External Email - Use Caution
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
> <matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@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.
>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@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.
>>>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@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.
>>>>>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@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.
>>>>>>> <DGREVE@mgh.harvard.edu <mailto:DGREVE@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.
>>>>>>>> <DGREVE@mgh.harvard.edu
>>>>>>>> <mailto:DGREVE@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
>>>>>>>>> <matthieuvanhoutte@gmail.com
>>>>>>>>> <mailto:matthieuvanhoutte@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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