0.01 --seg
>>  >> gtmseg.mgz --reg register.dof6.lta --default-seg-merge
>>  --mgx 0.01
>>  >> --o gtmpvc.output
>>  >>
>>  >> In the output directory "gtmpvc.output" where is the partial
>>  >> volume corrected PET image ?
>>  >>
>>  >> Thanks !
>>  >>
>>  >> Best regards,
>>  >> Matthieu
>>  >>
>>  >> 2015-12-15 21:07 GMT+01:00 Douglas N Greve
>>  >> >  
>>  >  >>:
>>  >>
>>  >> Not necessarily. It needs a good segmentation, so, to the
>>  >> extent that v6
>>  >> has a better segmentation then v6 is better.
>>  >>
>>  >> On 12/15/2015 02:57 PM, Matthieu Vanhoutte wrote:
>>  >> >
>>  >> > Thanks Douglas for the answer !
>>  >> >
>>  >> > But isn't PVC design for better working in terms of
>>  results
>>  >> with
>>  >> > v6_beta than v5.3 ?
>>  >> >
>>  >> > Best regards,
>>  >> >
>>  >> > Matthieu
>>  >> >
>>  >> > Le 15 déc. 2015 19:02, "Douglas N Greve"
>>  >> >  
>>  >
>>  >> > >  
>>  >> >  >  >> >
>>  >> > It is not subsegmented in 6.0 either:). When you run
>>  >> gtmseg, it will
>>  >> > create the new segmentation that include pons and
>>  a few
>>  >> other things
>>  >> >
>>  >> > On 12/15/2015 12:56 PM, Matthieu Vanhoutte wrote:
>>  >> > > Dear Douglas,
>>  >> > >
>>  >> > > Please see below :
>>  >> > >
>>  >> > > 2015-12-15 18:37 GMT+01:00 Douglas N Greve
>>  >> > >  
>>  >> >

Re: [Freesurfer] Use of PVC PET images (V6) : between versions compatibility and intensity normalisation

2016-01-11 Thread Matthieu Vanhoutte 

Le 11/01/2016 20:33, Douglas N Greve a écrit :


On 01/11/2016 02:14 PM, Matthieu Vanhoutte wrote:

Dear Douglas,

Sorry if I wasn't clear. With the PVC, voxels intensities are modified,
right ?

Not necessarily. The GTM does not work this way. MG and RBV do. For an
ROI analysis, the GTM is by far the preferred method.
I suppose I used MG method since I specified --mgx option (I would like 
to do an entire cortex analysis) ?

With MG PVC, voxels intensities are the modified ?

Best regards,
Matthieu

So, in the case of anatomical intensity normalization based on
gray matter of cerebellum, is the mean activity of gray cerebellum taken
from the original PET image or from the PVC'ed PET image ?

Again, not the right question for GTM

Best regards,
Matthieu

Le 11/01/2016 18:52, Douglas N Greve a écrit :

I'm not sure exactly what you mean. I guess you could set all voxels in
a given ROI to be the value of that ROI? This is not really a voxel-wise
correction and probably would not do what you want. You can use the mgx
data (corrected with muller-gartner method). There is also a --rbv
(region-based voxel-wise, Thomas 2012) option.


On 01/11/2016 12:34 PM, Matthieu Vanhoutte wrote:

Dear Douglas,

If the pons intensity used to normalize has been PVC'ed, couldn't we
have an output of mri_gtmpvc with the whole brain PVC'ed ?

Because the only files on output of mri_gtmpvc are :
mgx.ctxgm.nii.gz - pvc'ed cortex gm only
mgx.subctxgm.nii.gz - pvc'ed subcortical gm only
mgx.gm.nii.gz - pvc'ed all gm

Best regards,
Matthieu

2016-01-11 18:20 GMT+01:00 Douglas N Greve >:


   The pons intensity used to normalize has been PVC'ed. The file used is
   the input file.


