Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

[Matthieu Vanhoutte]

External Email - Use Caution

Hi Douglas,

Any advice ?

Best.

Le jeu. 7 févr. 2019 à 23:12, Matthieu Vanhoutte <
matthieuvanhou...@gmail.com> a écrit :

> Yes that's what I mean. But does this command provide an intensity
> normalized voxel-wise image ?
>
> Could you explain me the realign & reslice steps from the native PET to
> the voxel-wise PVC PET for MGX ans RBV ?
>
> Best,
> Matthieu
>
> Le jeu. 7 févr. 2019 à 23:06, Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> a écrit :
>
>> Do you mean the mean intensity not corrected for PVC? I would just run
>> mri_gtmpvc with --psf 0 --no-tfe to turn off PVC
>>
>> On 2/7/19 4:40 PM, Matthieu Vanhoutte wrote:
>> >
>> > External Email - Use Caution
>> >
>> > Hello experts,
>> >
>> > Anyone would have an advice on my previous questions ?
>> >
>> > Best,
>> > Matthieu
>> >
>> >
>> > Le mer. 30 janv. 2019 à 14:49, Matthieu Vanhoutte
>> > mailto:matthieuvanhou...@gmail.com>> a
>> > écrit :
>> >
>> > Hi Douglas,
>> >
>> > In order to apply intensity normalization to non-PVC PET images
>> > based on mean intensity from reference region in gtmseg.mgz, is it
>> > better to realign & reslice PET image onto gtmseg space or the
>> > reverse way ? How is it done when dealing with PVC images using
>> > gtmpvc command ?
>> >
>> > I would like to avoid too many reslicing operations before volume
>> > to surface projection, how would you deal with it ?
>> >
>> > Best,
>> > Matthieu
>> >
>> >> Le 28 janv. 2019 à 17:41, Greve, Douglas N.,Ph.D.
>> >> mailto:dgr...@mgh.harvard.edu>> a écrit :
>> >>
>> >> If you intend to use one of the aseg structures, then they are
>> >> the same.
>> >>
>> >> On 1/28/19 10:14 AM, Matthieu Vanhoutte wrote:
>> >>>
>> >>> External Email - Use Caution
>> >>>
>> >>> Hi Douglas,
>> >>>
>> >>>
>>  Le 25 janv. 2019 à 18:01, Greve, Douglas N.,Ph.D.
>>  mailto:dgr...@mgh.harvard.edu>> a
>> écrit :
>> 
>> 
>> 
>>  On 1/25/19 7:57 AM, Matthieu Vanhoutte wrote:
>> >
>> > External Email - Use Caution
>> >
>> > Dear Douglas,
>> >
>> > Could you precise me:
>> > 1) Is the intensity rescaling of PET image included in the
>> > mri_gtmpvc command based on reference region in gtmseg.mgz
>> > file rather than aseg.mgz ?
>>  It depends. If you are using pons, then that is not part of the
>>  aseg and is generated as part of the creation of gtmseg. But
>>  most of the rest of gtmseg is derived from the aseg and surfaces.
>> >>>
>> >>> Is it better to use gtmseg.mgz or aseg.mgz to extract reference
>> >>> region’s mean intensity ?
>> >>>
>> >>>
>> > 2) Is this rescaling applied before PVE correction or after
>> > (i.e. based on PVE corrected reference region’s mean intensity)
>> ?
>>  After
>> >
>> > Many thanks in advance for helping.
>> >
>> > Best,
>> > Matthieu
>> >
>> >> Le 7 janv. 2019 à 17:26, Greve, Douglas N.,Ph.D.
>> >> mailto:dgr...@mgh.harvard.edu>> a
>> >> écrit :
>> >>
>> >>
>> >>
>> >> On 1/7/19 11:18 AM, Matthieu Vanhoutte wrote:
>> >>>
>> >>> External Email - Use Caution
>> >>>
>> >>>
>> >>> I used the following command to obtain only rescaled
>> >>> voxel-wise PET image (with no PVC):
>> >>> /mri_gtmpvc --i PET.nii.gz --reg Pet2T1.register.dof6.lta
>> >>> --psf 0 --no-tfe --seg gtmseg.mgz --default-seg-merge
>> >>> --auto-mask PSF .01 --rbv --o  nopvc/
>> >>>
>> >>> If I omitted/--rbv/or/--mgx/option//I didn't get the
>> >>> rescaled voxel-wise PET image (without PVC). Could I obtain
>> >>> the rescaled voxel-wise PET image (without PVC) just by
>> >>> dividing each voxel of the native PET image by the mean of
>> >>> the reference region ?
>> >> Yes
>> >>>
>> >>> Best,
>> >>> Matt
>> >>>
>> >>> Le lun. 7 janv. 2019 à 16:01, Greve, Douglas N.,Ph.D.
>> >>> mailto:dgr...@mgh.harvard.edu>> a
>> >>> écrit :
>> >>>
>> >>> I'm not sure what you mean. If you are turning off PVC,
>> >>> why are you computing RBV and MGX? What is your command
>> >>> line? What do you mean that these options don't seem to
>> >>> work?
>> >>>
>> >>> On 12/21/18 2:22 PM, Matthieu Vanhoutte wrote:
>> 
>>  External Email - Use Caution
>> 
>>  Hi Douglas,
>> 
>>  Thanks for helping.
>> 
>>  To have an only rescaled voxel-wise PET image, these
>>  options seem to work only when -rbv method is used and
>>  not -mgx.
>> 
>>  Do you know why ?
>> 
>> 

Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

[Matthieu Vanhoutte]

External Email - Use Caution

Yes that's what I mean. But does this command provide an intensity
normalized voxel-wise image ?

Could you explain me the realign & reslice steps from the native PET to the
voxel-wise PVC PET for MGX ans RBV ?

