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Hi Douglas,
Could you answer to my previous question ?
Best, Matthieu
Le 30 janv. 2019 à 14:48, Matthieu Vanhoutte 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 CautionHi 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 CautionDear Douglas,
Could you precise me:
- 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 ?
- 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 >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 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 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 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 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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