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!
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!
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:
- 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 contrastshould 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:
- 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!
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Yes, actually, I just want to know what does that mean when we use *, for example Gender*Group, does this mean group and gender has a interaction? So what i want to know, if we can create design matrix like this: X = 1 + age + gender + group, I dont want the interact between group and gender
Hope to hear from you soon! Merci Hao ________________________________ De : freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Douglas Greve greve@nmr.mgh.harvard.edu Envoyé : mardi 14 juin 2016 04:20:18 À : freesurfer@nmr.mgh.harvard.edu Objet : Re: [Freesurfer] Define the design matrix by myself
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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu de la part de Hao wen hao.freesurfer@hotmail.commailto:hao.freesurfer@hotmail.com Envoyé : vendredi 10 juin 2016 11:10:37 À : freesurfer@nmr.mgh.harvard.edumailto: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!
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello:
To make it more clear!
I thought from FSGD file in mris_preproc, it will regard the group and gender as class, so in the X.dat will be gender*group; will not be possible to have the seperate columns for gender and group? do I understand it correctly?
Or the FSGD file used in mris-preproc has nothing to do with the design matrix? It is used just to gather the thickness info from all the subjects?
Thank you
________________________________ De : freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Hao wen hao.freesurfer@hotmail.com Envoyé : mardi 14 juin 2016 09:25:06 À : Freesurfer support list Objet : Re: [Freesurfer] Define the design matrix by myself
Yes, actually, I just want to know what does that mean when we use *, for example Gender*Group, does this mean group and gender has a interaction? So what i want to know, if we can create design matrix like this: X = 1 + age + gender + group, I dont want the interact between group and gender
Hope to hear from you soon! Merci Hao ________________________________ De : freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Douglas Greve greve@nmr.mgh.harvard.edu Envoyé : mardi 14 juin 2016 04:20:18 À : freesurfer@nmr.mgh.harvard.edu Objet : Re: [Freesurfer] Define the design matrix by myself
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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu de la part de Hao wen hao.freesurfer@hotmail.commailto:hao.freesurfer@hotmail.com Envoyé : vendredi 10 juin 2016 11:10:37 À : freesurfer@nmr.mgh.harvard.edumailto: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!
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
It turned out this is not possible, I got this error:
ERROR: matrix is ill-conditioned or badly scaled, condno = 1.34551e+07
here is my design matrix:
1 AD CN age male female
1.000 0.000 1.000 74.300 0.000 1.000; 1.000 0.000 1.000 73.700 0.000 1.000; 1.000 0.000 1.000 84.500 1.000 0.000; 1.000 0.000 1.000 78.500 1.000 0.000; 1.000 0.000 1.000 80.800 0.000 1.000; 1.000 0.000 1.000 65.400 0.000 1.000; 1.000 0.000 1.000 73.100 1.000 0.000; 1.000 0.000 1.000 72.600 1.000 0.000; 1.000 0.000 1.000 63.200 0.000 1.000; 1.000 0.000 1.000 71.700 0.000 1.000; 1.000 0.000 1.000 77.700 1.000 0.000; 1.000 0.000 1.000 76.900 0.000 1.000; 1.000 0.000 1.000 73.200 0.000 1.000; 1.000 0.000 1.000 76.200 0.000 1.000; 1.000 0.000 1.000 84.700 0.000 1.000; 1.000 0.000 1.000 69.600 1.000 0.000; 1.000 0.000 1.000 70.100 0.000 1.000; 1.000 0.000 1.000 70.900 1.000 0.000; 1.000 0.000 1.000 77.000 1.000 0.000; 1.000 0.000 1.000 74.500 0.000 1.000; 1.000 0.000 1.000 74.400 1.000 0.000; 1.000 0.000 1.000 72.900 0.000 1.000; 1.000 0.000 1.000 74.000 0.000 1.000; 1.000 0.000 1.000 70.600 0.000 1.000; 1.000 0.000 1.000 78.200 0.000 1.000; 1.000 0.000 1.000 70.600 0.000 1.000; 1.000 0.000 1.000 80.300 1.000 0.000; 1.000 0.000 1.000 65.100 0.000 1.000; 1.000 0.000 1.000 69.800 0.000 1.000; 1.000 0.000 1.000 71.100 0.000 1.000; 1.000 1.000 0.000 81.300 0.000 1.000; 1.000 1.000 0.000 75.400 0.000 1.000; 1.000 1.000 0.000 73.900 1.000 0.000; 1.000 1.000 0.000 64.100 0.000 1.000; 1.000 1.000 0.000 80.100 0.000 1.000; 1.000 1.000 0.000 78.300 0.000 1.000; 1.000 1.000 0.000 73.200 0.000 1.000; 1.000 1.000 0.000 75.300 1.000 0.000; 1.000 1.000 0.000 65.600 0.000 1.000; 1.000 1.000 0.000 62.400 0.000 1.000; 1.000 1.000 0.000 77.200 1.000 0.000; 1.000 1.000 0.000 70.700 1.000 0.000; 1.000 1.000 0.000 70.100 1.000 0.000; 1.000 1.000 0.000 82.600 1.000 0.000; 1.000 1.000 0.000 80.200 1.000 0.000; 1.000 1.000 0.000 65.900 1.000 0.000; 1.000 1.000 0.000 59.700 1.000 0.000; 1.000 1.000 0.000 71.800 0.000 1.000; 1.000 1.000 0.000 72.400 1.000 0.000; 1.000 1.000 0.000 80.500 1.000 0.000; 1.000 1.000 0.000 62.900 0.000 1.000; 1.000 1.000 0.000 67.400 0.000 1.000; 1.000 1.000 0.000 80.200 1.000 0.000; 1.000 1.000 0.000 85.500 0.000 1.000; 1.000 1.000 0.000 65.900 0.000 1.000; 1.000 1.000 0.000 89.100 1.000 0.000; 1.000 1.000 0.000 56.400 0.000 1.000; 1.000 1.000 0.000 82.700 0.000 1.000; 1.000 1.000 0.000 68.300 0.000 1.000; 1.000 1.000 0.000 74.000 0.000 1.000;
and my contrast is: -1 1 0 0 0,
So I think right now you should understand what I mean, sorry for the mess!