   On 01/11/2016 04:04 AM, Matthieu Vanhoutte wrote:
   > Dear Douglas,
   >
   > Just one more question : by default mri_gtmpvc uses pons for
   computing
   > rSUV, but is this intensity normalization done before or after
   partial
   > volume correction ? What file is used in input for intensity
   > normalization ?
   >
   > Thanks in advance !
   >
   > Best regards,
   > Matthieu
   >
   > 2015-12-18 18:26 GMT+01:00 Douglas Greve
   
   > >>:
   >
   > You'll see several files that begin with mgx:
   > mgx.ctxgm.nii.gz - pvc'ed cortex gm only
   > mgx.subctxgm.nii.gz - pvc'ed subcortical gm only
   > mgx.gm.nii.gz - pvc'ed all gm
   >
   >
   > On 12/18/15 6:08 AM, Matthieu Vanhoutte wrote:
   >> Hello Douglas,
   >>
   >> I have run mri_gtmpvc with static PET images using the
   following
   >> command :
   >> mri_gtmpvc --i PET.nii.gz --psf 6 --auto-mask 8 0.01 --seg
   >> gtmseg.mgz --reg register.dof6.lta --default-seg-merge
   --mgx 0.01
   >> --o gtmpvc.output
   >>
   >> In the output directory "gtmpvc.output" where is the partial
   >> volume corrected PET image ?
   >>
   >> Thanks !
   >>
   >> Best regards,
   >> Matthieu
   >>
   >> 2015-12-15 21:07 GMT+01:00 Douglas N Greve
   >> 
   >>:
   >>
   >> Not necessarily. It needs a good segmentation, so, to the
   >> extent that v6
   >> has a better segmentation then v6 is better.
   >>
   >> On 12/15/2015 02:57 PM, Matthieu Vanhoutte wrote:
   >> >
   >> > Thanks Douglas for the answer !
   >> >
   >> > But isn't PVC design for better working in terms of
   results
   >> with
   >> > v6_beta than v5.3 ?
   >> >
   >> > Best regards,
   >> >
   >> > Matthieu
   >> >
   >> > Le 15 déc. 2015 19:02, "Douglas N Greve"
   >> 
   >
   >> > 
   >> > >
   >> > It is not subsegmented in 6.0 either:). When you run
   >> gtmseg, it will
   >> > create the new segmentation that include pons and
   a few
   >> other things
   >> >
   >> > On 12/15/2015 12:56 PM, Matthieu Vanhoutte wrote:
   >> > > Dear Douglas,
   >> > >
   >>

Re: [Freesurfer] Use of PVC PET images (V6) : between versions compatibility and intensity normalisation

2015-12-18 Thread Matthieu Vanhoutte 
Hello Douglas,

I have run mri_gtmpvc with static PET images using the following command :
mri_gtmpvc --i PET.nii.gz --psf 6 --auto-mask 8 0.01 --seg gtmseg.mgz --reg
register.dof6.lta --default-seg-merge --mgx 0.01 --o gtmpvc.output

In the output directory "gtmpvc.output" where is the partial volume
corrected PET image ?

Thanks !

Best regards,
Matthieu

2015-12-15 21:07 GMT+01:00 Douglas N Greve :

