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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