Re: [Freesurfer] One Group (One Factor), Two Covariates

[Douglas N Greve]

The 2nd contrast (slope) is the one you want.


On 02/05/2018 01:21 PM, std...@virgilio.it wrote:
>
> Thanks.
>
> Only for I quick check of my understanding, if I'm using:
>
>
> FSGD File (g1v1.fsgd)
>
> GroupDescriptorFile 1
>
> Title OSGM
>
> Class Main
>
> Variables Age
>
> Input subject1 Main 30
>
> Input subject2 Main 40
>
> .
>
>
> A) Contrast 1 (intercept.mtx) 1 0
>
> B) Contrast 2 (slope.mtx) 0 1
>
> Considering that my goal is to obtain a map reporting the significant 
> clusters where the FC is positively/negatively associated with Age, is 
> this contrast exact? Or it shows the clusters where la FC between seed 
> and target regions is significant, regressing out the Age? This second 
> case in not of my interest.
> Please suggest a way to reach the first case.
>
> Thanks
>
>
> Stefano
>
>
>
>> Il 5 febbraio 2018 alle 18.27 Douglas Greve 
>>  ha scritto:
>>
>> If you have one class and two variables, then [0 1 0] and [0 0 1]
>>
>>
>> On 2/4/18 10:23 AM, std...@virgilio.it  wrote:
>>>
>>> I would like to find where the functional connectivity is correlated 
>>> to VARIABLE 1 regressing out the VARIABLE 2.
>>>
>>> How I should set my contrast.mtx?
>>>
>>> Thanks
>>>
>>>
>>> Stefano
>>>
 Il 3 febbraio 2018 alle 19.57 Douglas Greve 
   ha 
 scritto:



 On 2/2/18 7:47 AM, std...@virgilio.it  
 wrote:
>
> Hi list,
>
> in reference to One Group (One Factor), Two Covariates
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G2V#Contrast2age.mtx
>
> that has been applied on FS-FAST fcMRI data
>
> I obtain three folder, respectively, for "main", "covariate 1", 
> "covariate 2".
>
> What's meaning the sig.nii.gz that it is produced by mri_glmfit in 
> each folder?
> Please correct my conclusions if they are wrong.
>
> 1 - In the "Main" folder, the sig.nii.gz contains the results of 
> One-sample t test regressing out the effect of the two covariates.
>
 Correct
>
> 2 - In the "Covariate 1" folder, the sig.nii.gz contains the 
> significant cluster that are associated with the covariate 1 
> regressing out the effect for the covariate 2.
>
 Yes (and the main)
>
> 3 - In the "Covariate 2" folder, the sig.nii.gz contains the 
> significant cluster that are associated with the covariate 2 
> regressing out the effect for the covariate 1.
>
 Yes (and regressing out the main)
>
> Thanks
>
>
> Stefano
>
> *
> *
>
> *
> *
>
>
>
> ___
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>>>
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>>
>
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>>
>>
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>> HelpLine at
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>> and properly
>> dispose of the e-mail.

-- 
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
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Re: [Freesurfer] One Group (One Factor), Two Covariates

[stdp82]

Thanks.

Only for I quick check of my understanding, if I'm using:


FSGD File (g1v1.fsgd)

GroupDescriptorFile 1

Title OSGM

Class Main

Variables Age

Input subject1 Main 30

Input subject2 Main 40

.


A) Contrast 1 (intercept.mtx) 1 0

B) Contrast 2 (slope.mtx) 0 1

Considering that my goal is to obtain a map reporting the significant clusters 
where the FC is positively/negatively associated with Age, is this contrast 
exact? Or it shows the clusters where la FC between seed and target regions is 
significant, regressing out the Age? This second case in not of my interest.
Please suggest a way to reach the first case.