Best,
Matthieu

Le jeu. 7 févr. 2019 à 23:06, Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> a écrit :

> Do you mean the mean intensity not corrected for PVC? I would just run
> mri_gtmpvc with --psf 0 --no-tfe to turn off PVC
>
> On 2/7/19 4:40 PM, Matthieu Vanhoutte wrote:
> >
> > External Email - Use Caution
> >
> > Hello experts,
> >
> > Anyone would have an advice on my previous questions ?
> >
> > Best,
> > Matthieu
> >
> >
> > Le mer. 30 janv. 2019 à 14:49, Matthieu Vanhoutte
> > mailto:matthieuvanhou...@gmail.com>> a
> > écrit :
> >
> > Hi Douglas,
> >
> > In order to apply intensity normalization to non-PVC PET images
> > based on mean intensity from reference region in gtmseg.mgz, is it
> > better to realign & reslice PET image onto gtmseg space or the
> > reverse way ? How is it done when dealing with PVC images using
> > gtmpvc command ?
> >
> > I would like to avoid too many reslicing operations before volume
> > to surface projection, how would you deal with it ?
> >
> > Best,
> > Matthieu
> >
> >> Le 28 janv. 2019 à 17:41, Greve, Douglas N.,Ph.D.
> >> mailto:dgr...@mgh.harvard.edu>> a écrit :
> >>
> >> If you intend to use one of the aseg structures, then they are
> >> the same.
> >>
> >> On 1/28/19 10:14 AM, Matthieu Vanhoutte wrote:
> >>>
> >>> External Email - Use Caution
> >>>
> >>> Hi Douglas,
> >>>
> >>>
>  Le 25 janv. 2019 à 18:01, Greve, Douglas N.,Ph.D.
>  mailto:dgr...@mgh.harvard.edu>> a écrit
> :
> 
> 
> 
>  On 1/25/19 7:57 AM, Matthieu Vanhoutte wrote:
> >
> > External Email - Use Caution
> >
> > Dear Douglas,
> >
> > Could you precise me:
> > 1) Is the intensity rescaling of PET image included in the
> > mri_gtmpvc command based on reference region in gtmseg.mgz
> > file rather than aseg.mgz ?
>  It depends. If you are using pons, then that is not part of the
>  aseg and is generated as part of the creation of gtmseg. But
>  most of the rest of gtmseg is derived from the aseg and surfaces.
> >>>
> >>> Is it better to use gtmseg.mgz or aseg.mgz to extract reference
> >>> region’s mean intensity ?
> >>>
> >>>
> > 2) Is this rescaling applied before PVE correction or after
> > (i.e. based on PVE corrected reference region’s mean intensity) ?
>  After
> >
> > Many thanks in advance for helping.
> >
> > Best,
> > Matthieu
> >
> >> Le 7 janv. 2019 à 17:26, Greve, Douglas N.,Ph.D.
> >> mailto:dgr...@mgh.harvard.edu>> a
> >> écrit :
> >>
> >>
> >>
> >> On 1/7/19 11:18 AM, Matthieu Vanhoutte wrote:
> >>>
> >>> External Email - Use Caution
> >>>
> >>>
> >>> I used the following command to obtain only rescaled
> >>> voxel-wise PET image (with no PVC):
> >>> /mri_gtmpvc --i PET.nii.gz --reg Pet2T1.register.dof6.lta
> >>> --psf 0 --no-tfe --seg gtmseg.mgz --default-seg-merge
> >>> --auto-mask PSF .01 --rbv --o  nopvc/
> >>>
> >>> If I omitted/--rbv/or/--mgx/option//I didn't get the
> >>> rescaled voxel-wise PET image (without PVC). Could I obtain
> >>> the rescaled voxel-wise PET image (without PVC) just by
> >>> dividing each voxel of the native PET image by the mean of
> >>> the reference region ?
> >> Yes
> >>>
> >>> Best,
> >>> Matt
> >>>
> >>> Le lun. 7 janv. 2019 à 16:01, Greve, Douglas N.,Ph.D.
> >>> mailto:dgr...@mgh.harvard.edu>> a
> >>> écrit :
> >>>
> >>> I'm not sure what you mean. If you are turning off PVC,
> >>> why are you computing RBV and MGX? What is your command
> >>> line? What do you mean that these options don't seem to
> >>> work?
> >>>
> >>> On 12/21/18 2:22 PM, Matthieu Vanhoutte wrote:
> 
>  External Email - Use Caution
> 
>  Hi Douglas,
> 
>  Thanks for helping.
> 
>  To have an only rescaled voxel-wise PET image, these
>  options seem to work only when -rbv method is used and
>  not -mgx.
> 
>  Do you know why ?
> 
>  Best,
>  Matthieu
> 
> 
>  Le mar. 18 déc. 2018 à 17:58, Greve, Douglas N.,Ph.D.
>    > a écrit :
> 
>  You will need to 

Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

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

Do you mean the mean intensity not corrected for PVC? I would just run 
mri_gtmpvc with --psf 0 --no-tfe to turn off PVC

On 2/7/19 4:40 PM, Matthieu Vanhoutte wrote:
>
> External Email - Use Caution
>
> Hello experts,
>
> Anyone would have an advice on my previous questions ?
>
> Best,
> Matthieu
>
>
> Le mer. 30 janv. 2019 à 14:49, Matthieu Vanhoutte 
> mailto:matthieuvanhou...@gmail.com>> a 
> écrit :
>
> Hi Douglas,
>
> In order to apply intensity normalization to non-PVC PET images
> based on mean intensity from reference region in gtmseg.mgz, is it
> better to realign & reslice PET image onto gtmseg space or the
> reverse way ? How is it done when dealing with PVC images using
> gtmpvc command ?
>
> I would like to avoid too many reslicing operations before volume
> to surface projection, how would you deal with it ?
>
> Best,
> Matthieu
>
>> Le 28 janv. 2019 à 17:41, Greve, Douglas N.,Ph.D.
>> mailto:dgr...@mgh.harvard.edu>> a écrit :
>>
>> If you intend to use one of the aseg structures, then they are
>> the same.
>>
>> On 1/28/19 10:14 AM, Matthieu Vanhoutte wrote:
>>>
>>> External Email - Use Caution
>>>
>>> Hi Douglas,
>>>
>>>
 Le 25 janv. 2019 à 18:01, Greve, Douglas N.,Ph.D.
 mailto:dgr...@mgh.harvard.edu>> a écrit :