> Not necessarily. It needs a good segmentation, so, to the extent that v6
> has a better segmentation then v6 is better.
>
> On 12/15/2015 02:57 PM, Matthieu Vanhoutte wrote:
> >
> > Thanks Douglas for the answer !
> >
> > But isn't PVC design for better working in terms of results with
> > v6_beta than v5.3 ?
> >
> > Best regards,
> >
> > Matthieu
> >
> > Le 15 déc. 2015 19:02, "Douglas N Greve"  > > a écrit :
> >
> > It is not subsegmented in 6.0 either:). When you run gtmseg, it will
> > create the new segmentation that include pons and a few other things
> >
> > On 12/15/2015 12:56 PM, Matthieu Vanhoutte wrote:
> > > Dear Douglas,
> > >
> > > Please see below :
> > >
> > > 2015-12-15 18:37 GMT+01:00 Douglas N Greve
> > 
> > >  > >>:
> > >
> > >
> > >
> > > On 12/15/2015 04:46 AM, Matthieu Vanhoutte wrote:
> > > > Dear experts,
> > > >
> > > > Could anyone answer to my questions below ?
> > > >
> > > > Thanks !
> > > >
> > > > Best regards,
> > > > Matthieu
> > > >
> > > > 2015-12-10 10:10 GMT+01:00 Matthieu Vanhoutte
> > > >  > 
> > >  > >
> > >  > 
> > >  >  > > >
> > > > Dear FS experts,
> > > >
> > > > 1) First Is it possible to use the partial volume
> > correction
> > > > provided in the v6 beta version of FreeSurfer despite
> > the fact
> > > > that recon-all have been done for all subjects with
> > the v5.3 ?
> > > >
> > > Yes
> > >
> > >
> > > Great ! but isn't it a problem for computing rSUV with pons as
> > > reference structure since brainstem isn't sub-segmented in the
> > version
> > > 5.3 of recon-all ?
> > >
> > > >
> > > >
> > > > 2) Does this method supply an intensity normalisation for
> > > PET images ?
> > > >
> > > What do you mean by intensity normalization? For uptake
> > analysis,
> > > people
> > > usually use SUV (standard uptake values where the whole image
> is
> > > scaled
> > > by a value related to the injection mass and subject weight)
> > or you
> > > choose a reference structure to scale by (often called rSUV for
> > > relative). By default mri_gtmpvc uses pons, but you can
> > choose any
> > > structure you want with the --rescale flag
> > >
> > > >
> > > >
> > > > Best regards,
> > > > Matthieu
> > > >
> > > >
> > > >
> > > >
> > > > ___
> > > > Freesurfer mailing list
> > > > Freesurfer@nmr.mgh.harvard.edu
> > 
> > >  > >
> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > >
> > > --
> > >
> > >
> > > Best regards,
> > > Matthieu
> > >
> > > Douglas N. Greve, Ph.D.
> > > MGH-NMR Center
> > > gr...@nmr.mgh.harvard.edu 
> >  >>
> > > Phone Number: 617-724-2358 
> > >
> > > Fax: 617-726-7422   > >
> > >
> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > 
> > > 
> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > 
> > > 
> > > Outgoing:
> > >

Re: [Freesurfer] Use of PVC PET images (V6) : between versions compatibility and intensity normalisation

2015-12-18 Thread Matthieu Vanhoutte 
Many thanks !

Matthieu
Le 18 déc. 2015 18:27, "Douglas Greve"  a écrit :