Thanks


Stefano



> Il 5 febbraio 2018 alle 18.27 Douglas Greve  ha 
> scritto:
> 
> 
> If you have one class and two variables, then [0 1 0] and [0 0 1]
> 
> 
> On 2/4/18 10:23 AM, std...@virgilio.it mailto:std...@virgilio.it wrote:
> 
> > > 
> > I would like to find where the functional connectivity is 
> > correlated to VARIABLE 1 regressing out the VARIABLE 2.
> > 
> > How I should set my contrast.mtx?
> > 
> > Thanks
> > 
> > 
> > Stefano
> > 
> > > > > Il 3 febbraio 2018 alle 19.57 Douglas Greve 
> >  mailto:gr...@nmr.mgh.harvard.edu ha scritto:
> > > 
> > > 
> > > 
> > > 
> > > On 2/2/18 7:47 AM, std...@virgilio.it 
> > > mailto:std...@virgilio.it wrote:
> > > 
> > > > > > > 
> > > > Hi list,
> > > > 
> > > > in reference to One Group (One Factor), Two Covariates
> > > > 
> > > > 
> > > > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G2V#Contrast2age.mtx
> > > > 
> > > > that has been applied on FS-FAST fcMRI data
> > > > 
> > > > I obtain three folder, respectively, for "main", 
> > > > "covariate 1", "covariate 2".
> > > > 
> > > > What's meaning the sig.nii.gz that it is produced by 
> > > > mri_glmfit in each folder?
> > > > Please correct my conclusions if they are wrong.
> > > > 
> > > > 1 - In the "Main" folder, the sig.nii.gz contains the 
> > > > results of One-sample t test regressing out the effect of the two 
> > > > covariates.
> > > > 
> > > > > > > Correct
> > > 
> > > > > > > 
> > > > 2 - In the "Covariate 1" folder, the sig.nii.gz 
> > > > contains the significant cluster that are associated with the covariate 
> > > > 1 regressing out the effect for the covariate 2.
> > > > 
> > > > > > > Yes (and the main)
> > > 
> > > > > > > 
> > > > 3 - In the "Covariate 2" folder, the sig.nii.gz 
> > > > contains the significant cluster that are associated with the covariate 
> > > > 2 regressing out the effect for the covariate 1.
> > > > 
> > > > > > > Yes (and regressing out the main)
> > > 
> > > > > > > 
> > > > Thanks
> > > > 
> > > > 
> > > > Stefano
> > > > 
> > > > 
> > > > 
> > > > 
> > > > 
> > > > ___
> > > > Freesurfer mailing list
> > > > Freesurfer@nmr.mgh.harvard.edu 
> > > > mailto:Freesurfer@nmr.mgh.harvard.edu
> > > > 
> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > > 
> > > > > > > 
> > > > > 
> > 
> >  
> > 
> > > > > ___
> > > 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.
> > > 
> > > > > 
> > > 


 

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Re: [Freesurfer] One Group (One Factor), Two Covariates

[Douglas Greve]

If you have one class and two variables, then [0 1 0] and [0 0 1]


On 2/4/18 10:23 AM, std...@virgilio.it wrote:


I would like to find where the functional connectivity is correlated 
to VARIABLE 1 regressing out the VARIABLE 2.


How I should set my contrast.mtx?

Thanks


Stefano

Il 3 febbraio 2018 alle 19.57 Douglas Greve 
 ha scritto:




On 2/2/18 7:47 AM, std...@virgilio.it  wrote:


Hi list,

in reference to One Group (One Factor), Two Covariates

https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G2V#Contrast2age.mtx

that has been applied on FS-FAST fcMRI data

I obtain three folder, respectively, for "main", "covariate 1", 
"covariate 2".


What's meaning the sig.nii.gz that it is produced by mri_glmfit in 
each folder?

Please correct my conclusions if they are wrong.

1 - In the "Main" folder, the sig.nii.gz contains the results of 
One-sample t test regressing out the effect of the two covariates.



Correct


2 - In the "Covariate 1" folder, the sig.nii.gz contains the 
significant cluster that are associated with the covariate 1 
regressing out the effect for the covariate 2.



Yes (and the main)


3 - In the "Covariate 2" folder, the sig.nii.gz contains the 
significant cluster that are associated with the covariate 2 
regressing out the effect for the covariate 1.