 On 1/25/19 7:57 AM, Matthieu Vanhoutte wrote:
>
> External Email - Use Caution
>
> Dear Douglas,
>
> Could you precise me:
> 1) Is the intensity rescaling of PET image included in the
> mri_gtmpvc command based on reference region in gtmseg.mgz
> file rather than aseg.mgz ?
 It depends. If you are using pons, then that is not part of the
 aseg and is generated as part of the creation of gtmseg. But
 most of the rest of gtmseg is derived from the aseg and surfaces.
>>>
>>> Is it better to use gtmseg.mgz or aseg.mgz to extract reference
>>> region’s mean intensity ?
>>>
>>>
> 2) Is this rescaling applied before PVE correction or after
> (i.e. based on PVE corrected reference region’s mean intensity) ?
 After
>
> Many thanks in advance for helping.
>
> Best,
> Matthieu
>
>> Le 7 janv. 2019 à 17:26, Greve, Douglas N.,Ph.D.
>> mailto:dgr...@mgh.harvard.edu>> a
>> écrit :
>>
>>
>>
>> On 1/7/19 11:18 AM, Matthieu Vanhoutte wrote:
>>>
>>> External Email - Use Caution
>>>
>>>
>>> I used the following command to obtain only rescaled
>>> voxel-wise PET image (with no PVC):
>>> /mri_gtmpvc --i PET.nii.gz --reg Pet2T1.register.dof6.lta
>>> --psf 0 --no-tfe --seg gtmseg.mgz --default-seg-merge
>>> --auto-mask PSF .01 --rbv --o  nopvc/
>>>
>>> If I omitted/--rbv/or/--mgx/option//I didn't get the
>>> rescaled voxel-wise PET image (without PVC). Could I obtain
>>> the rescaled voxel-wise PET image (without PVC) just by
>>> dividing each voxel of the native PET image by the mean of
>>> the reference region ?
>> Yes
>>>
>>> Best,
>>> Matt
>>>
>>> Le lun. 7 janv. 2019 à 16:01, Greve, Douglas N.,Ph.D.
>>> mailto:dgr...@mgh.harvard.edu>> a
>>> écrit :
>>>
>>> I'm not sure what you mean. If you are turning off PVC,
>>> why are you computing RBV and MGX? What is your command
>>> line? What do you mean that these options don't seem to
>>> work?
>>>
>>> On 12/21/18 2:22 PM, Matthieu Vanhoutte wrote:

 External Email - Use Caution

 Hi Douglas,

 Thanks for helping.

 To have an only rescaled voxel-wise PET image, these
 options seem to work only when -rbv method is used and
 not -mgx.

 Do you know why ?

 Best,
 Matthieu


 Le mar. 18 déc. 2018 à 17:58, Greve, Douglas N.,Ph.D.
 >>> > a écrit :

 You will need to set --psf 0 and --no-tfe to fully
 turn off PVC.

 On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote:
>
> External Email - Use Caution
>
> Hi Douglas,
>
> Could you help me on this point ?
>
> Best,
> Matthieu
>
>
> Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte
>  > a écrit :
>
> Dear Douglas,
>

Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

[Matthieu Vanhoutte]

External Email - Use Caution

Hello experts,

Anyone would have an advice on my previous questions ?

Best,
Matthieu


Le mer. 30 janv. 2019 à 14:49, Matthieu Vanhoutte <
matthieuvanhou...@gmail.com> a écrit :

> Hi Douglas,
>
> In order to apply intensity normalization to non-PVC PET images based on
> mean intensity from reference region in gtmseg.mgz, is it better to realign
> & reslice PET image onto gtmseg space or the reverse way ? How is it done
> when dealing with PVC images using gtmpvc command ?
>
> I would like to avoid too many reslicing operations before volume to
> surface projection, how would you deal with it ?
>
> Best,
> Matthieu
>
> Le 28 janv. 2019 à 17:41, Greve, Douglas N.,Ph.D. 
> a écrit :
>
> If you intend to use one of the aseg structures, then they are the same.
>
> On 1/28/19 10:14 AM, Matthieu Vanhoutte wrote:
>
> External Email - Use Caution
> Hi Douglas,
>
>
> Le 25 janv. 2019 à 18:01, Greve, Douglas N.,Ph.D. 
> a écrit :
>
>
>
> On 1/25/19 7:57 AM, Matthieu Vanhoutte wrote:
>
> External Email - Use Caution
> Dear Douglas,
>
> Could you precise me:
> 1) Is the intensity rescaling of PET image included in the mri_gtmpvc
> command based on reference region in gtmseg.mgz file rather than aseg.mgz ?
>
> It depends. If you are using pons, then that is not part of the aseg and
> is generated as part of the creation of gtmseg. But most of the rest of
> gtmseg is derived from the aseg and surfaces.
>
>
> Is it better to use gtmseg.mgz or aseg.mgz to extract reference region’s
> mean intensity ?
>
>
> 2) Is this rescaling applied before PVE correction or after (i.e. based on
> PVE corrected reference region’s mean intensity) ?
>
> After
>
>
> Many thanks in advance for helping.
>
> Best,
> Matthieu
>
> Le 7 janv. 2019 à 17:26, Greve, Douglas N.,Ph.D. 
> a écrit :
>
>
>
> On 1/7/19 11:18 AM, Matthieu Vanhoutte wrote:
>
> External Email - Use Caution
>
> I used the following command to obtain only rescaled voxel-wise PET image
> (with no PVC):
> *mri_gtmpvc --i PET.nii.gz --reg Pet2T1.register.dof6.lta --psf 0 --no-tfe
> --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --rbv --o  nopvc*
>
> If I omitted *--rbv *or* --mgx* option I didn't get the rescaled
> voxel-wise PET image (without PVC). Could I obtain the rescaled voxel-wise
> PET image (without PVC) just by dividing each voxel of the native PET image
> by the mean of the reference region ?
>
> Yes
>
>
> Best,
> Matt
>
> Le lun. 7 janv. 2019 à 16:01, Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> a écrit :
>
>> I'm not sure what you mean. If you are turning off PVC, why are you
>> computing RBV and MGX? What is your command line? What do you mean that
>> these options don't seem to work?
>>
>> On 12/21/18 2:22 PM, Matthieu Vanhoutte wrote:
>>
>> External Email - Use Caution
>> Hi Douglas,
>>
>> Thanks for helping.
>>
>> To have an only rescaled voxel-wise PET image, these options seem to work
>> only when -rbv method is used and not -mgx.
>>
>> Do you know why ?
>>
>> Best,
>> Matthieu
>>
>>
>> Le mar. 18 déc. 2018 à 17:58, Greve, Douglas N.,Ph.D. <
>> dgr...@mgh.harvard.edu> a écrit :
>>
>>> You will need to set --psf 0 and --no-tfe to fully turn off PVC.
>>>
>>> On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote:
>>>
>>> External Email - Use Caution
>>> Hi Douglas,
>>>
>>> Could you help me on this point ?
>>>
>>> Best,
>>> Matthieu
>>>
>>>
>>> Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte <
>>> matthieuvanhou...@gmail.com> a écrit :
>>>
 Dear Douglas,

 Is it possible to use mri_gtmpvc command in order to intensity
 normalize PET images without applying PVE correction by setting --psf to 0 
 ?

