Hello,
We are currently doing a longitudinal Group Analysis using FreeSurfer, and were wondering if there is a way to run a 3 factor design (time is 2 levels, group is 2 levels, subject is 10 levels) using the mri_glmfit model, as i want to test the time by group interaction? Is there a way of writing this model in an FSDG file? If we can't do this using mri_glmfit, is it possible to do this using QDEC?
Regards, Harry
Hi Harry, I would do a time1-time2 subtraction (fscalc) and then do a 2 group analysis (search for "paired" on our wiki). doug
On 10/09/2012 12:45 AM, hhal5293@uni.sydney.edu.au wrote:
Hello,
We are currently doing a longitudinal Group Analysis using FreeSurfer, and were wondering if there is a way to run a 3 factor design (time is 2 levels, group is 2 levels, subject is 10 levels) using the mri_glmfit model, as i want to test the time by group interaction? Is there a way of writing this model in an FSDG file? If we can't do this using mri_glmfit, is it possible to do this using QDEC?
Regards, Harry
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Doug!
If i wanted to add a third time-point, what would u suggest would be a good method to use for time x group interaction?
Harry ________________________________________ 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: Wednesday, 10 October 2012 1:10 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] 3 Factor glm group analysis
Hi Harry, I would do a time1-time2 subtraction (fscalc) and then do a 2 group analysis (search for "paired" on our wiki). doug
On 10/09/2012 12:45 AM, hhal5293@uni.sydney.edu.au wrote:
Hello,
We are currently doing a longitudinal Group Analysis using FreeSurfer, and were wondering if there is a way to run a 3 factor design (time is 2 levels, group is 2 levels, subject is 10 levels) using the mri_glmfit model, as i want to test the time by group interaction? Is there a way of writing this model in an FSDG file? If we can't do this using mri_glmfit, is it possible to do this using QDEC?
Regards, Harry
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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
_______________________________________________ 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 Harry.
I have some scripts to compute a slope into the time thickness or volume (linear fits) and then run a standard glm on that .
However, we recommend to run a linear mixed effects model (external software). We are working on making that available.
Best Martin
Harry Hallock hhal5293@uni.sydney.edu.au wrote:
Thanks Doug!
If i wanted to add a third time-point, what would u suggest would be a good method to use for time x group interaction?
Harry ________________________________________ 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: Wednesday, 10 October 2012 1:10 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] 3 Factor glm group analysis
Hi Harry, I would do a time1-time2 subtraction (fscalc) and then do a 2 group analysis (search for "paired" on our wiki). doug
On 10/09/2012 12:45 AM, hhal5293@uni.sydney.edu.au wrote:
Hello,
We are currently doing a longitudinal Group Analysis using
FreeSurfer,
and were wondering if there is a way to run a 3 factor design (time
is
2 levels, group is 2 levels, subject is 10 levels) using the mri_glmfit model, as i want to test the time by group interaction? Is there a way of writing this model in an FSDG file? If we can't do
this
using mri_glmfit, is it possible to do this using QDEC?
Regards, Harry
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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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
Hi Harry
As Martin said, longitudinal linear mixed-effects models (lme) are the recommended tool for analyzing longitudinal data obtained from the Freesurfer longitudinal image processing pipeline. The increase in power can be dramatic. Coming up there is a paper about this subject. We are working on making our lme tools available and easy to use but in the mean time, if you are interested, I can make available a link for you to download our Matlab-based lme toolbox.
Best -Jorge
De: Martin Reuter mreuter@nmr.mgh.harvard.edu Para: Harry Hallock hhal5293@uni.sydney.edu.au; Douglas N Greve greve@nmr.mgh.harvard.edu; "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Enviado: Domingo 14 de octubre de 2012 21:06 Asunto: Re: [Freesurfer] 3 Factor glm group analysis
Hi Harry.
I have some scripts to compute a slope into the time thickness or volume (linear fits) and then run a standard glm on that .
However, we recommend to run a linear mixed effects model (external software). We are working on making that available.
Best Martin
Harry Hallock hhal5293@uni.sydney.edu.au wrote: Thanks Doug!
If i wanted to add a third time-point, what would u suggest would be a good method to use for time x group interaction?
Harry
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: Wednesday, 10 October 2012 1:10 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] 3 Factor glm group analysis
Hi Harry, I would do a time1-time2 subtraction (fscalc) and then do a 2 group analysis (search for "paired" on our wiki). doug
On 10/09/2012 12:45 AM, hhal5293@uni.sydney.edu.au wrote:
Hello,
We are currently doing a longitudinal Group Analysis using
FreeSurfer,
and were wondering if there is a way to run a 3 factor design (time is 2 levels, group is 2 levels, subject is 10 levels) using the mri_glmfit model, as i want to test the time by group interaction? Is there a way of writing this model in an FSDG file? If we can't do this using mri_glmfit, is it possible to do this using QDEC?
Regards, Harry
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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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
-- Sent from my phone, please excuse brevity. _______________________________________________ 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 Martin,
If you could make available that lme toolbox link, that would be great! Thanks for the help.
