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Hi Douglas,
Any advice ?
Best.
Le jeu. 7 févr. 2019 à 23:12, Matthieu Vanhoutte < matthieuvanhoutte@gmail.com> a écrit :
Yes that's what I mean. But does this command provide an intensity normalized voxel-wise image ?
Could you explain me the realign & reslice steps from the native PET to the voxel-wise PVC PET for MGX ans RBV ?
Best, Matthieu
Le jeu. 7 févr. 2019 à 23:06, Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> a écrit :
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 CautionHello 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, MatthieuLe 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>> aécrit :
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 >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:
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