---

From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
To: Antonella Kis <atorok9@yahoo.com>
Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Sent: Thursday, July 28, 2011 11:15 AM
Subject: Re: "orig surface" button

Hi Antonella,

if it's not active then it probably failed loading the orig surface. Can you send us the output of the tkmedit command? There is a multi-view button you can click in tkmedit to show 3 orthogonal views at the same time.

cheers
Bruce


On Thu, 28 Jul 2011, Antonella Kis wrote:

>
> Hi Bruce,
>
> Thanks again for your valuable information. I was trying to click on my "orig surface" button in the interface but it is not active. Is there
> a way that I can enable this option/button? I see more buttons are not active. How I can fix this?
>
> Second, using tkmedit, how I can see the same point that I choose in one view for example the coronal view in another view example horizontal
> view? How I can select this point in one view and make it visible in another view?
>
> Thanks,
> Antonella
>
> ______________________________________________________________________________________________________________________________________________
> From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
> To: Antonella Kis <atorok9@yahoo.com>
> Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
> Sent: Wednesday, July 27, 2011 4:35 PM
> Subject: Re: [Freesurfer] Corrections for the Pial surface
>
> Hi Antonella,
>
> 1. Can you load the lh.orig or rh.orig surface explicitly and see if it is shown? Is the "orig surface" button clicked in the interface?
>
> 2. the hippocampus and amygdala are not neocortical structures and shouldn't be included in the surfaces (in fact, the surfaces in those
> regions are somewhat arbitrary as they don't have the laminar architecture we are expecting).
>
> cheers
> Bruce
>
>
> On Wed, 27 Jul 2011, Antonella Kis wrote:
>
> > Hi Bruce,
> >
> > Thank again for your advice. I am not sure about the data collection but I will find out soon. In the mean time I have two more questions:
> > 1). The FS tutorial shows for the surface outlines  (by loading the -surfs) three line: the yellow indicating the white surface, the red for
> > the pial and a green line for the orig data. When I plot the surfs I have only the yellow and red line. Can I get the green line somehow?
> > 2). I suppose the two important brain structures,  amygdala and hippocampus must be included in the pial surface as a grey matter (I hope I
> am
> > right) .
> > If they are not enclosed in the pial surface is there a way to  resolve  this issue? How I should edit the pial surface in this case? How
> > important is to have them enclosed for my cortical thickness studies and for the GLM group analysi?
> >
> > Thank you very much.
> > Antonella
> >
> >
> >
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