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!