Cheers, Harry ________________________________ From: jorge luis [jbernal0019@yahoo.es] Sent: Tuesday, 16 October 2012 8:16 AM To: Martin Reuter; Harry Hallock [hhal5293@uni.sydney.edu.au] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Mixed-effects models for longitudinal data analysis in Freesurfer
Hi Harry
As Martin said, longitudinal linear mixed-effects models (lme) are the recommended tool for analyzing longitudinal data obtained from the Freesurfer longitudinal image processing pipeline. The increase in power can be dramatic. Coming up there is a paper about this subject. We are working on making our lme tools available and easy to use but in the mean time, if you are interested, I can make available a link for you to download our Matlab-based lme toolbox.
Best -Jorge
________________________________ De: Martin Reuter mreuter@nmr.mgh.harvard.edu Para: Harry Hallock hhal5293@uni.sydney.edu.au; Douglas N Greve greve@nmr.mgh.harvard.edu; "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Enviado: Domingo 14 de octubre de 2012 21:06 Asunto: Re: [Freesurfer] 3 Factor glm group analysis
Hi Harry.
I have some scripts to compute a slope into the time thickness or volume (linear fits) and then run a standard glm on that .
However, we recommend to run a linear mixed effects model (external software). We are working on making that available.
Best Martin
Harry Hallock hhal5293@uni.sydney.edu.au wrote:
Thanks Doug!
If i wanted to add a third time-point, what would u suggest would be a good method to use for time x group interaction?
Harry ________________________________
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: Wednesday, 10 October 2012 1:10 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] 3 Factor glm group analysis
Hi Harry, I would do a time1-time2 subtraction (fscalc) and then do a 2 group analysis (search for "paired" on our wiki). doug
On 10/09/2012 12:45 AM, hhal5293@uni.sydney.edu.au wrote: Hello,
We are currently doing a longitudinal Group Analysis using FreeSurfer, and were wondering if there is a way to run a 3 factor design (time is 2 levels, group is 2 levels, subject is 10 levels) using the mri_glmfit model, as i want to test the time by group interaction? Is there a way of writing this model in an FSDG file? If we can't do this using mri_glmfit, is it possible to do this using QDEC?
Regards, Harry
________________________________
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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
________________________________
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
-- Sent from my phone, please excuse brevity.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.
If you want to do a repeated measures ANOVA with more than two time points, I've put a page together here:
http://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova
doug
On 10/15/2012 08:24 PM, Harry Hallock [hhal5293@uni.sydney.edu.au] wrote:
Hi Martin,
If you could make available that lme toolbox link, that would be great! Thanks for the help.
Cheers, Harry
*From:* jorge luis [jbernal0019@yahoo.es] *Sent:* Tuesday, 16 October 2012 8:16 AM *To:* Martin Reuter; Harry Hallock [hhal5293@uni.sydney.edu.au] *Cc:* freesurfer@nmr.mgh.harvard.edu *Subject:* Mixed-effects models for longitudinal data analysis in Freesurfer
Hi Harry
As Martin said, longitudinal linear mixed-effects models (lme) are the recommended tool for analyzing longitudinal data obtained from the Freesurfer longitudinal image processing pipeline. The increase in power can be dramatic. Coming up there is a paper about this subject. We are working on making our lme tools available and easy to use but in the mean time, if you are interested, I can make available a link for you to download our Matlab-based lme toolbox.
Best -Jorge
------------------------------------------------------------------------ *De:* Martin Reuter <mreuter@nmr.mgh.harvard.edu> *Para:* Harry Hallock <hhal5293@uni.sydney.edu.au>; Douglas N Greve <greve@nmr.mgh.harvard.edu>; "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> *Enviado:* Domingo 14 de octubre de 2012 21:06 *Asunto:* Re: [Freesurfer] 3 Factor glm group analysis Hi Harry. I have some scripts to compute a slope into the time thickness or volume (linear fits) and then run a standard glm on that . However, we recommend to run a linear mixed effects model (external software). We are working on making that available. Best Martin Harry Hallock <hhal5293@uni.sydney.edu.au> wrote: Thanks Doug! If i wanted to add a third time-point, what would u suggest would be a good method to use for time x group interaction? Harry ------------------------------------------------------------------------ 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: Wednesday, 10 October 2012 1:10 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] 3 Factor glm group analysis Hi Harry, I would do a time1-time2 subtraction (fscalc) and then do a 2 group analysis (search for "paired" on our wiki). doug On 10/09/2012 12:45 AM, hhal5293@uni.sydney.edu.au wrote: Hello, We are currently doing a longitudinal Group Analysis using FreeSurfer, and were wondering if there is a way to run a 3 factor design (time is 2 levels, group is 2 levels, subject is 10 levels) using the mri_glmfit model, as i want to test the time by group interaction? Is there a way of writing this model in an FSDG file? If we can't do this using mri_glmfit, is it possible to do this using QDEC? Regards, Harry ------------------------------------------------------------------------ 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 <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop:www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> ------------------------------------------------------------------------ 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 -- Sent from my phone, please excuse brevity. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Harry Hallock -
Harry Hallock [hhal5293＠uni.sydney.edu.au]
-
hhal5293＠uni.sydney.edu.au
-
jorge luis -
Martin Reuter