 Best,
 Matthieu

>>>
>>>
>>> ___
>>> Freesurfer mailing 
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>>>
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>>
>>
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>> Freesurfer mailing 
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>>
>>
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>> Freesurfer mailing list
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>
>
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Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

[Matthieu Vanhoutte]

External Email - Use Caution

Hi Douglas,

Could you answer to my previous question ?

Best,
Matthieu

> Le 30 janv. 2019 à 14:48, Matthieu Vanhoutte  a 
> écrit :
> 
> Hi Douglas,
> 
> In order to apply intensity normalization to non-PVC PET images based on mean 
> intensity from reference region in gtmseg.mgz, is it better to realign & 
> reslice PET image onto gtmseg space or the reverse way ? How is it done when 
> dealing with PVC images using gtmpvc command ?
> 
> I would like to avoid too many reslicing operations before volume to surface 
> projection, how would you deal with it ?
> 
> Best,
> Matthieu
> 
>> Le 28 janv. 2019 à 17:41, Greve, Douglas N.,Ph.D. > > a écrit :
>> 
>> If you intend to use one of the aseg structures, then they are the same. 
>> 
>> On 1/28/19 10:14 AM, Matthieu Vanhoutte wrote:
>>> External Email - Use Caution
>>> 
>>> Hi Douglas,
>>> 
>>> 
 Le 25 janv. 2019 à 18:01, Greve, Douglas N.,Ph.D. >>> > a écrit :
 
 
 
 On 1/25/19 7:57 AM, Matthieu Vanhoutte wrote:
> External Email - Use Caution
> 
> Dear Douglas,
> 
> Could you precise me:
> 1) Is the intensity rescaling of PET image included in the mri_gtmpvc 
> command based on reference region in gtmseg.mgz file rather than aseg.mgz 
> ?
 It depends. If you are using pons, then that is not part of the aseg and 
 is generated as part of the creation of gtmseg. But most of the rest of 
 gtmseg is derived from the aseg and surfaces.
>>> 
>>> Is it better to use gtmseg.mgz or aseg.mgz to extract reference region’s 
>>> mean intensity ?
>>> 
>>> 
> 2) Is this rescaling applied before PVE correction or after (i.e. based 
> on PVE corrected reference region’s mean intensity) ?
 After
> 
> Many thanks in advance for helping.
> 
> Best,
> Matthieu
> 
>> Le 7 janv. 2019 à 17:26, Greve, Douglas N.,Ph.D. > > a écrit :
>> 
>> 
>> 
>> On 1/7/19 11:18 AM, Matthieu Vanhoutte wrote:
>>> External Email - Use Caution
>>> 
>>> 
>>> I used the following command to obtain only rescaled voxel-wise PET 
>>> image (with no PVC):
>>> mri_gtmpvc --i PET.nii.gz --reg Pet2T1.register.dof6.lta --psf 0 
>>> --no-tfe --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --rbv 
>>> --o  nopvc
>>> 
>>> If I omitted --rbv or --mgx option I didn't get the rescaled voxel-wise 
>>> PET image (without PVC). Could I obtain the rescaled voxel-wise PET 
>>> image (without PVC) just by dividing each voxel of the native PET image 
>>> by the mean of the reference region ?
>> Yes
>>> 
>>> Best,
>>> Matt
>>> 
>>> Le lun. 7 janv. 2019 à 16:01, Greve, Douglas N.,Ph.D. 
>>> mailto:dgr...@mgh.harvard.edu>> a écrit :
>>> I'm not sure what you mean. If you are turning off PVC, why are you 
>>> computing RBV and MGX? What is your command line? What do you mean that 
>>> these options don't seem to work?
>>> 
>>> On 12/21/18 2:22 PM, Matthieu Vanhoutte wrote:
 External Email - Use Caution
 
 Hi Douglas,
 
 Thanks for helping.
 
 To have an only rescaled voxel-wise PET image, these options seem to 
 work only when -rbv method is used and not -mgx.
 
 Do you know why ?
 
 Best,
 Matthieu 
 
 
 Le mar. 18 déc. 2018 à 17:58, Greve, Douglas N.,Ph.D. 
 mailto:dgr...@mgh.harvard.edu>> a écrit :
 You will need to set --psf 0 and --no-tfe to fully turn off PVC. 
 
 On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote:
> External Email - Use Caution
> 
> Hi Douglas,
> 
> Could you help me on this point ?
> 
> Best,
> Matthieu
> 
> 
> Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte 
> mailto:matthieuvanhou...@gmail.com>> a 
> écrit :
> Dear Douglas,
> 
> Is it possible to use mri_gtmpvc command in order to intensity 
> normalize PET images without applying PVE correction by setting --psf 
> to 0 ?
> 
> Best,
> Matthieu
> 
> 
> ___
> Freesurfer mailing list
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> 
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu 
 

Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

[Matthieu Vanhoutte]

External Email - Use Caution

Hi Douglas,

In order to apply intensity normalization to non-PVC PET images based on mean 
intensity from reference region in gtmseg.mgz, is it better to realign & 
reslice PET image onto gtmseg space or the reverse way ? How is it done when 
dealing with PVC images using gtmpvc command ?

I would like to avoid too many reslicing operations before volume to surface 
projection, how would you deal with it ?

Best,
Matthieu

> Le 28 janv. 2019 à 17:41, Greve, Douglas N.,Ph.D.  a 
> écrit :
> 
> If you intend to use one of the aseg structures, then they are the same. 
> 
> On 1/28/19 10:14 AM, Matthieu Vanhoutte wrote:
>> External Email - Use Caution
>> 
>> Hi Douglas,
>> 
>> 
>>> Le 25 janv. 2019 à 18:01, Greve, Douglas N.,Ph.D. >> > a écrit :
>>> 
>>> 
>>> 
>>> On 1/25/19 7:57 AM, Matthieu Vanhoutte wrote:
 External Email - Use Caution
 
 Dear Douglas,
 
 Could you precise me:
 1) Is the intensity rescaling of PET image included in the mri_gtmpvc 
 command based on reference region in gtmseg.mgz file rather than aseg.mgz ?
>>> It depends. If you are using pons, then that is not part of the aseg and is 
>>> generated as part of the creation of gtmseg. But most of the rest of gtmseg 
>>> is derived from the aseg and surfaces.
>> 
>> Is it better to use gtmseg.mgz or aseg.mgz to extract reference region’s 
>> mean intensity ?
>> 
>> 
 2) Is this rescaling applied before PVE correction or after (i.e. based on 
 PVE corrected reference region’s mean intensity) ?
>>> After
 
 Many thanks in advance for helping.
 
