Hi, Why not use total surface area to control for analyses involving area, and mean cortical thickness to control for thickness? I’ve posted to the list before regarding this, so you should be able to find those posts.
cheers, -MH
-- Michael Harms, Ph.D.
----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110Email: mharms@wustl.edu
On 7/4/16, 9:12 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Clara Kühn" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of ckuehn@cbs.mpg.de> wrote:
Do you know, if there are any publications concerning this matter? So far I've found only this http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0148852 that controls for tGM only for area and not CT.
Cheers Clara
----- Ursprüngliche Mail ----- Von: "Bruce Fischl" fischl@nmr.mgh.harvard.edu An: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 4. Juli 2016 15:37:57 Betreff: Re: [Freesurfer] controlling for total gray matter volume
sounds right to me Bruce On Mon, 4 Jul 2016, Clara Kühn wrote:
I have decided now to not control for ICV or total gray matter volume when looking at cortical thickness but to control for total gray matter volume when looking at surface area. Does that sound about right?
Cheers, Clara
----- Ursprüngliche Mail ----- Von: "Arkadiy Maksimovskiy" arkadiym@bu.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Samstag, 2. Juli 2016 18:36:51 Betreff: Re: [Freesurfer] controlling for total gray matter volume
Hi Clara,
If I am understanding your question correctly, you don't need to control for brain volume when looking at thickness analyses.
See quote below from this link:
http://www.freesurfer.net/fswiki/eTIV
"Note that this correction is only useful in situations where the structure scales with head size. Outside of this, correction just adds noise, or provides inaccurate data. In the case of the measures from Freesurfer, one would apply correction to the volume measures and not thickness measures. This is because volume scales with head size which is mostly due to changes in surface area, whereas thickness alone scales to a much less degree."
Best, Arkadiy
On Sat, Jul 2, 2016 at 12:00 PM, < freesurfer-request@nmr.mgh.harvard.edu > wrote:
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Today's Topics:
- controlling for total gray matter volume (Clara K?hn)
- cotrolling for total gray matter volume (Clara K?hn)
Message: 1 Date: Thu, 30 Jun 2016 15:19:43 +0200 (CEST) From: Clara K?hn < ckuehn@cbs.mpg.de > Subject: [Freesurfer] controlling for total gray matter volume To: Freesurfer support list < freesurfer@nmr.mgh.harvard.edu > Message-ID: < 600644700.119350.1467292783757.JavaMail.zimbra@cbs.mpg.de > Content-Type: text/plain; charset=utf-8
Dear FreeSurfer experts,
I would like to look at longitudinal thickness data and want to control for total gray matter volume. Should I use that information from the CROSS before anything has been registered and smoothed or from the LONG after they have been registered to the BASE? Also I was wondering if it is useful to control for total gray matter volume when looking at surface area?
Thanks for your help! Clara
Message: 2 Date: Thu, 30 Jun 2016 15:01:06 +0200 (CEST) From: Clara K?hn < ckuehn@cbs.mpg.de > Subject: [Freesurfer] cotrolling for total gray matter volume To: Freesurfer support list < freesurfer@nmr.mgh.harvard.edu > Message-ID: < 1473114832.117985.1467291666701.JavaMail.zimbra@cbs.mpg.de > Content-Type: text/plain; charset=utf-8
Dear FreeSurfer experts,
I would like to look at longitudinal thickness data and want to control for total gray matter volume. Should I use that information from the CROSS before anything has been registered and smoothed or from the LONG after they have been registered to the BASE? Also I was wondering if it is useful to control for total gray matter volume when looking at surface area?
Thanks for your help! Clara
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________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
yup, that is a reasonable approach Bruce
On Mon, 4 Jul 2016, Harms, Michael wrote:
Hi, Why not use total surface area to control for analyses involving area, and mean cortical thickness to control for thickness? I’ve posted to the list before regarding this, so you should be able to find those posts.
cheers, -MH
-- Michael Harms, Ph.D.
Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110Email: mharms@wustl.edu
On 7/4/16, 9:12 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Clara Kühn" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of ckuehn@cbs.mpg.de> wrote:
Do you know, if there are any publications concerning this matter? So far I've found only this http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0148852 that controls for tGM only for area and not CT.
Cheers Clara
----- Ursprüngliche Mail ----- Von: "Bruce Fischl" fischl@nmr.mgh.harvard.edu An: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 4. Juli 2016 15:37:57 Betreff: Re: [Freesurfer] controlling for total gray matter volume
sounds right to me Bruce On Mon, 4 Jul 2016, Clara Kühn wrote:
I have decided now to not control for ICV or total gray matter volume when looking at cortical thickness but to control for total gray matter volume when looking at surface area. Does that sound about right?
Cheers, Clara
----- Ursprüngliche Mail ----- Von: "Arkadiy Maksimovskiy" arkadiym@bu.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Samstag, 2. Juli 2016 18:36:51 Betreff: Re: [Freesurfer] controlling for total gray matter volume
Hi Clara,
If I am understanding your question correctly, you don't need to control for brain volume when looking at thickness analyses.
See quote below from this link:
http://www.freesurfer.net/fswiki/eTIV
"Note that this correction is only useful in situations where the structure scales with head size. Outside of this, correction just adds noise, or provides inaccurate data. In the case of the measures from Freesurfer, one would apply correction to the volume measures and not thickness measures. This is because volume scales with head size which is mostly due to changes in surface area, whereas thickness alone scales to a much less degree."
Best, Arkadiy
On Sat, Jul 2, 2016 at 12:00 PM, < freesurfer-request@nmr.mgh.harvard.edu > wrote:
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."
Today's Topics:
- controlling for total gray matter volume (Clara K?hn)
- cotrolling for total gray matter volume (Clara K?hn)
Message: 1 Date: Thu, 30 Jun 2016 15:19:43 +0200 (CEST) From: Clara K?hn < ckuehn@cbs.mpg.de > Subject: [Freesurfer] controlling for total gray matter volume To: Freesurfer support list < freesurfer@nmr.mgh.harvard.edu > Message-ID: < 600644700.119350.1467292783757.JavaMail.zimbra@cbs.mpg.de > Content-Type: text/plain; charset=utf-8
Dear FreeSurfer experts,
I would like to look at longitudinal thickness data and want to control for total gray matter volume. Should I use that information from the CROSS before anything has been registered and smoothed or from the LONG after they have been registered to the BASE? Also I was wondering if it is useful to control for total gray matter volume when looking at surface area?
Thanks for your help! Clara
Message: 2 Date: Thu, 30 Jun 2016 15:01:06 +0200 (CEST) From: Clara K?hn < ckuehn@cbs.mpg.de > Subject: [Freesurfer] cotrolling for total gray matter volume To: Freesurfer support list < freesurfer@nmr.mgh.harvard.edu > Message-ID: < 1473114832.117985.1467291666701.JavaMail.zimbra@cbs.mpg.de > Content-Type: text/plain; charset=utf-8
Dear FreeSurfer experts,
I would like to look at longitudinal thickness data and want to control for total gray matter volume. Should I use that information from the CROSS before anything has been registered and smoothed or from the LONG after they have been registered to the BASE? Also I was wondering if it is useful to control for total gray matter volume when looking at surface area?
Thanks for your help! Clara
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-
Bruce Fischl -
Harms, Michael