Yes (and regressing out the main)


Thanks


Stefano

*
*

*
*



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Re: [Freesurfer] One Group (One Factor), Two Covariates

[stdp82]

I would like to find where the functional connectivity is correlated to 
VARIABLE 1 regressing out the VARIABLE 2.

How I should set my contrast.mtx?

Thanks


Stefano

> Il 3 febbraio 2018 alle 19.57 Douglas Greve  ha 
> scritto:
> 
> 
> 
> 
> On 2/2/18 7:47 AM, std...@virgilio.it mailto:std...@virgilio.it wrote:
> 
> > > 
> > Hi list,
> > 
> > in reference to One Group (One Factor), Two Covariates
> > 
> > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G2V#Contrast2age.mtx
> > 
> > that has been applied on FS-FAST fcMRI data
> > 
> > I obtain three folder, respectively, for "main", "covariate 1", 
> > "covariate 2".
> > 
> > What's meaning the sig.nii.gz that it is produced by mri_glmfit in 
> > each folder?
> > Please correct my conclusions if they are wrong.
> > 
> > 1 - In the "Main" folder, the sig.nii.gz contains the results of 
> > One-sample t test regressing out the effect of the two covariates.
> > 
> > > Correct
> 
> > > 
> > 2 - In the "Covariate 1" folder, the sig.nii.gz contains the 
> > significant cluster that are associated with the covariate 1 regressing out 
> > the effect for the covariate 2.
> > 
> > > Yes (and the main)
> 
> > > 
> > 3 - In the "Covariate 2" folder, the sig.nii.gz contains the 
> > significant cluster that are associated with the covariate 2 regressing out 
> > the effect for the covariate 1.
> > 
> > > Yes (and regressing out the main)
> 
> > > 
> > Thanks
> > 
> > 
> > Stefano
> > 
> > 
> > 
> > 
> > 
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > 
> > > 


 

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> 
> 
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> is
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> e-mail
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Re: [Freesurfer] One Group (One Factor), Two Covariates

[Douglas Greve]

On 2/2/18 7:47 AM, std...@virgilio.it wrote:


Hi list,

in reference to One Group (One Factor), Two Covariates

https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G2V#Contrast2age.mtx

that has been applied on FS-FAST fcMRI data

I obtain three folder, respectively, for "main", "covariate 1", 
"covariate 2".


What's meaning the sig.nii.gz that it is produced by mri_glmfit in 
each folder?

Please correct my conclusions if they are wrong.

1 - In the "Main" folder, the sig.nii.gz contains the results of 
One-sample t test regressing out the effect of the two covariates.



Correct


2 - In the "Covariate 1" folder, the sig.nii.gz contains the 
significant cluster that are associated with the covariate 1 
regressing out the effect for the covariate 2.



Yes (and the main)


3 - In the "Covariate 2" folder, the sig.nii.gz contains the 
significant cluster that are associated with the covariate 2 
regressing out the effect for the covariate 1.



Yes (and regressing out the main)


Thanks


Stefano

*
*

*
*



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[Freesurfer] One Group (One Factor), Two Covariates

[stdp82]

Hi list,

in reference to One Group (One Factor), Two Covariates

https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G2V#Contrast2age.mtx

that has been applied on FS-FAST fcMRI data

I obtain three folder, respectively, for "main", "covariate 1", "covariate 2".

What's meaning the sig.nii.gz that it is produced by mri_glmfit in each folder?
Please correct my conclusions if they are wrong.

1 - In the "Main" folder, the sig.nii.gz contains the results of One-sample t 
test regressing out the effect of the two covariates.

2 - In the "Covariate 1" folder, the sig.nii.gz contains the significant 
cluster that are associated with the covariate 1 regressing out the effect for 
the covariate 2.

3 - In the "Covariate 2" folder, the sig.nii.gz contains the significant 
cluster that are associated with the covariate 2 regressing out the effect for 
the covariate 1.

Thanks


Stefano


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