 Best,
 Matthieu
 
> Le 7 janv. 2019 à 17:26, Greve, Douglas N.,Ph.D.  > a écrit :
> 
> 
> 
> On 1/7/19 11:18 AM, Matthieu Vanhoutte wrote:
>> External Email - Use Caution
>> 
>> 
>> I used the following command to obtain only rescaled voxel-wise PET 
>> image (with no PVC):
>> mri_gtmpvc --i PET.nii.gz --reg Pet2T1.register.dof6.lta --psf 0 
>> --no-tfe --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --rbv 
>> --o  nopvc
>> 
>> If I omitted --rbv or --mgx option I didn't get the rescaled voxel-wise 
>> PET image (without PVC). Could I obtain the rescaled voxel-wise PET 
>> image (without PVC) just by dividing each voxel of the native PET image 
>> by the mean of the reference region ?
> Yes
>> 
>> Best,
>> Matt
>> 
>> Le lun. 7 janv. 2019 à 16:01, Greve, Douglas N.,Ph.D. 
>> mailto:dgr...@mgh.harvard.edu>> a écrit :
>> I'm not sure what you mean. If you are turning off PVC, why are you 
>> computing RBV and MGX? What is your command line? What do you mean that 
>> these options don't seem to work?
>> 
>> On 12/21/18 2:22 PM, Matthieu Vanhoutte wrote:
>>> External Email - Use Caution
>>> 
>>> Hi Douglas,
>>> 
>>> Thanks for helping.
>>> 
>>> To have an only rescaled voxel-wise PET image, these options seem to 
>>> work only when -rbv method is used and not -mgx.
>>> 
>>> Do you know why ?
>>> 
>>> Best,
>>> Matthieu 
>>> 
>>> 
>>> Le mar. 18 déc. 2018 à 17:58, Greve, Douglas N.,Ph.D. 
>>> mailto:dgr...@mgh.harvard.edu>> a écrit :
>>> You will need to set --psf 0 and --no-tfe to fully turn off PVC. 
>>> 
>>> On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote:
 External Email - Use Caution
 
 Hi Douglas,
 
 Could you help me on this point ?
 
 Best,
 Matthieu
 
 
 Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte 
 mailto:matthieuvanhou...@gmail.com>> a 
 écrit :
 Dear Douglas,
 
 Is it possible to use mri_gtmpvc command in order to intensity 
 normalize PET images without applying PVE correction by setting --psf 
 to 0 ?
 
 Best,
 Matthieu
 
 
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Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

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

If you intend to use one of the aseg structures, then they are the same.

On 1/28/19 10:14 AM, Matthieu Vanhoutte wrote:

External Email - Use Caution

Hi Douglas,


Le 25 janv. 2019 à 18:01, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> a écrit :



On 1/25/19 7:57 AM, Matthieu Vanhoutte wrote:

External Email - Use Caution

Dear Douglas,

Could you precise me:
1) Is the intensity rescaling of PET image included in the mri_gtmpvc command 
based on reference region in gtmseg.mgz file rather than aseg.mgz ?
It depends. If you are using pons, then that is not part of the aseg and is 
generated as part of the creation of gtmseg. But most of the rest of gtmseg is 
derived from the aseg and surfaces.

Is it better to use gtmseg.mgz or aseg.mgz to extract reference region’s mean 
intensity ?


2) Is this rescaling applied before PVE correction or after (i.e. based on PVE 
corrected reference region’s mean intensity) ?
After

Many thanks in advance for helping.

Best,
Matthieu

Le 7 janv. 2019 à 17:26, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> a écrit :



On 1/7/19 11:18 AM, Matthieu Vanhoutte wrote:

External Email - Use Caution

I used the following command to obtain only rescaled voxel-wise PET image (with 
no PVC):
mri_gtmpvc --i PET.nii.gz --reg Pet2T1.register.dof6.lta --psf 0 --no-tfe --seg 
gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --rbv --o  nopvc

If I omitted --rbv or --mgx option I didn't get the rescaled voxel-wise PET 
image (without PVC). Could I obtain the rescaled voxel-wise PET image (without 
PVC) just by dividing each voxel of the native PET image by the mean of the 
reference region ?
Yes

Best,
Matt

Le lun. 7 janv. 2019 à 16:01, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> a écrit :
I'm not sure what you mean. If you are turning off PVC, why are you computing 
RBV and MGX? What is your command line? What do you mean that these options 
don't seem to work?

On 12/21/18 2:22 PM, Matthieu Vanhoutte wrote:

External Email - Use Caution

Hi Douglas,

Thanks for helping.

To have an only rescaled voxel-wise PET image, these options seem to work only 
when -rbv method is used and not -mgx.

Do you know why ?

Best,
Matthieu


Le mar. 18 déc. 2018 à 17:58, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> a écrit :
You will need to set --psf 0 and --no-tfe to fully turn off PVC.

On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote:

External Email - Use Caution

Hi Douglas,

Could you help me on this point ?

Best,
Matthieu


Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte 
mailto:matthieuvanhou...@gmail.com>> a écrit :
Dear Douglas,

Is it possible to use mri_gtmpvc command in order to intensity normalize PET 
images without applying PVE correction by setting --psf to 0 ?

Best,
Matthieu



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Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

[Matthieu Vanhoutte]

External Email - Use Caution

Hi Douglas,


> Le 25 janv. 2019 à 18:01, Greve, Douglas N.,Ph.D.  a 
> écrit :
> 
> 
> 
> On 1/25/19 7:57 AM, Matthieu Vanhoutte wrote:
>> External Email - Use Caution
>> 
>> Dear Douglas,
>> 
>> Could you precise me:
>> 1) Is the intensity rescaling of PET image included in the mri_gtmpvc 
>> command based on reference region in gtmseg.mgz file rather than aseg.mgz ?
> It depends. If you are using pons, then that is not part of the aseg and is 
> generated as part of the creation of gtmseg. But most of the rest of gtmseg 
> is derived from the aseg and surfaces.

