External Email - Use Caution
Hi Douglas,
Could you help me concerning my previous questions ?
Thanks, Matthieu
Le 11 févr. 2019 à 17:37, Matthieu VANHOUTTE matthieuvanhoutte@gmail.com a écrit :
Hi Douglas,
Thanks for clarification. Why use "nearest neighbor" instead of classical "trilinear" interpolation ?
Should it be done as well when projecting from volume to surface with mri_vol2surf ?
Best,
Matthieu
On 11/02/2019 17:32, Greve, Douglas N.,Ph.D. wrote:
It will not used trilinear interp. Try it with nearest neighbor
On 2/10/19 11:55 AM, Matthieu Vanhoutte wrote:
External Email - Use CautionDear Douglas,
Before using "mri_gtmpvc --psf 0 --no-tfe -- rbv" according your advice to obtain voxel-wise output rescaled without PVC correction, I have done sequentially the different steps to obtain this output. However, when comparing voxel-wise rescaled output (rbv.nii.gz) between the two methods, final values at each voxel are not the same…
To obtain first rescaled voxel-wise output I have used sequentially these steps:
- Concatenate transforms from PET space to gtmseg.mgz
- Register native PET into gtmseg space (trilin. interpolation)
- Compute mean PET inside reference regions (with regions masks from gtmseg.mgz)
- Compute intensity normalized PET images in gtmseg space
Doesn’t the "mri_gtmpvc --psf 0 --no-tfe -- rdv" command use these same steps ?
Best, Matthieu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The GTM operates on regions, so you can't do trilin interp. The operations that you describe below are not used in mri_gtmpvc. If you are trying to get something close to what the GTM does, then use nearest neighbor
On 2/14/19 3:43 AM, Matthieu Vanhoutte wrote:
External Email - Use CautionHi Douglas,
Could you help me concerning my previous questions ?
Thanks, Matthieu
Le 11 févr. 2019 à 17:37, Matthieu VANHOUTTE matthieuvanhoutte@gmail.com a écrit :
Hi Douglas,
Thanks for clarification. Why use "nearest neighbor" instead of classical "trilinear" interpolation ?
Should it be done as well when projecting from volume to surface with mri_vol2surf ?
Best,
Matthieu
On 11/02/2019 17:32, Greve, Douglas N.,Ph.D. wrote:
It will not used trilinear interp. Try it with nearest neighbor
On 2/10/19 11:55 AM, Matthieu Vanhoutte wrote:
External Email - Use CautionDear Douglas,
Before using "mri_gtmpvc --psf 0 --no-tfe -- rbv" according your advice to obtain voxel-wise output rescaled without PVC correction, I have done sequentially the different steps to obtain this output. However, when comparing voxel-wise rescaled output (rbv.nii.gz) between the two methods, final values at each voxel are not the same…
To obtain first rescaled voxel-wise output I have used sequentially these steps:
- Concatenate transforms from PET space to gtmseg.mgz
- Register native PET into gtmseg space (trilin. interpolation)
- Compute mean PET inside reference regions (with regions masks from gtmseg.mgz)
- Compute intensity normalized PET images in gtmseg space
Doesn’t the "mri_gtmpvc --psf 0 --no-tfe -- rdv" command use these same steps ?
Best, Matthieu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi Douglas,
So to register PET to gtmseg space mri_gtmpvc command use nearest neighbor, interpolation right ?
And what about the interpolation method to use when projecting PVE corrected PET on surface ?
Thanks,
Matthieu
On 14/02/2019 17:44, Greve, Douglas N.,Ph.D. wrote:
The GTM operates on regions, so you can't do trilin interp. The operations that you describe below are not used in mri_gtmpvc. If you are trying to get something close to what the GTM does, then use nearest neighbor
On 2/14/19 3:43 AM, Matthieu Vanhoutte wrote:
External Email - Use CautionHi Douglas,
Could you help me concerning my previous questions ?
Thanks, Matthieu
Le 11 févr. 2019 à 17:37, Matthieu VANHOUTTE matthieuvanhoutte@gmail.com a écrit :
Hi Douglas,
Thanks for clarification. Why use "nearest neighbor" instead of classical "trilinear" interpolation ?
Should it be done as well when projecting from volume to surface with mri_vol2surf ?
