The pons intensity used to normalize has been PVC'ed. The file used is
the input file.
On 01/11/2016 04:04 AM, Matthieu Vanhoutte wrote:
> 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
> <mailto: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 <mailto: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 <mailto:greve@nmr.mgh.harvard.edu>
>> > <mailto:greve@nmr.mgh.harvard.edu
>> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422>> <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>>
>> > > <mailto:greve@nmr.mgh.harvard.edu
>> <mailto:greve@nmr.mgh.harvard.edu>
>> > <mailto:greve@nmr.mgh.harvard.edu
>> <mailto: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>>>
>> > > <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
>> <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
>> 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
>> > > greve@nmr.mgh.harvard.edu
>> <mailto:greve@nmr.mgh.harvard.edu>
>> <mailto:greve@nmr.mgh.harvard.edu
>> <mailto:greve@nmr.mgh.harvard.edu>>
>> > <mailto:greve@nmr.mgh.harvard.edu
>> <mailto:greve@nmr.mgh.harvard.edu>
>> <mailto:greve@nmr.mgh.harvard.edu
>> <mailto:greve@nmr.mgh.harvard.edu>>>
>> > > Phone Number:617-724-2358 <tel:617-724-2358> <tel:617-724-2358
>> <tel:617-724-2358>>
>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358
>> <tel:617-724-2358>>>
>> > > Fax: 617-726-7422 <tel:617-726-7422>
>> <tel:617-726-7422>
>> > <tel:617-726-7422 <tel:617-726-7422>>>
>> > >
>> > > Bugs:
>> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>> > >
>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
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>> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>> >
>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>> > >
>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>> > > Outgoing:
>> > >
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>> > >
>> > > _______________________________________________
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>> > <mailto: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
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>> >
>> > --
>> > Douglas N. Greve, Ph.D.
>> > MGH-NMR Center
>> > greve@nmr.mgh.harvard.edu
>> <mailto:greve@nmr.mgh.harvard.edu>
>> <mailto:greve@nmr.mgh.harvard.edu
>> <mailto:greve@nmr.mgh.harvard.edu>>
>> > Phone Number: 617-724-2358 <tel:617-724-2358>
>> <tel:617-724-2358 <tel:617-724-2358>>
>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422
>> <tel:617-726-7422>>
>> >
>> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> <http://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>
>> >
>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>> > Outgoing:
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>> >
>> > _______________________________________________
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>> >
>> >
>> >
> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > _______________________________________________
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>>
>> --
>> 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
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>>
>>
>>
>>
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>
>
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>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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