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

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

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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. <DGREVE@mgh.harvard.edu> a écrit :

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

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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> 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:

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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> 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:

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Hi Douglas,

Could you help me on this point ?

Best,

Matthieu

Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte <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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