Best,
Matthieu
On 11/02/2019 17:32, Greve, Douglas N.,Ph.D. wrote:
It will not used trilinear interp. Try it with nearest neighbor
On 2/10/19 11:55 AM, Matthieu Vanhoutte wrote:
External Email - Use CautionDear Douglas,
Before using "mri_gtmpvc --psf 0 --no-tfe -- rbv" according your advice to obtain voxel-wise output rescaled without PVC correction, I have done sequentially the different steps to obtain this output. However, when comparing voxel-wise rescaled output (rbv.nii.gz) between the two methods, final values at each voxel are not the same…
To obtain first rescaled voxel-wise output I have used sequentially these steps:
- Concatenate transforms from PET space to gtmseg.mgz
- Register native PET into gtmseg space (trilin. interpolation)
- Compute mean PET inside reference regions (with regions masks from gtmseg.mgz)
- Compute intensity normalized PET images in gtmseg space
Doesn’t the "mri_gtmpvc --psf 0 --no-tfe -- rdv" command use these same steps ?
Best, Matthieu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
On 2/14/19 12:16 PM, Matthieu VANHOUTTE wrote:
External Email - Use CautionHi Douglas,
So to register PET to gtmseg space mri_gtmpvc command use nearest neighbor, interpolation right ?
It does not map the PET to the gtmseg space. It maps the gtmseg to the PET space. Since this is a segmentation, it uses nearest neighbor. But the algorithm is much more complicated; see the paper.
And what about the interpolation method to use when projecting PVE corrected PET on surface ?
I usually use nearest neighbor to avoid interpolation
Thanks,
Matthieu
On 14/02/2019 17:44, Greve, Douglas N.,Ph.D. wrote:
The GTM operates on regions, so you can't do trilin interp. The operations that you describe below are not used in mri_gtmpvc. If you are trying to get something close to what the GTM does, then use nearest neighbor
On 2/14/19 3:43 AM, Matthieu Vanhoutte wrote:
External Email - Use CautionHi Douglas,
Could you help me concerning my previous questions ?
Thanks, Matthieu
Le 11 févr. 2019 à 17:37, Matthieu VANHOUTTE matthieuvanhoutte@gmail.com a écrit :
Hi Douglas,
Thanks for clarification. Why use "nearest neighbor" instead of classical "trilinear" interpolation ?
Should it be done as well when projecting from volume to surface with mri_vol2surf ?
Best,
Matthieu
On 11/02/2019 17:32, Greve, Douglas N.,Ph.D. wrote:
It will not used trilinear interp. Try it with nearest neighbor
On 2/10/19 11:55 AM, Matthieu Vanhoutte wrote:
External Email - Use CautionDear Douglas,
Before using "mri_gtmpvc --psf 0 --no-tfe -- rbv" according your advice to obtain voxel-wise output rescaled without PVC correction, I have done sequentially the different steps to obtain this output. However, when comparing voxel-wise rescaled output (rbv.nii.gz) between the two methods, final values at each voxel are not the same…
To obtain first rescaled voxel-wise output I have used sequentially these steps:
- Concatenate transforms from PET space to gtmseg.mgz
- Register native PET into gtmseg space (trilin. interpolation)
- Compute mean PET inside reference regions (with regions masks from gtmseg.mgz)
- Compute intensity normalized PET images in gtmseg space
Doesn’t the "mri_gtmpvc --psf 0 --no-tfe -- rdv" command use these same steps ?
Best, Matthieu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Le jeu. 14 févr. 2019 à 18:31, Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> a écrit :
On 2/14/19 12:16 PM, Matthieu VANHOUTTE wrote:
External Email - Use CautionHi Douglas,
So to register PET to gtmseg space mri_gtmpvc command use nearest neighbor, interpolation right ?
It does not map the PET to the gtmseg space. It maps the gtmseg to the PET space. Since this is a segmentation, it uses nearest neighbor. But the algorithm is much more complicated; see the paper.
Thank you I will look into the paper, I was wondering how not to loose the gtmseg resolution ?
Concerning RBV PVC in which order and what type of interpolation are used since PVE corrected output is on gtmseg_space ?
And what about the interpolation method to use when projecting PVE corrected PET on surface ?
