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> 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>> 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.

>
>>> 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>>
>>>     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
>>>>>>>>>
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