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 <gr...@nmr.mgh.harvard.edu
<mailto:gr...@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"
<gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
> <mailto:gr...@nmr.mgh.harvard.edu
<mailto:gr...@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
> <gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>
<mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>
> > <mailto:gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>
> <mailto:gr...@nmr.mgh.harvard.edu
<mailto:gr...@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
> > > <matthieuvanhou...@gmail.com
<mailto:matthieuvanhou...@gmail.com>
> <mailto:matthieuvanhou...@gmail.com
<mailto:matthieuvanhou...@gmail.com>>
> > <mailto:matthieuvanhou...@gmail.com
<mailto:matthieuvanhou...@gmail.com>
> <mailto:matthieuvanhou...@gmail.com
<mailto:matthieuvanhou...@gmail.com>>>
> > <mailto:matthieuvanhou...@gmail.com
<mailto:matthieuvanhou...@gmail.com>
> <mailto:matthieuvanhou...@gmail.com
<mailto:matthieuvanhou...@gmail.com>>
> > <mailto:matthieuvanhou...@gmail.com
<mailto:matthieuvanhou...@gmail.com>
> <mailto:matthieuvanhou...@gmail.com
<mailto:matthieuvanhou...@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
normalisation for
> > PET images ?
> > >
> > What do you mean by intensity normalization? For uptake
> analysis,
> > people
> > usually use SUV (standard uptake values where the
whole image is
> > scaled
> > by a value related to the injection mass and subject
weight)
> or you
> > choose a reference structure to scale by (often called
rSUV for
> > 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>>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>>
> > >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > --
> >
> >
> > Best regards,
> > Matthieu
> >
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>
<mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>
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> >
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> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
<mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>
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<tel:617-726-7422>>
>
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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
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Fax: 617-726-7422
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