> You'll see several files that begin with mgx:
> mgx.ctxgm.nii.gz - pvc'ed cortex gm only
> mgx.subctxgm.nii.gz - pvc'ed subcortical gm only
> mgx.gm.nii.gz - pvc'ed all gm
>
> On 12/18/15 6:08 AM, Matthieu Vanhoutte wrote:
>
> Hello Douglas,
>
> I have run mri_gtmpvc with static PET images using the following command :
> mri_gtmpvc --i PET.nii.gz --psf 6 --auto-mask 8 0.01 --seg gtmseg.mgz
> --reg register.dof6.lta --default-seg-merge --mgx 0.01 --o gtmpvc.output
>
> In the output directory "gtmpvc.output" where is the partial volume
> corrected PET image ?
>
> Thanks !
>
> Best regards,
> Matthieu
>
> 2015-12-15 21:07 GMT+01:00 Douglas N Greve :
>
>> Not necessarily. It needs a good segmentation, so, to the extent that v6
>> has a better segmentation then v6 is better.
>>
>> On 12/15/2015 02:57 PM, Matthieu Vanhoutte wrote:
>> >
>> > Thanks Douglas for the answer !
>> >
>> > But isn't PVC design for better working in terms of results with
>> > v6_beta than v5.3 ?
>> >
>> > Best regards,
>> >
>> > Matthieu
>> >
>> > Le 15 déc. 2015 19:02, "Douglas N Greve" > > > a écrit :
>> >
>> > It is not subsegmented in 6.0 either:). When you run gtmseg, it will
>> > create the new segmentation that include pons and a few other things
>> >
>> > On 12/15/2015 12:56 PM, Matthieu Vanhoutte wrote:
>> > > Dear Douglas,
>> > >
>> > > Please see below :
>> > >
>> > > 2015-12-15 18:37 GMT+01:00 Douglas N Greve
>> > 
>> > > > > >>:
>> > >
>> > >
>> > >
>> > > On 12/15/2015 04:46 AM, Matthieu Vanhoutte wrote:
>> > > > Dear experts,
>> > > >
>> > > > Could anyone answer to my questions below ?
>> > > >
>> > > > Thanks !
>> > > >
>> > > > Best regards,
>> > > > Matthieu
>> > > >
>> > > > 2015-12-10 10:10 GMT+01:00 Matthieu Vanhoutte
>> > > > > > 
>> > > > > >
>> > > > > 
>> > > > > > > > >
>> > > > Dear FS experts,
>> > > >
>> > > > 1) First Is it possible to use the partial volume
>> > correction
>> > > > provided in the v6 beta version of FreeSurfer despite
>> > the fact
>> > > > that recon-all have been done for all subjects with
>> > the v5.3 ?
>> > > >
>> > > Yes
>> > >
>> > >
>> > > Great ! but isn't it a problem for computing rSUV with pons as
>> > > reference structure since brainstem isn't sub-segmented in the
>> > version
>> > > 5.3 of recon-all ?
>> > >
>> > > >
>> > > >
>> > > > 2) Does this method supply an intensity normalisation
>> for
>> > > PET images ?
>> > > >
>> > > What do you mean by intensity normalization? For uptake
>> > analysis,
>> > > people
>> > > usually use SUV (standard uptake values where the whole image
>> is
>> > > scaled
>> > > by a value related to the injection mass and subject weight)
>> > or you
>> > > choose a reference structure to scale by (often called rSUV
>> for
>> > > relative). By default mri_gtmpvc uses pons, but you can
>> > choose any
>> > > structure you want with the --rescale flag
>> > >
>> > > >
>> > > >
>> > > > Best regards,
>> > > > Matthieu
>> > > >
>> > > >
>> > > >
>> > > >
>> > > > ___
>> > > > Freesurfer mailing list
>> > > > Freesurfer@nmr.mgh.harvard.edu
>> > 
>> > > > > >
>> > > >
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> > >
>> > > --
>> > >
>> > >
>> > > Best regards,
>> > > Matthieu
>> > >
>> > > Douglas N. Greve, Ph.D.
>> > > MGH-NMR Center
>> > > gr...@nmr.mgh.harvard.edu 
>> > > >>
>> > > Phone Number: 617-724-2358 
>> > >
>> > > Fax: 617-726-7422  > > >
>> > >
>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> >

Re: [Freesurfer] Use of PVC PET images (V6) : between versions compatibility and intensity normalisation

2015-12-18 Thread Douglas Greve 

You'll see several files that begin with mgx:
mgx.ctxgm.nii.gz - pvc'ed cortex gm only
mgx.subctxgm.nii.gz - pvc'ed subcortical gm only
mgx.gm.nii.gz - pvc'ed all gm

On 12/18/15 6:08 AM, Matthieu Vanhoutte wrote:

Hello Douglas,

I have run mri_gtmpvc with static PET images using the following command :
mri_gtmpvc --i PET.nii.gz --psf 6 --auto-mask 8 0.01 --seg gtmseg.mgz 
--reg register.dof6.lta --default-seg-merge --mgx 0.01 --o gtmpvc.output


In the output directory "gtmpvc.output" where is the partial volume 
corrected PET image ?


Thanks !

Best regards,
Matthieu

2015-12-15 21:07 GMT+01:00 Douglas N Greve >:


Not necessarily. It needs a good segmentation, so, to the extent
that v6
has a better segmentation then v6 is better.

On 12/15/2015 02:57 PM, Matthieu Vanhoutte wrote:
>
> Thanks Douglas for the answer !
>
> But isn't PVC design for better working in terms of results with
> v6_beta than v5.3 ?
>
> Best regards,
>
> Matthieu
>
> Le 15 déc. 2015 19:02, "Douglas N Greve"

