Re: [Freesurfer] Reporting Cohen's D for a significant cluster

Hi Bruce,

I am including the previous correspondence below, but here is a quick summary:

My goal is to get the Cohen’s D value for a max vertex of a significant cluster.

I entered the max vertex number in the bottom left of the freeview window (cursor window), where it says vertex. When I hit enter, RAS coordinates change, but the vertex # goes back to what it was previously and Cohen’s D (loaded as an overlay) does not change. The cohen’s D only changes when I move the mouse and click manually. I am attaching two screenshots of the before, during entry, and after to illustrate the process.

* arkadiy

[cid:image001.png@01D455A5.FF5396E0][cid:image002.png@01D455A5.FF5396E0][cid:image003.png@01D455A5.FF5396E0]

Previous Correspondence:

Hi Arkadiy

can you include the previous correspondance so we have context? And what window did you enter numbers? Was it the left hand side of the info window (under "cursor")?

cheers Bruce

On Wed, 26 Sep 2018, Maksimovskiy, Arkadiy wrote:

Hi Bruce,

I wanted to follow up on this as I was unsuccessful in doing what you suggested using Freeview (2.0)- entering numbers into the window does not change anything. Might there be another way to find out the Cohen’s D?

Thank you for your help,

Arkadiy

--

Arkadiy L. Maksimovskiy, Ph.D.

Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School

Re: [Freesurfer] Reporting Cohen's D for a significant clusterhttps://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg59519.html 2018-09-20https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=date:20180920&o=newest&f=1 Threadhttps://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=subject:%22%5C%5BFreesurfer%5C%5D+Reporting+Cohen%27s+D+for+a+significant+cluster%22&o=newest&f=1 Maksimovskiy, Arkadiyhttps://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=from:%22Maksimovskiy%2C+Arkadiy%22&o=newest&f=1

Hi Bruce,

Thank you so much for the tip and the quick response.

For some reason, the position and Cohen’s D value do not change when I input

the vertex and I think this might be due to an outdated Freeview version (2.0)

that I am using.

I attempted to load the new one from this link:

https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview

But I am getting an error: The requested URL

/pub/dist/freesurfer/freeview/freeview_osx.tar.gz was not found on this server.

I was wondering if you have this file available at another location?

Thanks again,

arkadiy

--

Arkadiy L. Maksimovskiy, Ph.D.

Postdoctoral Research Fellow

McLean Imaging Center, McLean Hospital

Department of Psychiatry, Harvard Medical School

--

Arkadiy L. Maksimovskiy, Ph.D.

Postdoctoral Research Fellow

McLean Imaging Center, McLean Hospital

Department of Psychiatry, Harvard Medical School

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Re: [Freesurfer] Reporting Cohen's D for a significant clusterhttps://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg59515.html 2018-09-20https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=date:20180920&o=newest&f=1 Threadhttps://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=subject:%22%5C%5BFreesurfer%5C%5D+Reporting+Cohen%27s+D+for+a+significant+cluster%22&o=newest&f=1 Bruce Fischlhttps://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=from:%22Bruce+Fischl%22&o=newest&f=1

Hi Arkadiy

if you have the surface loaded you can always type a vertex number into

the info field (that shows the current selected vertex) at the bottom of

the freeview window. It will then jump to that vertex, and adjust the views

accordingly

cheers

Bruce

On Thu, 20 Sep 2018, Maksimovskiy, Arkadiy wrote:

Update: It occurred to me that reporting it for the max verted might be the

best idea. In this case,

might anyone know what is the best way to navigate the Freeview to a specific

vertex number (is

there a place where I can input that number). Thanks again.

From: "Maksimovskiy, Arkadiy"

Date: Thursday, September 20, 2018 at 10:56 AM

To: "freesurfer@nmr.mgh.harvard.edu"

Subject: Reporting Cohen's D for a significant cluster

Dear Experts,

I was requested to report the Cohen’s D value for a significant cluster, which

resulted from a

cortical thickness analysis. I was able to calculate it and open the resulting

Cohen’s D mgh file in

Freeview, together with the file, indicating a significant cluster.

As expected, when I move the cursor within the significant cluster, Cohen’s D

value changes with

every vertex. I was wondering if you might have any recommendations for which

of the Cohen’s D

values to report, and how best to obtain that value?

Thank you for your help,

arkadiy

--

Arkadiy L. Maksimovskiy, Ph.D.

Postdoctoral Research Fellow

McLean Imaging Center, McLean Hospital

Department of Psychiatry, Harvard Medical School

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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.

Re: [Freesurfer] Reporting Cohen's D for a significant clusterhttps://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg59514.html 2018-09-20https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=date:20180920&o=newest&f=1 Threadhttps://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=subject:%22%5C%5BFreesurfer%5C%5D+Reporting+Cohen%27s+D+for+a+significant+cluster%22&o=newest&f=1 Maksimovskiy, Arkadiyhttps://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=from:%22Maksimovskiy%2C+Arkadiy%22&o=newest&f=1

Update: It occurred to me that reporting it for the max verted might be the

best idea. In this case, might anyone know what is the best way to navigate the

Freeview to a specific vertex number (is there a place where I can input that

number). Thanks again.

From: "Maksimovskiy, Arkadiy"

Date: Thursday, September 20, 2018 at 10:56 AM

To: "freesurfer@nmr.mgh.harvard.edu"

Subject: Reporting Cohen's D for a significant cluster

Dear Experts,

I was requested to report the Cohen’s D value for a significant cluster, which

resulted from a cortical thickness analysis. I was able to calculate it and

open the resulting Cohen’s D mgh file in Freeview, together with the file,

indicating a significant cluster.

As expected, when I move the cursor within the significant cluster, Cohen’s D

value changes with every vertex. I was wondering if you might have any

recommendations for which of the Cohen’s D values to report, and how best to

obtain that value?

Thank you for your help,

arkadiy

--

Arkadiy L. Maksimovskiy, Ph.D.

Postdoctoral Research Fellow

McLean Imaging Center, McLean Hospital

Department of Psychiatry, Harvard Medical School

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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.

-- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School