[Freesurfer] Convert mgh to gii

[David.Mackarthy]

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Hi FS experts,
I ran surface based analysis between two groups. The final output "is 
cache.th13.pos.sig.cluster.mgh" I would like to convert this file to gii format 
using "mris_convert" I tried:

mris_convert -c cache.th13.pos.sig.cluster.mgh cache.th13.pos.sig.cluster.gii

Please what I am doing wrong?
Thanks for help
-Dev___
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[Freesurfer] Pet Surfer

[David.Mackarthy]

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Dear Dr Greeve,
I am following petsurfer pipeline to do surface based analysis of PET-FDG data 
and I have interest in doing partial volume correction. I would like to inquire 
about:

1) Can partial volume correction be applied on white mater, or just on gray 
matter?

2) Can partial volume correction be applied between gray matter and CSF?

According to Muller-Gartner (MG) Method we segment the brain to gray/white and 
csf, then we apply partial volume correction only on gray matter. why not on 
the other parts.

I apologies if my question is basics and I appreciate your input.

Thanks for publishing this valuable manuscript

https://www.ncbi.nlm.nih.gov/pubmed/26915497

With all respect!
Dev___
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Re: [Freesurfer] Pet Surfer

[David.Mackarthy]

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Dear Dr Greve, thank you for the response
This is for a map-based study. Absolutely, this is clear, I appreciate the 
response. I just have one additional question and I appreciate your patience.

Is it recommended to apply PVC on white matter or csf? does it make sense to 
apply PVC on WM and CSF?

Thank you so much!



‐‐‐ Original Message ‐‐‐
On Wednesday, October 10, 2018 2:17 PM, Greve, Douglas N.,Ph.D. 
 wrote:

> Is this for an ROI-based study or a map-based study? For ROI, we use the
> GTM, and it PV corrects for all structures (including WM and CSF). For
> map-based, we use MG. MG removes WM (and CSF) entirely. In theory, it
> can be run in a way to keep WM and throw GM and CSF away, but that is
> not implemented. Does this answer your questions?
>
> On 10/10/2018 07:31 AM, David.Mackarthy wrote:
>
> > Dear Dr Greeve,
> > I am following petsurfer pipeline to do surface based analysis of
> > PET-FDG data and I have interest in doing partial volume correction. I
> > would like to inquire about:
> >
> > 1.  Can partial volume correction be applied on white mater, or just on
> > gray matter?
> >
> > 2.  Can partial volume correction be applied between gray matter and CSF?
> >
> >
> > According to Muller-Gartner (MG) Method we segment the brain to
> > gray/white and csf, then we apply partial volume correction only on
> > gray matter. why not on the other parts.
> > I apologies if my question is basics and I appreciate your input.
> > Thanks for publishing this valuable manuscript
> > https://www.ncbi.nlm.nih.gov/pubmed/26915497
> > With all respect!
> > Dev
> >
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



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