> >> a écrit :
>
> It is not subsegmented in 6.0 either:). When you run gtmseg,
it will
> create the new segmentation that include pons and a few
other things
>
> On 12/15/2015 12:56 PM, Matthieu Vanhoutte wrote:
> > Dear Douglas,
> >
> > Please see below :
> >
> > 2015-12-15 18:37 GMT+01:00 Douglas N Greve
> 
>
> > 
>  >
> >
> >
> > On 12/15/2015 04:46 AM, Matthieu Vanhoutte wrote:
> > > Dear experts,
> > >
> > > Could anyone answer to my questions below ?
> > >
> > > Thanks !
> > >
> > > Best regards,
> > > Matthieu
> > >
> > > 2015-12-10 10:10 GMT+01:00 Matthieu Vanhoutte
> > > 
> >
> > 
> >>
> > 
> >
> > 
> :
> > >
> > > Dear FS experts,
> > >
> > > 1) First Is it possible to use the partial volume
> correction
> > > provided in the v6 beta version of FreeSurfer
despite
> the fact
> > > that recon-all have been done for all subjects with
> the v5.3 ?
> > >
> > Yes
> >
> >
> > Great ! but isn't it a problem for computing rSUV with pons as
> > reference structure since brainstem isn't sub-segmented in the
> version
> > 5.3 of recon-all ?
> >
> > >
> > >
> > > 2) Does this method supply an intensity
normalisation for
> > PET images ?
> > >
> > What do you mean by intensity normalization? For uptake
> analysis,
> > people
> > usually use SUV (standard uptake values where the
whole image is
> > scaled
> > by a value related to the injection mass and subject
weight)
> or you
> > choose a reference structure to scale by (often called
rSUV for
> > relative). By default mri_gtmpvc uses pons, but you can
> choose any
> > structure you want with the --rescale flag
> >
> > >
> > >
> > > Best regards,
> > > Matthieu
> > >
> > >
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu

> >
> >

Re: [Freesurfer] Use of PVC PET images (V6) : between versions compatibility and intensity normalisation

2015-12-15 Thread Douglas N Greve 
It is not subsegmented in 6.0 either:). When you run gtmseg, it will 
create the new segmentation that include pons and a few other things

On 12/15/2015 12:56 PM, Matthieu Vanhoutte wrote:
> Dear Douglas,
>
> Please see below :
>
> 2015-12-15 18:37 GMT+01:00 Douglas N Greve  >:
>
>
>
> On 12/15/2015 04:46 AM, Matthieu Vanhoutte wrote:
> > Dear experts,
> >
> > Could anyone answer to my questions below ?
> >
> > Thanks !
> >
> > Best regards,
> > Matthieu
> >
> > 2015-12-10 10:10 GMT+01:00 Matthieu Vanhoutte
> >  
>  >>:
> >
> > Dear FS experts,
> >
> > 1) First Is it possible to use the partial volume correction
> > provided in the v6 beta version of FreeSurfer despite the fact
> > that recon-all have been done for all subjects with the v5.3 ?
> >
> Yes
>
>
> Great ! but isn't it a problem for computing rSUV with pons as 
> reference structure since brainstem isn't sub-segmented in the version 
> 5.3 of recon-all ?
>
> >
> >
> > 2) Does this method supply an intensity normalisation for
> PET images ?
> >
> What do you mean by intensity normalization? For uptake analysis,
> people
> usually use SUV (standard uptake values where the whole image is
> scaled
> by a value related to the injection mass and subject weight) or you
> choose a reference structure to scale by (often called rSUV for
> relative). By default mri_gtmpvc uses pons, but you can choose any
> structure you want with the --rescale flag
>
> >
> >
> > Best regards,
> > Matthieu
> >
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
>
>
> Best regards,
> Matthieu
>
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358 
> Fax: 617-726-7422 
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to
> whom it is
> addressed. If you believe this e-mail was sent to you in error and
> the e-mail
> contains patient information, please contact the Partners
> Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to
> you in error
> but does not contain patient information, please contact the
> sender and properly
> dispose of the e-mail.
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] Use of PVC PET images (V6) : between versions compatibility and intensity normalisation

2015-12-15 Thread Douglas N Greve 
Not necessarily. It needs a good segmentation, so, to the extent that v6 
has a better segmentation then v6 is better.

