Hi Bruce, Resending without attachments (I believe those prevented me from posting.
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.
* arkadiy
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the vertex and I think this might be due to an outdated Freeview version (2.0)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
___
Freesurfer mailing list
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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.
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
___
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.
-- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School