Is it better to use gtmseg.mgz or aseg.mgz to extract reference region’s mean 
intensity ?


>> 2) Is this rescaling applied before PVE correction or after (i.e. based on 
>> PVE corrected reference region’s mean intensity) ?
> After
>> 
>> Many thanks in advance for helping.
>> 
>> Best,
>> Matthieu
>> 
>>> Le 7 janv. 2019 à 17:26, Greve, Douglas N.,Ph.D. >> > a écrit :
>>> 
>>> 
>>> 
>>> On 1/7/19 11:18 AM, Matthieu Vanhoutte wrote:
 External Email - Use Caution
 
 
 I used the following command to obtain only rescaled voxel-wise PET image 
 (with no PVC):
 mri_gtmpvc --i PET.nii.gz --reg Pet2T1.register.dof6.lta --psf 0 --no-tfe 
 --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --rbv --o  nopvc
 
 If I omitted --rbv or --mgx option I didn't get the rescaled voxel-wise 
 PET image (without PVC). Could I obtain the rescaled voxel-wise PET image 
 (without PVC) just by dividing each voxel of the native PET image by the 
 mean of the reference region ?
>>> Yes
 
 Best,
 Matt
 
 Le lun. 7 janv. 2019 à 16:01, Greve, Douglas N.,Ph.D. 
 mailto:dgr...@mgh.harvard.edu>> a écrit :
 I'm not sure what you mean. If you are turning off PVC, why are you 
 computing RBV and MGX? What is your command line? What do you mean that 
 these options don't seem to work?
 
 On 12/21/18 2:22 PM, Matthieu Vanhoutte wrote:
> External Email - Use Caution
> 
> Hi Douglas,
> 
> Thanks for helping.
> 
> To have an only rescaled voxel-wise PET image, these options seem to work 
> only when -rbv method is used and not -mgx.
> 
> Do you know why ?
> 
> Best,
> Matthieu 
> 
> 
> Le mar. 18 déc. 2018 à 17:58, Greve, Douglas N.,Ph.D. 
> mailto:dgr...@mgh.harvard.edu>> a écrit :
> You will need to set --psf 0 and --no-tfe to fully turn off PVC. 
> 
> On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote:
>> External Email - Use Caution
>> 
>> Hi Douglas,
>> 
>> Could you help me on this point ?
>> 
>> Best,
>> Matthieu
>> 
>> 
>> Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte 
>> mailto:matthieuvanhou...@gmail.com>> a 
>> écrit :
>> Dear Douglas,
>> 
>> Is it possible to use mri_gtmpvc command in order to intensity normalize 
>> PET images without applying PVE correction by setting --psf to 0 ?
>> 
>> Best,
>> Matthieu
>> 
>> 
>> ___
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
>> 
> ___
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> 
> 
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>>> ___
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>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
>>> 
>> 
>> 

Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

[Matthieu Vanhoutte]

External Email - Use Caution

Hi Douglas,

Please find comments inline below.

best,
Matthieu

> Le 25 janv. 2019 à 18:01, Greve, Douglas N.,Ph.D.  a 
> écrit :
> 
> 
> 
> On 1/25/19 7:57 AM, Matthieu Vanhoutte wrote:
>> External Email - Use Caution
>> 
>> Dear Douglas,
>> 
>> Could you precise me:
>> 1) Is the intensity rescaling of PET image included in the mri_gtmpvc 
>> command based on reference region in gtmseg.mgz file rather than aseg.mgz ?
> It depends. If you are using pons, then that is not part of the aseg and is 
> generated as part of the creation of gtmseg. But most of the rest of gtmseg 
> is derived from the aseg and surfaces.
>> 2) Is this rescaling applied before PVE correction or after (i.e. based on 
>> PVE corrected reference region’s mean intensity) ?
> After

Thank you for this clarification. But do you use mean PET signal inside the 
reference region after the PVE correction, since in the particular case of pons 
there is no PVE correction applied to white matter ?

Do you see any objection whether intensity normalization was done before PVE 
correction based on the mean PET signal inside the reference region ?

>> 
>> Many thanks in advance for helping.
>> 
>> Best,
>> Matthieu
>> 
>>> Le 7 janv. 2019 à 17:26, Greve, Douglas N.,Ph.D. >> > a écrit :
>>> 
>>> 
>>> 
>>> On 1/7/19 11:18 AM, Matthieu Vanhoutte wrote:
 External Email - Use Caution
 
 
 I used the following command to obtain only rescaled voxel-wise PET image 
 (with no PVC):
 mri_gtmpvc --i PET.nii.gz --reg Pet2T1.register.dof6.lta --psf 0 --no-tfe 
 --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --rbv --o  nopvc
 
 If I omitted --rbv or --mgx option I didn't get the rescaled voxel-wise 
 PET image (without PVC). Could I obtain the rescaled voxel-wise PET image 
 (without PVC) just by dividing each voxel of the native PET image by the 
 mean of the reference region ?
>>> Yes
 
 Best,
 Matt
 
 Le lun. 7 janv. 2019 à 16:01, Greve, Douglas N.,Ph.D. 
 mailto:dgr...@mgh.harvard.edu>> a écrit :
 I'm not sure what you mean. If you are turning off PVC, why are you 
 computing RBV and MGX? What is your command line? What do you mean that 
 these options don't seem to work?
 
 On 12/21/18 2:22 PM, Matthieu Vanhoutte wrote:
> External Email - Use Caution
> 
> Hi Douglas,
> 
> Thanks for helping.
> 
> To have an only rescaled voxel-wise PET image, these options seem to work 
> only when -rbv method is used and not -mgx.
> 
> Do you know why ?
> 
> Best,
> Matthieu 
> 
> 
> Le mar. 18 déc. 2018 à 17:58, Greve, Douglas N.,Ph.D. 
> mailto:dgr...@mgh.harvard.edu>> a écrit :
> You will need to set --psf 0 and --no-tfe to fully turn off PVC. 
> 
> On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote:
>> External Email - Use Caution
>> 
>> Hi Douglas,
>> 
>> Could you help me on this point ?
>> 
>> Best,
>> Matthieu
>> 
>> 
>> Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte 
>> mailto:matthieuvanhou...@gmail.com>> a 
>> écrit :
>> Dear Douglas,
>> 
>> Is it possible to use mri_gtmpvc command in order to intensity normalize 
>> PET images without applying PVE correction by setting --psf to 0 ?
>> 
>> Best,
>> Matthieu
>> 
>> 
>> ___
>> Freesurfer mailing list
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>> 
> ___
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> 
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Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

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

On 1/25/19 7:57 AM, Matthieu Vanhoutte wrote:

External Email - Use Caution

Dear Douglas,

Could you precise me:
1) Is the intensity rescaling of PET image included in the mri_gtmpvc command 
based on reference region in gtmseg.mgz file rather than aseg.mgz ?
It depends. If you are using pons, then that is not part of the aseg and is 
generated as part of the creation of gtmseg. But most of the rest of gtmseg is 
derived from the aseg and surfaces.
2) Is this rescaling applied before PVE correction or after (i.e. based on PVE 
corrected reference region’s mean intensity) ?
After

Many thanks in advance for helping.