I usually use nearest neighbor to avoid interpolation
Should you precise this on PETSurfer wiki since on the mri_vol2surf command trilinear interpolation is used by default ?
Best.
Thanks,
Matthieu
On 14/02/2019 17:44, Greve, Douglas N.,Ph.D. wrote:
The GTM operates on regions, so you can't do trilin interp. The operations that you describe below are not used in mri_gtmpvc. If you are trying to get something close to what the GTM does, then use nearest neighbor
On 2/14/19 3:43 AM, Matthieu Vanhoutte wrote:
External Email - Use CautionHi Douglas,
Could you help me concerning my previous questions ?
Thanks, Matthieu
Le 11 févr. 2019 à 17:37, Matthieu VANHOUTTE <
matthieuvanhoutte@gmail.com> a écrit :
Hi Douglas,
Thanks for clarification. Why use "nearest neighbor" instead of
classical "trilinear" interpolation ?
Should it be done as well when projecting from volume to surface with
mri_vol2surf ?
Best,
Matthieu
On 11/02/2019 17:32, Greve, Douglas N.,Ph.D. wrote:
It will not used trilinear interp. Try it with nearest neighbor
On 2/10/19 11:55 AM, Matthieu Vanhoutte wrote: > External Email - Use Caution > > Dear Douglas, > > Before using "mri_gtmpvc --psf 0 --no-tfe -- rbv" according your
advice to obtain voxel-wise output rescaled without PVC correction, I have done sequentially the different steps to obtain this output. However, when comparing voxel-wise rescaled output (rbv.nii.gz) between the two methods, final values at each voxel are not the same…
> > To obtain first rescaled voxel-wise output I have used sequentially
these steps:
> 1. Concatenate transforms from PET space to gtmseg.mgz > 2. Register native PET into gtmseg space (trilin.
interpolation)
> 3. Compute mean PET inside reference regions (with regions
masks from gtmseg.mgz)
> 4. Compute intensity normalized PET images in gtmseg space > > Doesn’t the "mri_gtmpvc --psf 0 --no-tfe -- rdv" command use these
same steps ?
> > Best, > Matthieu > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
On 2/14/19 1:14 PM, Matthieu Vanhoutte wrote:
External Email - Use Caution
Le jeu. 14 févr. 2019 à 18:31, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> a écrit :
On 2/14/19 12:16 PM, Matthieu VANHOUTTE wrote: > External Email - Use Caution > > Hi Douglas, > > So to register PET to gtmseg space mri_gtmpvc command use nearest > neighbor, interpolation right ? It does not map the PET to the gtmseg space. It maps the gtmseg to the PET space. Since this is a segmentation, it uses nearest neighbor. But the algorithm is much more complicated; see the paper.Thank you I will look into the paper, I was wondering how not to loose the gtmseg resolution ?
I thought you wanted to turn off all PVC? If you want to correct for the tissue fraction effect, then don't use --no-tfe
Concerning RBV PVC in which order and what type of interpolation are used since PVE corrected output is on gtmseg_space ?
This question does not make sense in the context of RBV. Each ROI gets a value, and this value is then assigned to all the voxels in that ROI in gtmseg prior to apply the RBV algorithm.
> > And what about the interpolation method to use when projecting PVE > corrected PET on surface ? I usually use nearest neighbor to avoid interpolationShould you precise this on PETSurfer wiki since on the mri_vol2surf command trilinear interpolation is used by default ?
By default, mri_vol2surf uses nearest neighbor. mri_vol2vol uses trilin by default. An unfortunate inconsistency I made about 15 years ago and have been too afraid to change it:)
Best.