On 12/15/2015 02:57 PM, Matthieu Vanhoutte wrote:
>
> Thanks Douglas for the answer !
>
> But isn't PVC design for better working in terms of results with 
> v6_beta than v5.3 ?
>
> Best regards,
>
> Matthieu
>
> Le 15 déc. 2015 19:02, "Douglas N Greve"  > a écrit :
>
> It is not subsegmented in 6.0 either:). When you run gtmseg, it will
> create the new segmentation that include pons and a few other things
>
> On 12/15/2015 12:56 PM, Matthieu Vanhoutte wrote:
> > Dear Douglas,
> >
> > Please see below :
> >
> > 2015-12-15 18:37 GMT+01:00 Douglas N Greve
> 
> >  >>:
> >
> >
> >
> > On 12/15/2015 04:46 AM, Matthieu Vanhoutte wrote:
> > > Dear experts,
> > >
> > > Could anyone answer to my questions below ?
> > >
> > > Thanks !
> > >
> > > Best regards,
> > > Matthieu
> > >
> > > 2015-12-10 10:10 GMT+01:00 Matthieu Vanhoutte
> > >  
> >  >
> >  
> >   > >
> > > Dear FS experts,
> > >
> > > 1) First Is it possible to use the partial volume
> correction
> > > provided in the v6 beta version of FreeSurfer despite
> the fact
> > > that recon-all have been done for all subjects with
> the v5.3 ?
> > >
> > Yes
> >
> >
> > Great ! but isn't it a problem for computing rSUV with pons as
> > reference structure since brainstem isn't sub-segmented in the
> version
> > 5.3 of recon-all ?
> >
> > >
> > >
> > > 2) Does this method supply an intensity normalisation for
> > PET images ?
> > >
> > What do you mean by intensity normalization? For uptake
> analysis,
> > people
> > usually use SUV (standard uptake values where the whole image is
> > scaled
> > by a value related to the injection mass and subject weight)
> or you
> > choose a reference structure to scale by (often called rSUV for
> > relative). By default mri_gtmpvc uses pons, but you can
> choose any
> > structure you want with the --rescale flag
> >
> > >
> > >
> > > Best regards,
> > > Matthieu
> > >
> > >
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> 
> >  >
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > --
> >
> >
> > Best regards,
> > Matthieu
> >
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu 
> >
> > Phone Number: 617-724-2358 
> >
> > Fax: 617-726-7422   >
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> > 
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> > 
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
>  >
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > The information in this e-mail is intended only for the
> person to
> > whom it is
> > addressed. If you believe this e-mail was sent to you in
> error and
> > the e-mail
> > contains patient information, please contact the Partners
> > Compliance

Re: [Freesurfer] Use of PVC PET images (V6) : between versions compatibility and intensity normalisation

2015-12-15 Thread Douglas N Greve 


On 12/15/2015 04:46 AM, Matthieu Vanhoutte wrote:
> Dear experts,
>
> Could anyone answer to my questions below ?
>
> Thanks !
>
> Best regards,
> Matthieu
>
> 2015-12-10 10:10 GMT+01:00 Matthieu Vanhoutte 
> >:
>
> Dear FS experts,
>
> 1) First Is it possible to use the partial volume correction
> provided in the v6 beta version of FreeSurfer despite the fact
> that recon-all have been done for all subjects with the v5.3 ?
>
Yes
>
>
> 2) Does this method supply an intensity normalisation for PET images ?
>
What do you mean by intensity normalization? For uptake analysis, people 
usually use SUV (standard uptake values where the whole image is scaled 
by a value related to the injection mass and subject weight) or you 
choose a reference structure to scale by (often called rSUV for 
relative). By default mri_gtmpvc uses pons, but you can choose any 
structure you want with the --rescale flag
>
>
> Best regards,
> Matthieu
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Use of PVC PET images (V6) : between versions compatibility and intensity normalisation

2015-12-15 Thread Matthieu Vanhoutte 
Dear Douglas,

Please see below :

2015-12-15 18:37 GMT+01:00 Douglas N Greve :

>
>
> On 12/15/2015 04:46 AM, Matthieu Vanhoutte wrote:
> > Dear experts,
> >
> > Could anyone answer to my questions below ?
> >
> > Thanks !
> >
> > Best regards,
> > Matthieu
> >
> > 2015-12-10 10:10 GMT+01:00 Matthieu Vanhoutte
> > >:
> >
> > Dear FS experts,
> >
> > 1) First Is it possible to use the partial volume correction
> > provided in the v6 beta version of FreeSurfer despite the fact
> > that recon-all have been done for all subjects with the v5.3 ?
> >
> Yes
>

Great ! but isn't it a problem for computing rSUV with pons as reference
structure since brainstem isn't sub-segmented in the version 5.3 of
recon-all ?