Best,
Matthieu

Le 7 janv. 2019 à 17:26, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> a écrit :



On 1/7/19 11:18 AM, Matthieu Vanhoutte wrote:

External Email - Use Caution

I used the following command to obtain only rescaled voxel-wise PET image (with 
no PVC):
mri_gtmpvc --i PET.nii.gz --reg Pet2T1.register.dof6.lta --psf 0 --no-tfe --seg 
gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --rbv --o  nopvc

If I omitted --rbv or --mgx option I didn't get the rescaled voxel-wise PET 
image (without PVC). Could I obtain the rescaled voxel-wise PET image (without 
PVC) just by dividing each voxel of the native PET image by the mean of the 
reference region ?
Yes

Best,
Matt

Le lun. 7 janv. 2019 à 16:01, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> a écrit :
I'm not sure what you mean. If you are turning off PVC, why are you computing 
RBV and MGX? What is your command line? What do you mean that these options 
don't seem to work?

On 12/21/18 2:22 PM, Matthieu Vanhoutte wrote:

External Email - Use Caution

Hi Douglas,

Thanks for helping.

To have an only rescaled voxel-wise PET image, these options seem to work only 
when -rbv method is used and not -mgx.

Do you know why ?

Best,
Matthieu


Le mar. 18 déc. 2018 à 17:58, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> a écrit :
You will need to set --psf 0 and --no-tfe to fully turn off PVC.

On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote:

External Email - Use Caution

Hi Douglas,

Could you help me on this point ?

Best,
Matthieu


Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte 
mailto:matthieuvanhou...@gmail.com>> a écrit :
Dear Douglas,

Is it possible to use mri_gtmpvc command in order to intensity normalize PET 
images without applying PVE correction by setting --psf to 0 ?

Best,
Matthieu



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Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

[Matthieu Vanhoutte]

External Email - Use Caution

Dear Douglas,

Could you precise me:
1) Is the intensity rescaling of PET image included in the mri_gtmpvc command 
based on reference region in gtmseg.mgz file rather than aseg.mgz ?
2) Is this rescaling applied before PVE correction or after (i.e. based on PVE 
corrected reference region’s mean intensity) ?

Many thanks in advance for helping.

Best,
Matthieu

> Le 7 janv. 2019 à 17:26, Greve, Douglas N.,Ph.D.  a 
> écrit :
> 
> 
> 
> On 1/7/19 11:18 AM, Matthieu Vanhoutte wrote:
>> External Email - Use Caution
>> 
>> 
>> I used the following command to obtain only rescaled voxel-wise PET image 
>> (with no PVC):
>> mri_gtmpvc --i PET.nii.gz --reg Pet2T1.register.dof6.lta --psf 0 --no-tfe 
>> --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --rbv --o  nopvc
>> 
>> If I omitted --rbv or --mgx option I didn't get the rescaled voxel-wise PET 
>> image (without PVC). Could I obtain the rescaled voxel-wise PET image 
>> (without PVC) just by dividing each voxel of the native PET image by the 
>> mean of the reference region ?
> Yes
>> 
>> Best,
>> Matt
>> 
>> Le lun. 7 janv. 2019 à 16:01, Greve, Douglas N.,Ph.D. 
>> mailto:dgr...@mgh.harvard.edu>> a écrit :
>> I'm not sure what you mean. If you are turning off PVC, why are you 
>> computing RBV and MGX? What is your command line? What do you mean that 
>> these options don't seem to work?
>> 
>> On 12/21/18 2:22 PM, Matthieu Vanhoutte wrote:
>>> External Email - Use Caution
>>> 
>>> Hi Douglas,
>>> 
>>> Thanks for helping.
>>> 
>>> To have an only rescaled voxel-wise PET image, these options seem to work 
>>> only when -rbv method is used and not -mgx.
>>> 
>>> Do you know why ?
>>> 
>>> Best,
>>> Matthieu 
>>> 
>>> 
>>> Le mar. 18 déc. 2018 à 17:58, Greve, Douglas N.,Ph.D. 
>>> mailto:dgr...@mgh.harvard.edu>> a écrit :
>>> You will need to set --psf 0 and --no-tfe to fully turn off PVC. 
>>> 
>>> On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote:
 External Email - Use Caution
 
 Hi Douglas,
 
 Could you help me on this point ?
 
 Best,
 Matthieu
 
 
 Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte 
 mailto:matthieuvanhou...@gmail.com>> a écrit 
 :
 Dear Douglas,
 
 Is it possible to use mri_gtmpvc command in order to intensity normalize 
 PET images without applying PVE correction by setting --psf to 0 ?
 
 Best,
 Matthieu
 
 
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
 
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>>> 
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Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

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

On 1/7/19 11:18 AM, Matthieu Vanhoutte wrote:

External Email - Use Caution

I used the following command to obtain only rescaled voxel-wise PET image (with 
no PVC):
mri_gtmpvc --i PET.nii.gz --reg Pet2T1.register.dof6.lta --psf 0 --no-tfe --seg 
gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --rbv --o  nopvc

If I omitted --rbv or --mgx option I didn't get the rescaled voxel-wise PET 
image (without PVC). Could I obtain the rescaled voxel-wise PET image (without 
PVC) just by dividing each voxel of the native PET image by the mean of the 
reference region ?
Yes

Best,
Matt

Le lun. 7 janv. 2019 à 16:01, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> a écrit :
I'm not sure what you mean. If you are turning off PVC, why are you computing 
RBV and MGX? What is your command line? What do you mean that these options 
don't seem to work?