> > Thanks, > > Matthieu > > On 14/02/2019 17:44, Greve, Douglas N.,Ph.D. wrote: >> The GTM operates on regions, so you can't do trilin interp. The >> operations that you describe below are not used in mri_gtmpvc. If you >> are trying to get something close to what the GTM does, then use nearest >> neighbor >> >> On 2/14/19 3:43 AM, Matthieu Vanhoutte wrote: >>> External Email - Use Caution >>> >>> Hi Douglas, >>> >>> Could you help me concerning my previous questions ? >>> >>> Thanks, >>> Matthieu >>> >>>> Le 11 févr. 2019 à 17:37, Matthieu VANHOUTTE <matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> a écrit : >>>> >>>> Hi Douglas, >>>> >>>> Thanks for clarification. Why use "nearest neighbor" instead of classical "trilinear" interpolation ? >>>> >>>> Should it be done as well when projecting from volume to surface with mri_vol2surf ? >>>> >>>> Best, >>>> >>>> Matthieu >>>> >>>> On 11/02/2019 17:32, Greve, Douglas N.,Ph.D. wrote: >>>>> It will not used trilinear interp. Try it with nearest neighbor >>>>> >>>>> On 2/10/19 11:55 AM, Matthieu Vanhoutte wrote: >>>>>> External Email - Use Caution >>>>>> >>>>>> Dear Douglas, >>>>>> >>>>>> Before using "mri_gtmpvc --psf 0 --no-tfe -- rbv" according your advice to obtain voxel-wise output rescaled without PVC correction, I have done sequentially the different steps to obtain this output. However, when comparing voxel-wise rescaled output (rbv.nii.gz) between the two methods, final values at each voxel are not the same… >>>>>> >>>>>> To obtain first rescaled voxel-wise output I have used sequentially these steps: >>>>>> 1. Concatenate transforms from PET space to gtmseg.mgz >>>>>> 2. Register native PET into gtmseg space (trilin. interpolation) >>>>>> 3. Compute mean PET inside reference regions (with regions masks from gtmseg.mgz) >>>>>> 4. Compute intensity normalized PET images in gtmseg space >>>>>> >>>>>> Doesn’t the "mri_gtmpvc --psf 0 --no-tfe -- rdv" command use these same steps ? >>>>>> >>>>>> Best, >>>>>> Matthieu >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Le 14 févr. 2019 à 19:37, Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu a écrit :
On 2/14/19 1:14 PM, Matthieu Vanhoutte wrote:
External Email - Use CautionLe jeu. 14 févr. 2019 à 18:31, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> a écrit :
On 2/14/19 12:16 PM, Matthieu VANHOUTTE wrote:
External Email - Use CautionHi Douglas,
So to register PET to gtmseg space mri_gtmpvc command use nearest neighbor, interpolation right ?
It does not map the PET to the gtmseg space. It maps the gtmseg to the PET space. Since this is a segmentation, it uses nearest neighbor. But the algorithm is much more complicated; see the paper.
Thank you I will look into the paper, I was wondering how not to loose the gtmseg resolution ?
I thought you wanted to turn off all PVC? If you want to correct for the tissue fraction effect, then don't use --no-tfe
Oh, I had to miss something. I didn’t know PVC had several components, whose one is tissue fraction effect… What are the different corrections applied during PVC ? When papers mention no PVC they principally don’t correct for tissue fraction effect ?
I wanted to know what is the interest of computing a high resolution segmentation (gtmseg) if it goes to PET space and resliced to its lower resolution ?
Concerning RBV PVC in which order and what type of interpolation are used since PVE corrected output is on gtmseg_space ?
This question does not make sense in the context of RBV. Each ROI gets a value, and this value is then assigned to all the voxels in that ROI in gtmseg prior to apply the RBV algorithm.
Ok thank you, so in RBV case native PET is interpolated (trilinear?) first to gtmseg space ?
And what about the interpolation method to use when projecting PVE corrected PET on surface ?
I usually use nearest neighbor to avoid interpolation
Should you precise this on PETSurfer wiki since on the mri_vol2surf command trilinear interpolation is used by default ?
By default, mri_vol2surf uses nearest neighbor. mri_vol2vol uses trilin by default. An unfortunate inconsistency I made about 15 years ago and have been too afraid to change it:)
Thank you I didn’t know this one and supposed the trilinear as default as it is done in moi_vol2vol. Good to know it :)
Best.
Thanks,
Matthieu
On 14/02/2019 17:44, Greve, Douglas N.,Ph.D. wrote:
The GTM operates on regions, so you can't do trilin interp. The operations that you describe below are not used in mri_gtmpvc.
If you
are trying to get something close to what the GTM does, then
use nearest
neighbor
On 2/14/19 3:43 AM, Matthieu Vanhoutte wrote:
External Email - Use CautionHi Douglas,
Could you help me concerning my previous questions ?
