Le 11/01/2016 20:33, Douglas N Greve a écrit :

On 01/11/2016 02:14 PM, Matthieu Vanhoutte wrote:
Dear Douglas,

Sorry if I wasn't clear. With the PVC, voxels intensities are modified,
right ?
Not necessarily. The GTM does not work this way. MG and RBV do. For an 
ROI analysis, the GTM is by far the preferred method.
I suppose I used MG method since I specified  --mgx option (I would like to do an entire cortex analysis) ?
With MG PVC, voxels intensities are the modified ?

Best regards,
Matthieu


      
So, in the case of anatomical intensity normalization based on
gray matter of cerebellum, is the mean activity of gray cerebellum taken
from the original PET image or from the PVC'ed PET image ?
Again, not the right question for GTM
Best regards,
Matthieu

Le 11/01/2016 18:52, Douglas N Greve a écrit :
I'm not sure exactly what you mean. I guess you could set all voxels in
a given ROI to be the value of that ROI? This is not really a voxel-wise
correction and probably would not do what you want. You can use the mgx
data (corrected with muller-gartner method). There is also a --rbv
(region-based voxel-wise, Thomas 2012) option.


On 01/11/2016 12:34 PM, Matthieu Vanhoutte wrote:
Dear Douglas,

If the pons intensity used to normalize has been PVC'ed, couldn't we
have an output of mri_gtmpvc with the whole brain PVC'ed ?

Because the only files on output of mri_gtmpvc are :
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

Best regards,
Matthieu

2016-01-11 18:20 GMT+01:00 Douglas N Greve <greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>:


      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>
      > <mailto: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>
      <mailto: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 <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>>>> 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>>>
      >>         >     > <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
      <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>>>>
      >>         >     >     <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
      <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>>>
      >>         >     >     <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
      <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>>>
      >>         >     <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
      <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>>>
      >>         >     <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 <tel:617-724-2358>>>>
      >>         >     >     Fax: 617-726-7422 <tel:617-726-7422>
      <tel:617-726-7422 <tel:617-726-7422>>
      >>         <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422
      <tel: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>
      >>         >     >
      >>          <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>
      >>         >
      >>
      <http://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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      <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>
      >>         <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
      >>         >     >
      >>         >     >
      >>         >     >     The information in this e-mail is intended only
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      >>         >     person to
      >>         >     >     whom it is
      >>         >     >     addressed. If you believe this e-mail was
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      >>         >     > _______________________________________________
      >>         >     > Freesurfer mailing list
      >>         >     > Freesurfer@nmr.mgh.harvard.edu
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      >>         <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
      >>         >
      >>         >     --
      >>         >     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>>
      >>         >     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>
      >>         >
       <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>
      >>         >
      >>
      <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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      >>         <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
      >>         >
      >>         >
      >>         >
      >>         > _______________________________________________
      >>         > Freesurfer mailing list
      >>         > Freesurfer@nmr.mgh.harvard.edu
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      <mailto:Freesurfer@nmr.mgh.harvard.edu>>
      >>         >
      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>
      <mailto: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>
      >>         <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:
      >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
      >>
      >>  _______________________________________________
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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 <mailto:greve@nmr.mgh.harvard.edu>
      Phone Number: 617-724-2358
      Fax: 617-726-7422

      Bugs: 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>
      Outgoing:
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