On 12/21/18 2:22 PM, Matthieu Vanhoutte wrote:

External Email - Use Caution

Hi Douglas,

Thanks for helping.

To have an only rescaled voxel-wise PET image, these options seem to work only 
when -rbv method is used and not -mgx.

Do you know why ?

Best,
Matthieu


Le mar. 18 déc. 2018 à 17:58, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> a écrit :
You will need to set --psf 0 and --no-tfe to fully turn off PVC.

On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote:

External Email - Use Caution

Hi Douglas,

Could you help me on this point ?

Best,
Matthieu


Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte 
mailto:matthieuvanhou...@gmail.com>> a écrit :
Dear Douglas,

Is it possible to use mri_gtmpvc command in order to intensity normalize PET 
images without applying PVE correction by setting --psf to 0 ?

Best,
Matthieu



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Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

[Matthieu Vanhoutte]

External Email - Use Caution

I used the following command to obtain only rescaled voxel-wise PET image
(with no PVC):
*mri_gtmpvc --i PET.nii.gz --reg Pet2T1.register.dof6.lta --psf 0 --no-tfe
--seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --rbv --o  nopvc*

If I omitted *--rbv *or* --mgx* option I didn't get the rescaled voxel-wise
PET image (without PVC). Could I obtain the rescaled voxel-wise PET image
(without PVC) just by dividing each voxel of the native PET image by the
mean of the reference region ?

Best,
Matt

Le lun. 7 janv. 2019 à 16:01, Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> a écrit :

> I'm not sure what you mean. If you are turning off PVC, why are you
> computing RBV and MGX? What is your command line? What do you mean that
> these options don't seem to work?
>
> On 12/21/18 2:22 PM, Matthieu Vanhoutte wrote:
>
> External Email - Use Caution
> Hi Douglas,
>
> Thanks for helping.
>
> To have an only rescaled voxel-wise PET image, these options seem to work
> only when -rbv method is used and not -mgx.
>
> Do you know why ?
>
> Best,
> Matthieu
>
>
> Le mar. 18 déc. 2018 à 17:58, Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> a écrit :
>
>> You will need to set --psf 0 and --no-tfe to fully turn off PVC.
>>
>> On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote:
>>
>> External Email - Use Caution
>> Hi Douglas,
>>
>> Could you help me on this point ?
>>
>> Best,
>> Matthieu
>>
>>
>> Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte <
>> matthieuvanhou...@gmail.com> a écrit :
>>
>>> Dear Douglas,
>>>
>>> Is it possible to use mri_gtmpvc command in order to intensity normalize
>>> PET images without applying PVE correction by setting --psf to 0 ?
>>>
>>> Best,
>>> Matthieu
>>>
>>
>>
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Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

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

I'm not sure what you mean. If you are turning off PVC, why are you computing 
RBV and MGX? What is your command line? What do you mean that these options 
don't seem to work?

On 12/21/18 2:22 PM, Matthieu Vanhoutte wrote:

External Email - Use Caution

Hi Douglas,

Thanks for helping.

To have an only rescaled voxel-wise PET image, these options seem to work only 
when -rbv method is used and not -mgx.

Do you know why ?

Best,
Matthieu


Le mar. 18 déc. 2018 à 17:58, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> a écrit :
You will need to set --psf 0 and --no-tfe to fully turn off PVC.

On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote:

External Email - Use Caution

Hi Douglas,

Could you help me on this point ?

Best,
Matthieu


Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte 
mailto:matthieuvanhou...@gmail.com>> a écrit :
Dear Douglas,

Is it possible to use mri_gtmpvc command in order to intensity normalize PET 
images without applying PVE correction by setting --psf to 0 ?

Best,
Matthieu



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Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

[Matthieu Vanhoutte]

External Email - Use Caution

Hi Douglas,

Could you answer to my previous request ?

Best,
Matt

> Le 21 déc. 2018 à 20:22, Matthieu Vanhoutte  a 
> écrit :
> 
> Hi Douglas,
> 
> Thanks for helping.
> 
> To have an only rescaled voxel-wise PET image, these options seem to work 
> only when -rbv method is used and not -mgx.
> 
> Do you know why ?
> 
> Best,
> Matthieu 
> 
> 
> Le mar. 18 déc. 2018 à 17:58, Greve, Douglas N.,Ph.D.  > a écrit :
> You will need to set --psf 0 and --no-tfe to fully turn off PVC. 
> 
> On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote:
>> External Email - Use Caution
>> 
>> Hi Douglas,
>> 
>> Could you help me on this point ?
>> 
>> Best,
>> Matthieu
>> 
>> 
>> Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte 
>> mailto:matthieuvanhou...@gmail.com>> a écrit :
>> Dear Douglas,
>> 
>> Is it possible to use mri_gtmpvc command in order to intensity normalize PET 
>> images without applying PVE correction by setting --psf to 0 ?
>> 
>> Best,
>> Matthieu
>> 
>> 
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Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

[Matthieu Vanhoutte]

External Email - Use Caution

Hi Douglas,

Thanks for helping.

To have an only rescaled voxel-wise PET image, these options seem to work
only when -rbv method is used and not -mgx.

Do you know why ?

Best,
Matthieu


Le mar. 18 déc. 2018 à 17:58, Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> a écrit :

> You will need to set --psf 0 and --no-tfe to fully turn off PVC.
>
> On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote:
>
> External Email - Use Caution
> Hi Douglas,
>
> Could you help me on this point ?
>
> Best,
> Matthieu
>
>
> Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte <
> matthieuvanhou...@gmail.com> a écrit :
>
>> Dear Douglas,
>>
>> Is it possible to use mri_gtmpvc command in order to intensity normalize
>> PET images without applying PVE correction by setting --psf to 0 ?
>>
>> Best,
>> Matthieu
>>
>
>
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Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

[Matthieu Vanhoutte]

External Email - Use Caution

Hi Douglas,

Could you help me on this point ?

Best,
Matthieu


Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte <
matthieuvanhou...@gmail.com> a écrit :

> Dear Douglas,
>
> Is it possible to use mri_gtmpvc command in order to intensity normalize
> PET images without applying PVE correction by setting --psf to 0 ?
>
> Best,
> Matthieu
>
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[Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

[Matthieu Vanhoutte]

External Email - Use Caution

Dear Douglas,

Is it possible to use mri_gtmpvc command in order to intensity normalize
PET images without applying PVE correction by setting --psf to 0 ?

Best,
Matthieu
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