Thanks, Matthieu
Le 11 févr. 2019 à 17:37, Matthieu VANHOUTTE
<matthieuvanhoutte@gmail.com mailto:matthieuvanhoutte@gmail.com> a écrit :
Hi Douglas,
Thanks for clarification. Why use "nearest neighbor" instead
of classical "trilinear" interpolation ?
Should it be done as well when projecting from volume to
surface with mri_vol2surf ?
Best,
Matthieu
On 11/02/2019 17:32, Greve, Douglas N.,Ph.D. wrote: > It will not used trilinear interp. Try it with nearest neighbor > > On 2/10/19 11:55 AM, Matthieu Vanhoutte wrote: >> External Email - Use Caution >> >> Dear Douglas, >> >> Before using "mri_gtmpvc --psf 0 --no-tfe -- rbv" according
your advice to obtain voxel-wise output rescaled without PVC correction, I have done sequentially the different steps to obtain this output. However, when comparing voxel-wise rescaled output (rbv.nii.gz) between the two methods, final values at each voxel are not the same…
>> >> To obtain first rescaled voxel-wise output I have used
sequentially these steps:
>> 1. Concatenate transforms from PET space to gtmseg.mgz >> 2. Register native PET into gtmseg space (trilin.
interpolation)
>> 3. Compute mean PET inside reference regions (with
regions masks from gtmseg.mgz)
>> 4. Compute intensity normalized PET images in gtmseg
space
>> >> Doesn’t the "mri_gtmpvc --psf 0 --no-tfe -- rdv" command
use these same steps ?
>> >> Best, >> Matthieu >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
On 2/14/19 2:25 PM, Matthieu Vanhoutte wrote:
External Email - Use CautionLe 14 févr. 2019 à 19:37, Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu a écrit :
On 2/14/19 1:14 PM, Matthieu Vanhoutte wrote:
External Email - Use CautionLe jeu. 14 févr. 2019 à 18:31, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> a écrit :
On 2/14/19 12:16 PM, Matthieu VANHOUTTE wrote:External Email - Use CautionHi Douglas,
So to register PET to gtmseg space mri_gtmpvc command use nearest neighbor, interpolation right ?
It does not map the PET to the gtmseg space. It maps the gtmseg to the PET space. Since this is a segmentation, it uses nearest neighbor. But the algorithm is much more complicated; see the paper.Thank you I will look into the paper, I was wondering how not to loose the gtmseg resolution ?
I thought you wanted to turn off all PVC? If you want to correct for the tissue fraction effect, then don't use --no-tfe
Oh, I had to miss something. I didn’t know PVC had several components, whose one is tissue fraction effect… What are the different corrections applied during PVC ?
Tissue fraction effect and correction for blur induced by the low res nature of pet. See the paper.
When papers mention no PVC they principally don’t correct for tissue fraction effect ?
I don't know. Generally, people don't give many details on their method.
I wanted to know what is the interest of computing a high resolution segmentation (gtmseg) if it goes to PET space and resliced to its lower resolution ?
As I said before, this is not what happens. PETsurfer takes the TFE into account. Please see the paper for how it is done.
Concerning RBV PVC in which order and what type of interpolation are used since PVE corrected output is on gtmseg_space ?
This question does not make sense in the context of RBV. Each ROI gets a value, and this value is then assigned to all the voxels in that ROI in gtmseg prior to apply the RBV algorithm.
Ok thank you, so in RBV case native PET is interpolated (trilinear?) first to gtmseg space ?
And what about the interpolation method to use when projecting PVE corrected PET on surface ?
I usually use nearest neighbor to avoid interpolationShould you precise this on PETSurfer wiki since on the mri_vol2surf command trilinear interpolation is used by default ?
By default, mri_vol2surf uses nearest neighbor. mri_vol2vol uses trilin by default. An unfortunate inconsistency I made about 15 years ago and have been too afraid to change it:)
Thank you I didn’t know this one and supposed the trilinear as default as it is done in moi_vol2vol. Good to know it :)
Best.
Thanks,
Matthieu
On 14/02/2019 17:44, Greve, Douglas N.,Ph.D. wrote:
The GTM operates on regions, so you can't do trilin interp. The operations that you describe below are not used in mri_gtmpvc.
