yes doug On 05/31/2013 12:16 PM, Fotiadis, Panagiotis wrote:

Hey Doug,

Great, but besides the unbalanced numbers in each cohort, the fact that we have a cross sectional analysis instead of a longitudinal one doesn't matter right? Would it be correct to say that we still apply the same group analysis described in the wiki?

Thanks, Panos ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, May 31, 2013 11:59 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Group Analysis

Hi Panos, are you asking whether theunbalanced design will leadto one slope being different than another just because the numbers are different? That is not a problem. You can simply follow the instructions on the wiki. doug

On 05/31/2013 11:26 AM, Fotiadis, Panagiotis wrote:

...

Hey Doug,

Sorry for the overwhelming amount of questions. I wanted to confirm something. Suppose you want to do group analysis between two groups say a healthy cohort vs a diseased cohort. Each cohort has ~40 and ~30 subjects each (different people), and you want to compare how for instance the cortical thickness decreases over age in the one group versus the other. Do you still set the contrast vector as [0 0 1 -1] ([intercept 1 intercept 2 slope 1 slope 2]) and follow the analysis described in https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis or do you go on a different way since there are different subjects instead of one with 40 (or 30) different longitudinal data for each cohort? Don't we need to correct the age slopes for the fact that we have 40 (and 30) different subjects in each cohort?

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

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

---

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

---

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

Hey Doug,

Is there any need to co-register the subjects (of the two cohorts) destined for group analysis to the fsaverage space first in order to be able to compare their cortical thickness on the same space, or does mri_glmfit do that?

Thanks again, Panos ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Fotiadis, Panagiotis Sent: Friday, May 31, 2013 12:28 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Group Analysis

Thanks! Panos ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, May 31, 2013 12:22 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Group Analysis

yes doug On 05/31/2013 12:16 PM, Fotiadis, Panagiotis wrote:

Hey Doug,

Great, but besides the unbalanced numbers in each cohort, the fact that we have a cross sectional analysis instead of a longitudinal one doesn't matter right? Would it be correct to say that we still apply the same group analysis described in the wiki?

Thanks, Panos ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, May 31, 2013 11:59 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Group Analysis

Hi Panos, are you asking whether theunbalanced design will leadto one slope being different than another just because the numbers are different? That is not a problem. You can simply follow the instructions on the wiki. doug

On 05/31/2013 11:26 AM, Fotiadis, Panagiotis wrote:

...

Hey Doug,

Sorry for the overwhelming amount of questions. I wanted to confirm something. Suppose you want to do group analysis between two groups say a healthy cohort vs a diseased cohort. Each cohort has ~40 and ~30 subjects each (different people), and you want to compare how for instance the cortical thickness decreases over age in the one group versus the other. Do you still set the contrast vector as [0 0 1 -1] ([intercept 1 intercept 2 slope 1 slope 2]) and follow the analysis described in https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis or do you go on a different way since there are different subjects instead of one with 40 (or 30) different longitudinal data for each cohort? Don't we need to correct the age slopes for the fact that we have 40 (and 30) different subjects in each cohort?

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

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

---

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

---

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

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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

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

Thank you! ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, May 31, 2013 1:27 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Group Analysis

mri_glmfit does not do it. Run mris_preproc. See the tutorial doug

On 05/31/2013 01:13 PM, Fotiadis, Panagiotis wrote:

Hey Doug,

Is there any need to co-register the subjects (of the two cohorts) destined for group analysis to the fsaverage space first in order to be able to compare their cortical thickness on the same space, or does mri_glmfit do that?

Thanks again, Panos ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Fotiadis, Panagiotis Sent: Friday, May 31, 2013 12:28 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Group Analysis

Thanks! Panos ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, May 31, 2013 12:22 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Group Analysis

yes doug On 05/31/2013 12:16 PM, Fotiadis, Panagiotis wrote:

...

Hey Doug,

Great, but besides the unbalanced numbers in each cohort, the fact that we have a cross sectional analysis instead of a longitudinal one doesn't matter right? Would it be correct to say that we still apply the same group analysis described in the wiki?

Thanks, Panos ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, May 31, 2013 11:59 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Group Analysis

Hi Panos, are you asking whether theunbalanced design will leadto one slope being different than another just because the numbers are different? That is not a problem. You can simply follow the instructions on the wiki. doug

On 05/31/2013 11:26 AM, Fotiadis, Panagiotis wrote:

...

Hey Doug,

Sorry for the overwhelming amount of questions. I wanted to confirm something. Suppose you want to do group analysis between two groups say a healthy cohort vs a diseased cohort. Each cohort has ~40 and ~30 subjects each (different people), and you want to compare how for instance the cortical thickness decreases over age in the one group versus the other. Do you still set the contrast vector as [0 0 1 -1] ([intercept 1 intercept 2 slope 1 slope 2]) and follow the analysis described in https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis or do you go on a different way since there are different subjects instead of one with 40 (or 30) different longitudinal data for each cohort? Don't we need to correct the age slopes for the fact that we have 40 (and 30) different subjects in each cohort?

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

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

---

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

---

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

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

---

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

---

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

---

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

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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