> >
> >
> > 2) Does this method supply an intensity normalisation for PET images
> ?
> >
> What do you mean by intensity normalization? For uptake analysis, people
> usually use SUV (standard uptake values where the whole image is scaled
> by a value related to the injection mass and subject weight) or you
> choose a reference structure to scale by (often called rSUV for
> relative). By default mri_gtmpvc uses pons, but you can choose any
> structure you want with the --rescale flag
>
>
> >
> > Best regards,
> > Matthieu
> >
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
>

Best regards,
Matthieu


> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Use of PVC PET images (V6) : between versions compatibility and intensity normalisation

2015-12-15 Thread Matthieu Vanhoutte 
Thanks Douglas for the answer !

But isn't PVC design for better working in terms of results with v6_beta
than v5.3 ?

Best regards,

Matthieu
Le 15 déc. 2015 19:02, "Douglas N Greve"  a
écrit :

> It is not subsegmented in 6.0 either:). When you run gtmseg, it will
> create the new segmentation that include pons and a few other things
>
> On 12/15/2015 12:56 PM, Matthieu Vanhoutte wrote:
> > Dear Douglas,
> >
> > Please see below :
> >
> > 2015-12-15 18:37 GMT+01:00 Douglas N Greve  > >:
> >
> >
> >
> > On 12/15/2015 04:46 AM, Matthieu Vanhoutte wrote:
> > > Dear experts,
> > >
> > > Could anyone answer to my questions below ?
> > >
> > > Thanks !
> > >
> > > Best regards,
> > > Matthieu
> > >
> > > 2015-12-10 10:10 GMT+01:00 Matthieu Vanhoutte
> > >  > 
> >  > >>:
> > >
> > > Dear FS experts,
> > >
> > > 1) First Is it possible to use the partial volume correction
> > > provided in the v6 beta version of FreeSurfer despite the fact
> > > that recon-all have been done for all subjects with the v5.3 ?
> > >
> > Yes
> >
> >
> > Great ! but isn't it a problem for computing rSUV with pons as
> > reference structure since brainstem isn't sub-segmented in the version
> > 5.3 of recon-all ?
> >
> > >
> > >
> > > 2) Does this method supply an intensity normalisation for
> > PET images ?
> > >
> > What do you mean by intensity normalization? For uptake analysis,
> > people
> > usually use SUV (standard uptake values where the whole image is
> > scaled
> > by a value related to the injection mass and subject weight) or you
> > choose a reference structure to scale by (often called rSUV for
> > relative). By default mri_gtmpvc uses pons, but you can choose any
> > structure you want with the --rescale flag
> >
> > >
> > >
> > > Best regards,
> > > Matthieu
> > >
> > >
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > 
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > --
> >
> >
> > Best regards,
> > Matthieu
> >
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu 
> > Phone Number: 617-724-2358 
> > Fax: 617-726-7422 
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > 
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > 
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu  Freesurfer@nmr.mgh.harvard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > The information in this e-mail is intended only for the person to
> > whom it is
> > addressed. If you believe this e-mail was sent to you in error and
> > the e-mail
> > contains patient information, please contact the Partners
> > Compliance HelpLine at
> > http://www.partners.org/complianceline . If the e-mail was sent to
> > you in error
> > but does not contain patient information, please contact the
> > sender and properly
> > dispose of the e-mail.
> >
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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Re: [Freesurfer] Use of PVC PET images (V6) : between versions compatibility and intensity normalisation

2015-12-15 Thread Matthieu Vanhoutte 
Dear experts,

Could anyone answer to my questions below ?

Thanks !

Best regards,
Matthieu

2015-12-10 10:10 GMT+01:00 Matthieu Vanhoutte :

> Dear FS experts,
>
> 1) First Is it possible to use the partial volume correction provided in
> the v6 beta version of FreeSurfer despite the fact that recon-all have been
> done for all subjects with the v5.3 ?
>
> 2) Does this method supply an intensity normalisation for PET images ?
>
> Best regards,
> Matthieu
>
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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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