If youare trying to get something close to what the GTM does, then
use nearestneighbor
On 2/14/19 3:43 AM, Matthieu Vanhoutte wrote:
External Email - Use CautionHi Douglas,
Could you help me concerning my previous questions ?
Thanks, Matthieu
> Le 11 févr. 2019 à 17:37, Matthieu VANHOUTTE
<matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> a écrit :> Hi Douglas, > > Thanks for clarification. Why use "nearest neighbor" instead
of classical "trilinear" interpolation ?> Should it be done as well when projecting from volume to
surface with mri_vol2surf ?> Best, > > Matthieu > > On 11/02/2019 17:32, Greve, Douglas N.,Ph.D. wrote: >> It will not used trilinear interp. Try it with nearest neighbor >> >> On 2/10/19 11:55 AM, Matthieu Vanhoutte wrote: >>> External Email - Use Caution >>> >>> Dear Douglas, >>> >>> Before using "mri_gtmpvc --psf 0 --no-tfe -- rbv" according
your advice to obtain voxel-wise output rescaled without PVC correction, I have done sequentially the different steps to obtain this output. However, when comparing voxel-wise rescaled output (rbv.nii.gz) between the two methods, final values at each voxel are not the same…>>> To obtain first rescaled voxel-wise output I have used
sequentially these steps:>>> 1. Concatenate transforms from PET space to gtmseg.mgz >>> 2. Register native PET into gtmseg space (trilin.
interpolation)>>> 3. Compute mean PET inside reference regions (with
regions masks from gtmseg.mgz)>>> 4. Compute intensity normalized PET images in gtmseg
space>>> Doesn’t the "mri_gtmpvc --psf 0 --no-tfe -- rdv" command
use these same steps ?>>> Best, >>> Matthieu >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu
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Le jeu. 14 févr. 2019 à 21:36, Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> a écrit :
On 2/14/19 2:25 PM, Matthieu Vanhoutte wrote:
External Email - Use CautionLe 14 févr. 2019 à 19:37, Greve, Douglas N.,Ph.D. <
DGREVE@mgh.harvard.edu> a écrit :
On 2/14/19 1:14 PM, Matthieu Vanhoutte wrote:
External Email - Use CautionLe jeu. 14 févr. 2019 à 18:31, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> a écrit :
On 2/14/19 12:16 PM, Matthieu VANHOUTTE wrote:External Email - Use CautionHi Douglas,
So to register PET to gtmseg space mri_gtmpvc command use nearest neighbor, interpolation right ?
It does not map the PET to the gtmseg space. It maps the gtmseg to the PET space. Since this is a segmentation, it uses nearest neighbor. But the algorithm is much more complicated; see the paper.Thank you I will look into the paper, I was wondering how not to loose the gtmseg resolution ?
I thought you wanted to turn off all PVC? If you want to correct for the tissue fraction effect, then don't use --no-tfe
Oh, I had to miss something. I didn’t know PVC had several components,
whose one is tissue fraction effect… What are the different corrections applied during PVC ? Tissue fraction effect and correction for blur induced by the low res nature of pet. See the paper.
When papers mention no PVC they principally don’t correct for tissue
fraction effect ? I don't know. Generally, people don't give many details on their method.
I wanted to know what is the interest of computing a high resolution
segmentation (gtmseg) if it goes to PET space and resliced to its lower resolution ? As I said before, this is not what happens. PETsurfer takes the TFE into account. Please see the paper for how it is done.
But in the case where --psf 0 --no-tfe are specified, isn't the high resolution of gtmseg lost when rescaling intensities to mean reference region ?
Concerning RBV PVC in which order and what type of interpolation are used since PVE corrected output is on gtmseg_space ?
This question does not make sense in the context of RBV. Each ROI gets a value, and this value is then assigned to all the voxels in that ROI in gtmseg prior to apply the RBV algorithm.
Ok thank you, so in RBV case native PET is interpolated (trilinear?)
first to gtmseg space ?
And what about the interpolation method to use when projecting PVE corrected PET on surface ?
I usually use nearest neighbor to avoid interpolationShould you precise this on PETSurfer wiki since on the mri_vol2surf command trilinear interpolation is used by default ?
