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:
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Hi Douglas,
Le 25 janv. 2019 à 18:01, Greve, Douglas N.,Ph.D.
<dgr...@mgh.harvard.edu<mailto:dgr...@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.
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.
<dgr...@mgh.harvard.edu<mailto:dgr...@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.
<dgr...@mgh.harvard.edu<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:
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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.
<dgr...@mgh.harvard.edu<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:
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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
<matthieuvanhou...@gmail.com<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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