Re: [Freesurfer] Qdec: group differences covaring for age and sex {Disarmed}

2015-09-22 Thread Douglas Greve
Yes, that is fine as long as they are listed as discrete variables (as 
is the case below).

doug

On 9/22/15 7:59 AM, pablo najt wrote:

Hello Douglas,
If I understand your comment about defining all discrete variables as 
classes (e.g. PT_F, PT_M, HC_F, HC_M) *only applies* to glm command 
line stream not qdec. If I am using qdec I can have discrete variables 
defined separately (e.g. Sex, Diagnosis) specified in the qdec.table 
text file as I am not required to specify classes as in the FS 
descriptor file.  I am following here the instructions as shown below. 
Do I understand correct?

Thanks,
Pablo

qdec.table example from FSpage



> To: freesurfer@nmr.mgh.harvard.edu
> From: gr...@nmr.mgh.harvard.edu
> Date: Mon, 21 Sep 2015 17:39:14 -0400
> Subject: Re: [Freesurfer] Qdec: group differences covaring for age 
and sex

>
> Yes, it is addressing that question. The contrast should be the same as
> your Group Diff below. Although I'm not sure you're using the proper
> design. It looks like you are using Sex as a continuous covariate? That
> is not correct. It should be discrete. So you should have 4 classes
> (HC-M, HC-F, PT-M, PT-F)
>
> On 09/21/2015 09:31 AM, pablo najt wrote:
> > Hello FS experts,
> > I would like to understand the results from qdec in a GLM model with
> > Group (PT/HC), and two covariates (Age, gender).
> > I set up my contrast as follow:
> >
> > Group Diff
> > HC PT AgeHC AgePT SexHC SexPT
> > 1 -1 0 0 0 0
> >
> > Group x Age effect
> > HC PT AgeHC AgePT SexHC SexPT
> > 0 0 1 -1 0 0
> >
> > Group X Sex effect
> > HC PT AgeHC AgePT SexHC SexPT
> > 0 0 0 0 1 -1
> > Continues just as indicated in the "2 Groups 2 Covariates example"
> >
> > What I would like to find out: /If there are group differences while
> > controlling for age and sex/.
> >
> > In Qdec I selected Group, Gender, and Age. (Age as normal variable,
> > not as nuisance)
> > However, when I open my results with Qdec I am not quite sure it is
> > answering my question.
> >
> > From all the questions listed I thought that the following was
> > addressing what I need, but would like to clarify.
> > "/Does the thickness, --Age correlation, accounting for Gender, 
differ

> > between HC and PT?"/
> > Would you mind confirming this for me?
> > Thanks!!
> > Pablo
> >
> >
> > ___
> > 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
> gr...@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
>
>
> 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.
>


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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
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Re: [Freesurfer] Qdec: group differences covaring for age and sex {Disarmed}

2015-09-22 Thread pablo najt
Hello Douglas,
If I understand your comment about defining all discrete variables as classes 
(e.g. PT_F, PT_M, HC_F, HC_M) *only applies* to glm command line stream not 
qdec. If I am using qdec I can have discrete variables defined separately (e.g. 
Sex, Diagnosis) specified in the qdec.table text file as I am not required to 
specify classes as in the FS descriptor file.  I am following here the 
instructions as shown below. Do I understand correct?
Thanks,
Pablo

qdec.table example from FSpage
  


> To: freesurfer@nmr.mgh.harvard.edu
> From: gr...@nmr.mgh.harvard.edu
> Date: Mon, 21 Sep 2015 17:39:14 -0400
> Subject: Re: [Freesurfer] Qdec: group differences covaring for age and sex
> 
> Yes, it is addressing that question. The contrast should be the same as 
> your Group Diff below. Although I'm not sure you're using the proper 
> design. It looks like you are using Sex as a continuous covariate? That 
> is not correct. It should be discrete. So you should have 4 classes 
> (HC-M, HC-F, PT-M, PT-F)
> 
> On 09/21/2015 09:31 AM, pablo najt wrote:
> > Hello FS experts,
> > I would like to understand the results from qdec in a GLM model with 
> > Group (PT/HC), and two covariates (Age, gender).
> > I set up my contrast as follow:
> >
> > Group Diff
> > HC  PT  AgeHC  AgePT  SexHC SexPT
> >  1 -10   0  0   0
> >
> > Group x Age effect
> > HC  PT  AgeHC  AgePT  SexHC SexPT
> >  0  0 1  -1 00
> >
> > Group X Sex effect
> > HC  PT  AgeHC  AgePT  SexHC SexPT
> >  0  0 0   0  1   -1
> > Continues just as indicated in the "2 Groups 2 Covariates example"
> >
> > What I would like to find out: /If there are group differences while 
> > controlling for age and sex/.
> >
> > In Qdec I selected Group, Gender, and Age. (Age as normal variable, 
> > not as nuisance)
> > However, when I open my results with Qdec I am not quite sure it is 
> > answering my question.
> >
> > From all the questions listed I thought that the following was 
> > addressing what I need, but would like to clarify.
> > "/Does the thickness, --Age correlation, accounting for Gender, differ 
> > between HC and PT?"/
> > Would you mind confirming this for me?
> > Thanks!!
> > Pablo
> >
> >
> > ___
> > 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
> gr...@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
> 
> 
> 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.
> 
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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.