sorry, I don't understand the question. It looks like the design matrix is right. It looks like the contrasts tests for a diff between AD and controls. What else do you need?

On 6/13/16 8:49 AM, Hao wen wrote:

Hello:

I am still confused about how to make the design matrix in FS for group analysis:

I want to create a design matrix like this: X = 1 + TermAge + TermGender * TermGroup (this should be like

Age

Female

*

AD

Male

*

AD

Female

*

CN

Male

*

CN

)

There are just 5 columns, not like DODS, we have 8 columns:

Here is my commandline process:

1) in mris_preproc, we gathered the thickness info from every subjects, the cml is as below:

mris_preproc --fsgd AD_CN_COVARIATES_AGE_GENDER.fsgd \

--cache-in thickness.fwhm15.fsaverage \

--target fsaverage \

--hemi lh \

--out lh.AD_CN_COVARIATES_AGE_GENDER_thickness_15.mgh

after this we use mri_glmfit :

mri_glmfit --glmdir lh.AD_CN_COVARIAETS_AGE_GENDER.glmdir\

--y lh.AD_CN_COVARIATES_AGE_GENDER_thickness_15.mgh \

--C Contrast.mtx \

--X X_5_intersect.mat\

--surf fsaverage lh \

--cortex

After this command:

In the command here, the Contrast.mtx is +0.00000 +1.00000 +1.00000 -1.00000 -1.00000 ,but it the result turns out that the contrast should be +0.00000 -1.00000 -1.00000 +1.00000 +1.00000, cuz the thickness of CN should be bigger than that of AD, so my question is how to know which colomn in the contrast should be Female*CN, Male*CN, Female*AD, Male*AD, I know in DODS, DOSS, this is related how do you how you order your class in the FSGD file, but here, I just have 5 columns, I dont know how to make the correspondences, I can just deduce it from my results, so I attached my FSGD file for you!

the design matrix is , Xg.dat, I ceate the design matrix, design_matrix.mat from matlab:

+74.30000 +0.00000 +0.00000 +0.00000 +1.00000

+73.70000 +0.00000 +0.00000 +0.00000 +1.00000

+84.50000 +0.00000 +0.00000 +1.00000 +0.00000

+78.50000 +0.00000 +0.00000 +1.00000 +0.00000

+80.80000 +0.00000 +0.00000 +0.00000 +1.00000

+65.40000 +0.00000 +0.00000 +0.00000 +1.00000

+73.10000 +0.00000 +0.00000 +1.00000 +0.00000

+72.60000 +0.00000 +0.00000 +1.00000 +0.00000

+63.20000 +0.00000 +0.00000 +0.00000 +1.00000

+71.70000 +0.00000 +0.00000 +0.00000 +1.00000

+77.70000 +0.00000 +0.00000 +1.00000 +0.00000

+76.90000 +0.00000 +0.00000 +0.00000 +1.00000

+73.20000 +0.00000 +0.00000 +0.00000 +1.00000

+76.20000 +0.00000 +0.00000 +0.00000 +1.00000

+84.70000 +0.00000 +0.00000 +0.00000 +1.00000

+69.60000 +0.00000 +0.00000 +1.00000 +0.00000

+70.10000 +0.00000 +0.00000 +0.00000 +1.00000

+70.90000 +0.00000 +0.00000 +1.00000 +0.00000

+77.00000 +0.00000 +0.00000 +1.00000 +0.00000

+74.50000 +0.00000 +0.00000 +0.00000 +1.00000

+74.40000 +0.00000 +0.00000 +1.00000 +0.00000

+72.90000 +0.00000 +0.00000 +0.00000 +1.00000

+74.00000 +0.00000 +0.00000 +0.00000 +1.00000

+70.60000 +0.00000 +0.00000 +0.00000 +1.00000

+78.20000 +0.00000 +0.00000 +0.00000 +1.00000

+70.60000 +0.00000 +0.00000 +0.00000 +1.00000

+80.30000 +0.00000 +0.00000 +1.00000 +0.00000

+65.10000 +0.00000 +0.00000 +0.00000 +1.00000

+69.80000 +0.00000 +0.00000 +0.00000 +1.00000

+71.10000 +0.00000 +0.00000 +0.00000 +1.00000

+81.30000 +0.00000 +1.00000 +0.00000 +0.00000

+75.40000 +0.00000 +1.00000 +0.00000 +0.00000

+73.90000 +1.00000 +0.00000 +0.00000 +0.00000

+64.10000 +0.00000 +1.00000 +0.00000 +0.00000

+80.10000 +0.00000 +1.00000 +0.00000 +0.00000

+78.30000 +0.00000 +1.00000 +0.00000 +0.00000

+73.20000 +0.00000 +1.00000 +0.00000 +0.00000

+75.30000 +1.00000 +0.00000 +0.00000 +0.00000

+65.60000 +0.00000 +1.00000 +0.00000 +0.00000

+62.40000 +0.00000 +1.00000 +0.00000 +0.00000

+77.20000 +1.00000 +0.00000 +0.00000 +0.00000

+70.70000 +1.00000 +0.00000 +0.00000 +0.00000

+70.10000 +1.00000 +0.00000 +0.00000 +0.00000

+82.60000 +1.00000 +0.00000 +0.00000 +0.00000

+80.20000 +1.00000 +0.00000 +0.00000 +0.00000

+65.90000 +1.00000 +0.00000 +0.00000 +0.00000

+59.70000 +1.00000 +0.00000 +0.00000 +0.00000

+71.80000 +0.00000 +1.00000 +0.00000 +0.00000

+72.40000 +1.00000 +0.00000 +0.00000 +0.00000

+80.50000 +1.00000 +0.00000 +0.00000 +0.00000

+62.90000 +0.00000 +1.00000 +0.00000 +0.00000

+67.40000 +0.00000 +1.00000 +0.00000 +0.00000

+80.20000 +1.00000 +0.00000 +0.00000 +0.00000

+85.50000 +0.00000 +1.00000 +0.00000 +0.00000

+65.90000 +0.00000 +1.00000 +0.00000 +0.00000

+89.10000 +1.00000 +0.00000 +0.00000 +0.00000

+56.40000 +0.00000 +1.00000 +0.00000 +0.00000

+82.70000 +0.00000 +1.00000 +0.00000 +0.00000

+68.30000 +0.00000 +1.00000 +0.00000 +0.00000

+74.00000 +0.00000 +1.00000 +0.00000 +0.00000

So my question is how to correspond the different column to the contrast matrix and this (

Age

Female

*

AD

Male

*

AD

Female

*

CN

Male

*

CN

)

So , do you have some specific tutorial for this kind of analysis, if not, can you clarify this to me a little and I would like to make a tutorial for this, cuz

De : freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> de la part de Hao wen <hao.freesurfer@hotmail.com>
Envoyé : vendredi 10 juin 2016 11:10:37
À : freesurfer@nmr.mgh.harvard.edu
Objet : [Freesurfer] GLM: Define the design matrix by myself

Hello, Freesurfer experts:
I want to define the design matrix by myself in GLM, I know that in FS, when we deal with the categorized factors, we treat them as classes, So basically, I want to make a design matrix like this:

1) formula_EffectOnGroupWithAgeGenderCovariates = 1 + TermGroup + TermAge + TermGender

and

2) formula_EffectOnGroupWithAgeGenderInterectionCovariates = 1 + TermAge + TermGender * TermGroup

Here, TermGroup and TermGender are categorized factors, so I know that we can make the design matrix like 2) in FS, cuz here we define it as intersection, but my question is that if wen can define a matrix like the first one? I know in SurfStat, we can define it like 1)

Hope to hear from you soon:)

thank you in advance!
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