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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Dear  Bruce,

In fact, when I run:

tkmedit subject2 brainmask.mgz lh.orig lh.white -aux wm.mgz -aux-surface rh.orig rh.white

it gave me an error saying that tkmedit does not recognize lh.orig but the green line pops up and the orig surface button is now active. Why I still get the error message I don't know.

I want to ask one more favour:

1).Can you please briefly describe the difference between the following files: orig.mgz    brain.mgz    brainmask.mgz    T1.mgz

2) What is the difference between wm.mgz and filled.mgz

3) What represents the nu.mgz?

Thank you. 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: 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

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

Hi Antonella, When you load the files that those buttons are associated with, then they become active. When you loaded the orig surfaces, the orig surface button still was not active?

If you choose any button besides the Navigate button, when you left click, that will move the cursor (red crosshair) and then when you click one of the buttons to switch views, the cursor will be located on the same slice as it was in the other view.

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

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.