New subject: FS V6.0 GTM PVC ROI definition

10 Aug 2016

      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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Re: [Freesurfer] FS V6.0 GTM PVC ROI definition