which "native" space? the pet native? the anatomical native?

On 08/09/2016 05:46 PM, Pradeep wrote:
> Hello Doug,
>
> The aux/seg.nii image which has all the ROI's defined does not seem to
> be in the subject's native space or the CVS template space.
>
> How do I bring it to the subjects native space?
>
> Thanks,
> Pradeep
>
> Screenshot from 2016-08-09 14:42:10.png
>
> On Tue, Jul 19, 2016 at 5:03 PM Pradeep <tpradeep@gmail.com
> <mailto:tpradeep@gmail.com>> wrote:
>
>     Thanks responding Doug!
>
>     I am interested us using centrum semiovale as reference region. Is
>     there a way I can save the unsegmented white matter [5001& 5002]
>     during the gtmseg step or what would be its equivalent label in
>     the gtm_pvc results table?
>
>     Thanks,
>     Pradeep
>
>     On Thu, Jul 7, 2016 at 11:20 AM Douglas N Greve
>     <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
>
>
>         On 06/20/2016 08:25 PM, Pradeep wrote:
>         > Hello Freesrufer Team,
>         >
>         > I am trying to use the Partial volume correction procedure
>         implemented
>         > in the freesurfer 6 beta version and have a few questions.
>         >
>         > In your recent Neuroimaging paper, the left and right
>         hemispheres were
>         > combined by taking the average of the two as they did not
>         show any
>         > age-by-hemisphere interaction.
>         >
>         > I might have interpreted the Supplementary figure 1
>         incorrectly, but
>         > the Geometric transfer matrix seem to show around 52 ROI's,
>         So were
>         > the L and R ROIs combined for the PVC results you reported
>         in  that
>         > paper? Or were the same 52 used for the general PVC in the
>         FS pipeline?
>         They were combined only after the PVC calculation. For the
>         figure, I
>         changed the GTM to show the combined GTM.
>         >
>         > Do you have any concrete results to examine the effects of
>         the size
>         > variation over the ROIs used for PVC?
>         Not sure what you mean here. You can get the variance
>         reduction factor
>         for each ROI in the gtm.stats.dat file. This indicates how
>         much noise
>         reduction you can expect (assuming gaussian noise, etc) in
>         each ROI
>         given the size and anatomical distribution of the ROIs and PSF.
>         > Should a threshold be set for the sizes of these ROIs?
>         What do you mean?
>         >
>         > How were the white matter hypo-intensities dealt with while
>         generating
>         > the ROI masks?
>         I merged them with WM. I tried it with and without, and it did
>         not make
>         much of a difference.
>         doug
>         >
>         >
>         > Thanks,
>         > Pradeep
>         >
>         >
>         >
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>         --
>         Douglas N. Greve, Ph.D.
>         MGH-NMR Center
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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

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