Dear Douglas,
Just one more question : by default mri_gtmpvc uses pons for computing rSUV, but is this intensity normalization done before or after partial volume correction ? What file is used in input for intensity normalization ?
Thanks in advance !
Best regards, Matthieu
2015-12-18 18:26 GMT+01:00 Douglas Greve greve@nmr.mgh.harvard.edu:
You'll see several files that begin with mgx: mgx.ctxgm.nii.gz - pvc'ed cortex gm only mgx.subctxgm.nii.gz - pvc'ed subcortical gm only mgx.gm.nii.gz - pvc'ed all gm
On 12/18/15 6:08 AM, Matthieu Vanhoutte wrote:
Hello Douglas,
I have run mri_gtmpvc with static PET images using the following command : mri_gtmpvc --i PET.nii.gz --psf 6 --auto-mask 8 0.01 --seg gtmseg.mgz --reg register.dof6.lta --default-seg-merge --mgx 0.01 --o gtmpvc.output
In the output directory "gtmpvc.output" where is the partial volume corrected PET image ?
Thanks !
Best regards, Matthieu
2015-12-15 21:07 GMT+01:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
Not necessarily. It needs a good segmentation, so, to the extent that v6 has a better segmentation then v6 is better.
On 12/15/2015 02:57 PM, Matthieu Vanhoutte wrote:
Thanks Douglas for the answer !
But isn't PVC design for better working in terms of results with v6_beta than v5.3 ?
Best regards,
Matthieu
Le 15 déc. 2015 19:02, "Douglas N Greve" < greve@nmr.mgh.harvard.edu
greve@nmr.mgh.harvard.edu
mailto:greve@nmr.mgh.harvard.edu> a écrit :
It is not subsegmented in 6.0 either:). When you run gtmseg, it will create the new segmentation that include pons and a few other things On 12/15/2015 12:56 PM, Matthieu Vanhoutte wrote: > Dear Douglas, > > Please see below : > > 2015-12-15 18:37 GMT+01:00 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto: <greve@nmr.mgh.harvard.edu>greve@nmr.mgh.harvard.edu>>>: > > > > On 12/15/2015 04:46 AM, Matthieu Vanhoutte wrote: > > Dear experts, > > > > Could anyone answer to my questions below ? > > > > Thanks ! > > > > Best regards, > > Matthieu > > > > 2015-12-10 10:10 GMT+01:00 Matthieu Vanhoutte > > <matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com> > <mailto:matthieuvanhoutte@gmail.com <mailto:matthieuvanhoutte@gmail.com>>>>: > > > > Dear FS experts, > > > > 1) First Is it possible to use the partial volume correction > > provided in the v6 beta version of FreeSurfer despite the fact > > that recon-all have been done for all subjects with the v5.3 ? > > > Yes > > > Great ! but isn't it a problem for computing rSUV with pons as > reference structure since brainstem isn't sub-segmented in the version > 5.3 of recon-all ? > > > > > > > 2) Does this method supply an intensity normalisationfor
> PET images ? > > > What do you mean by intensity normalization? For uptake analysis, > people > usually use SUV (standard uptake values where the whole imageis
> scaled > by a value related to the injection mass and subject weight) or you > choose a reference structure to scale by (often called rSUVfor
> relative). By default mri_gtmpvc uses pons, but you can choose any > structure you want with the --rescale flag > > > > > > > Best regards, > > Matthieu > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: <Freesurfer@nmr.mgh.harvard.edu>Freesurfer@nmr.mgh.harvard.edu>>
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.