On 08/10/2017 11:35 AM, John Anderson wrote:
>
> Dear Dr Greve,
>
> Thank you very much for the great explanation. I will definitely 
> correct for PVC using PET surfer.
>
> Kindly I have one follow-up question and I highly appreciate your input.
>
> I have PET data for two groups. I studied the difference in PET signal 
> using  voxel-wise ( FSL/randomise) and surface-based using PET surfer.
>
> My question is about PVC. We correct for PVC in surface based because 
> we re-sample PET data to the brain surface which is an output of 
> segmentation process, meaning we expect partial volume effects between 
> the grey/white  for a possible contamination between them during 
> segmentation.

>
> We don't do PVE in voxel-wise because we don't worry about the 
> contamination meaning there are no segmentation lines to separate 
> between brain regions.

>
> Kindly is my understanding for this fact correct ( i.e. why we correct 
> in surface based and we don't correct in voxel-wise).
It is not correct. You do PVC to remove interactions between the anatomy 
and the PET through PVEs. Those will be there in both surface-based and 
volume-based analysis.  If you perform smoothing in volume-based 
analysis, you will make the PVEs worse. Doing MG PVC then volume-based 
smoothing will result in a disaster. In my opinion, the only way to do 
PVC in a map-based analysis (vs ROI) is to do it on the surface. For 
subcortical, you can do volume-based smoothing within a GM mask.

> By the way, I ran voxel-wise using randomise with TFCE and 5000 
> permutations.
For the surface, you can use mri_glmfit with the --perm option.
>
> Thank you again for any clarification
> John
>
>
>
>
> The PET signalcan change with a lot of anatomical changes in the brain 
> including thickness, surface area, and gyrification. There is no known 
> regressor that will account for this. Right right way to account for 
> it is with partialvolume correction (PVC). It is best to do PVC 
> simultaneously with the recon, but software is not available to 
> perform this. You can do it on a post-hoc basis in PETsurfer using the 
> PVC options in mri_gtmpvc. See the wiki.
>
>
>
> On 08/10/2017 04:11 AM, John Anderson wrote:
>
> >
>
> > Hi Dr Greve,
>
> >
>
> > I have PET data for two groups and I used PET surfer in FSV 6.0 to run
>
> > the analyses. The pipeline is straightforward and the analysis ran
>
> > smoothly without any issues.
>
> >
>
> > Is it correct procedure to adjust PET signal to differences in gray
>
> > matter volume or cortical thinness between two groups?
>
> >
>
> > In other words, is it correct if gray matter volume or cortical
>
> > thickness for subjects be included as EVs in GLM or a nausiance factor
>
> > in QDEC?
>
> >
>
> > Specifically, is the PET signal changeable depending ondifferences
>
> > in cortical thickness.
>
> > or differences in gray matter volume?
>
> >
>
> > Thank youfor any clarification
>
> >
>
> >> Thank you !
>
> >> Jon
>
> >>
>
> >
>
> >
>
> >
>
> > _______________________________________________
>
> > Freesurfer mailing list
>
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>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> --
>
> Douglas N. Greve, Ph.D.
>
> MGH-NMR Center
>
> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
>
> Phone Number: 617-724-2358
>
> Fax: 617-726-7422
>
>
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> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>
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>
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html 
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>
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>
>
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>> -------- Original Message --------
>> Subject: PET surfer
>> Local Time: August 10, 2017 4:11 AM
>> UTC Time: August 10, 2017 8:11 AM
>> From: john.ande...@protonmail.com
>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>>
>> Hi Dr Greve,
>>
>> I have PET data for two groups and I used PET surfer in FSV 6.0 to 
>> run the analyses. The pipeline is straightforward and the analysis 
>> ran smoothly without any issues.
>>
>> Is it correct procedure to adjust PET signal to differences in gray 
>> matter volume or cortical thinness between two groups?
>>
>> In other words, is it correct if gray matter volume or cortical 
>> thickness for subjects be included as EVs in GLM or a nausiance 
>> factor in QDEC?
>>
>> Specifically, is the PET signal changeable depending on  differences 
>> in cortical thickness.
>> or differences in gray matter volume?
>>
>> Thank you  for any clarification
>>
>>> Thank you !
>>> Jon
>>>
>>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@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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www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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