By default, mri_vol2surf uses nearest neighbor. mri_vol2vol uses trilin by default. An unfortunate inconsistency I made about 15 years ago and have been too afraid to change it:)
Thank you I didn’t know this one and supposed the trilinear as default
as it is done in moi_vol2vol. Good to know it :)
Best.
Thanks,
Matthieu
On 14/02/2019 17:44, Greve, Douglas N.,Ph.D. wrote:
The GTM operates on regions, so you can't do trilin interp. The operations that you describe below are not used in mri_gtmpvc.
If youare trying to get something close to what the GTM does, then
use nearestneighbor
On 2/14/19 3:43 AM, Matthieu Vanhoutte wrote: > External Email - Use Caution > > Hi Douglas, > > Could you help me concerning my previous questions ? > > Thanks, > Matthieu > >> Le 11 févr. 2019 à 17:37, Matthieu VANHOUTTE
<matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> a écrit :>> Hi Douglas, >> >> Thanks for clarification. Why use "nearest neighbor" instead
of classical "trilinear" interpolation ?>> Should it be done as well when projecting from volume to
surface with mri_vol2surf ?>> Best, >> >> Matthieu >> >> On 11/02/2019 17:32, Greve, Douglas N.,Ph.D. wrote: >>> It will not used trilinear interp. Try it with nearest neighbor >>> >>> On 2/10/19 11:55 AM, Matthieu Vanhoutte wrote: >>>> External Email - Use Caution >>>> >>>> Dear Douglas, >>>> >>>> Before using "mri_gtmpvc --psf 0 --no-tfe -- rbv" according
your advice to obtain voxel-wise output rescaled without PVC correction, I have done sequentially the different steps to obtain this output. However, when comparing voxel-wise rescaled output (rbv.nii.gz) between the two methods, final values at each voxel are not the same…>>>> To obtain first rescaled voxel-wise output I have used
sequentially these steps:>>>> 1. Concatenate transforms from PET space to gtmseg.mgz >>>> 2. Register native PET into gtmseg space (trilin.
interpolation)>>>> 3. Compute mean PET inside reference regions (with
regions masks from gtmseg.mgz)>>>> 4. Compute intensity normalized PET images in gtmseg
space>>>> Doesn’t the "mri_gtmpvc --psf 0 --no-tfe -- rdv" command
use these same steps ?>>>> Best, >>>> Matthieu >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
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But in the case where --psf 0 --no-tfe are specified, isn't the high
resolution of gtmseg lost when rescaling intensities to mean reference region ? Yes
On 2/14/19 5:25 PM, Matthieu Vanhoutte wrote:
External Email - Use Caution
Le jeu. 14 févr. 2019 à 21:36, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> a écrit :
On 2/14/19 2:25 PM, Matthieu Vanhoutte wrote: > External Email - Use Caution > >> Le 14 févr. 2019 à 19:37, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> a écrit : >> >> >> >> On 2/14/19 1:14 PM, Matthieu Vanhoutte wrote: >>> External Email - Use Caution >>> >>> >>> >>> Le jeu. 14 févr. 2019 à 18:31, Greve, Douglas N.,Ph.D. >>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> a écrit : >>> >>> >>> >>> On 2/14/19 12:16 PM, Matthieu VANHOUTTE wrote: >>>> External Email - Use Caution >>>> >>>> Hi Douglas, >>>> >>>> So to register PET to gtmseg space mri_gtmpvc command use nearest >>>> neighbor, interpolation right ? >>> It does not map the PET to the gtmseg space. It maps the gtmseg to >>> the >>> PET space. Since this is a segmentation, it uses nearest neighbor. >>> But >>> the algorithm is much more complicated; see the paper. >>> >>> >>> Thank you I will look into the paper, I was wondering how not to loose >>> the gtmseg resolution ? >> I thought you wanted to turn off all PVC? If you want to correct for the >> tissue fraction effect, then don't use --no-tfe > Oh, I had to miss something. I didn’t know PVC had several components, whose one is tissue fraction effect… What are the different corrections applied during PVC ? Tissue fraction effect and correction for blur induced by the low res nature of pet. See the paper. > When papers mention no PVC they principally don’t correct for tissue fraction effect ? I don't know. Generally, people don't give many details on their method. > > I wanted to know what is the interest of computing a high resolution segmentation (gtmseg) if it goes to PET space and resliced to its lower resolution ? As I said before, this is not what happens. PETsurfer takes the TFE into account. Please see the paper for how it is done.But in the case where --psf 0 --no-tfe are specified, isn't the high resolution of gtmseg lost when rescaling intensities to mean reference region ?
> >>> Concerning RBV PVC in which order and what type of interpolation are >>> used since PVE corrected output is on gtmseg_space ? >> This question does not make sense in the context of RBV. Each ROI gets a >> value, and this value is then assigned to all the voxels in that ROI in >> gtmseg prior to apply the RBV algorithm. > Ok thank you, so in RBV case native PET is interpolated (trilinear?) first to gtmseg space ? > >>>> And what about the interpolation method to use when projecting PVE >>>> corrected PET on surface ? >>> I usually use nearest neighbor to avoid interpolation >>> >>> >>> Should you precise this on PETSurfer wiki since on the mri_vol2surf >>> command trilinear interpolation is used by default ? >> By default, mri_vol2surf uses nearest neighbor. mri_vol2vol uses trilin >> by default. An unfortunate inconsistency I made about 15 years ago and >> have been too afraid to change it:) > Thank you I didn’t know this one and supposed the trilinear as default as it is done in moi_vol2vol. Good to know it :) > >>> Best. >>> >>>> Thanks, >>>> >>>> Matthieu >>>> >>>> On 14/02/2019 17:44, Greve, Douglas N.,Ph.D. wrote: >>>>> The GTM operates on regions, so you can't do trilin interp. The >>>>> operations that you describe below are not used in mri_gtmpvc. >>> If you >>>>> are trying to get something close to what the GTM does, then >>> use nearest >>>>> neighbor >>>>> >>>>> On 2/14/19 3:43 AM, Matthieu Vanhoutte wrote: >>>>>> External Email - Use Caution >>>>>> >>>>>> Hi Douglas, >>>>>> >>>>>> Could you help me concerning my previous questions ? >>>>>> >>>>>> Thanks, >>>>>> Matthieu >>>>>> >>>>>>> Le 11 févr. 2019 à 17:37, Matthieu VANHOUTTE >>> <matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>> >>> a écrit : >>>>>>> Hi Douglas, >>>>>>> >>>>>>> Thanks for clarification. Why use "nearest neighbor" instead >>> of classical "trilinear" interpolation ? >>>>>>> Should it be done as well when projecting from volume to >>> surface with mri_vol2surf ? >>>>>>> Best, >>>>>>> >>>>>>> Matthieu >>>>>>> >>>>>>> On 11/02/2019 17:32, Greve, Douglas N.,Ph.D. wrote: >>>>>>>> It will not used trilinear interp. Try it with nearest neighbor >>>>>>>> >>>>>>>> On 2/10/19 11:55 AM, Matthieu Vanhoutte wrote: >>>>>>>>> External Email - Use Caution >>>>>>>>> >>>>>>>>> Dear Douglas, >>>>>>>>> >>>>>>>>> Before using "mri_gtmpvc --psf 0 --no-tfe -- rbv" according >>> your advice to obtain voxel-wise output rescaled without PVC >>> correction, I have done sequentially the different steps to obtain >>> this output. However, when comparing voxel-wise rescaled output >>> (rbv.nii.gz) between the two methods, final values at each voxel >>> are not the same… >>>>>>>>> To obtain first rescaled voxel-wise output I have used >>> sequentially these steps: >>>>>>>>> 1. Concatenate transforms from PET space to gtmseg.mgz >>>>>>>>> 2. Register native PET into gtmseg space (trilin. >>> interpolation) >>>>>>>>> 3. Compute mean PET inside reference regions (with >>> regions masks from gtmseg.mgz) >>>>>>>>> 4. Compute intensity normalized PET images in gtmseg >>> space >>>>>>>>> Doesn’t the "mri_gtmpvc --psf 0 --no-tfe -- rdv" command >>> use these same steps ? >>>>>>>>> Best, >>>>>>>>> Matthieu >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Freesurfer mailing list >>>>>>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>> _______________________________________________ >>>>>>>> Freesurfer mailing list >>>>>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Matthieu Vanhoutte -
Matthieu VANHOUTTE