In SurfStat, they treat these variables as main effect, and gender*group as interaction, so my question is in FS, do we have a way to do this like main effect for the categorized factor?
Hope to hear from you soon!
________________________________ De : freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Hao wen hao.freesurfer@hotmail.com Envoyé : mardi 14 juin 2016 12:10:38 À : Freesurfer support list Objet : Re: [Freesurfer] Define the design matrix by myself
Hello:
To make it more clear!
I thought from FSGD file in mris_preproc, it will regard the group and gender as class, so in the X.dat will be gender*group; will not be possible to have the seperate columns for gender and group? do I understand it correctly?
Or the FSGD file used in mris-preproc has nothing to do with the design matrix? It is used just to gather the thickness info from all the subjects?
Thank you
________________________________ De : freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Hao wen hao.freesurfer@hotmail.com Envoyé : mardi 14 juin 2016 09:25:06 À : Freesurfer support list Objet : Re: [Freesurfer] Define the design matrix by myself
Yes, actually, I just want to know what does that mean when we use *, for example Gender*Group, does this mean group and gender has a interaction? So what i want to know, if we can create design matrix like this: X = 1 + age + gender + group, I dont want the interact between group and gender
Hope to hear from you soon! Merci Hao ________________________________ De : freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Douglas Greve greve@nmr.mgh.harvard.edu Envoyé : mardi 14 juin 2016 04:20:18 À : freesurfer@nmr.mgh.harvard.edu Objet : Re: [Freesurfer] Define the design matrix by myself
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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu de la part de Hao wen hao.freesurfer@hotmail.commailto:hao.freesurfer@hotmail.com Envoyé : vendredi 10 juin 2016 11:10:37 À : freesurfer@nmr.mgh.harvard.edumailto: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!
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
remove the 1st column and it will be ok
On 6/14/16 6:24 AM, Hao wen wrote:
It turned out this is not possible, I got this error:
ERROR: matrix is ill-conditioned or badly scaled, condno = 1.34551e+07
here is my design matrix:
1 AD CN age male female
1.000 0.000 1.000 74.300 0.000 1.000; 1.000 0.000 1.000 73.700 0.000 1.000; 1.000 0.000 1.000 84.500 1.000 0.000; 1.000 0.000 1.000 78.500 1.000 0.000; 1.000 0.000 1.000 80.800 0.000 1.000; 1.000 0.000 1.000 65.400 0.000 1.000; 1.000 0.000 1.000 73.100 1.000 0.000; 1.000 0.000 1.000 72.600 1.000 0.000; 1.000 0.000 1.000 63.200 0.000 1.000; 1.000 0.000 1.000 71.700 0.000 1.000; 1.000 0.000 1.000 77.700 1.000 0.000; 1.000 0.000 1.000 76.900 0.000 1.000; 1.000 0.000 1.000 73.200 0.000 1.000; 1.000 0.000 1.000 76.200 0.000 1.000; 1.000 0.000 1.000 84.700 0.000 1.000; 1.000 0.000 1.000 69.600 1.000 0.000; 1.000 0.000 1.000 70.100 0.000 1.000; 1.000 0.000 1.000 70.900 1.000 0.000; 1.000 0.000 1.000 77.000 1.000 0.000; 1.000 0.000 1.000 74.500 0.000 1.000; 1.000 0.000 1.000 74.400 1.000 0.000; 1.000 0.000 1.000 72.900 0.000 1.000; 1.000 0.000 1.000 74.000 0.000 1.000; 1.000 0.000 1.000 70.600 0.000 1.000; 1.000 0.000 1.000 78.200 0.000 1.000; 1.000 0.000 1.000 70.600 0.000 1.000; 1.000 0.000 1.000 80.300 1.000 0.000; 1.000 0.000 1.000 65.100 0.000 1.000; 1.000 0.000 1.000 69.800 0.000 1.000; 1.000 0.000 1.000 71.100 0.000 1.000; 1.000 1.000 0.000 81.300 0.000 1.000; 1.000 1.000 0.000 75.400 0.000 1.000; 1.000 1.000 0.000 73.900 1.000 0.000; 1.000 1.000 0.000 64.100 0.000 1.000; 1.000 1.000 0.000 80.100 0.000 1.000; 1.000 1.000 0.000 78.300 0.000 1.000; 1.000 1.000 0.000 73.200 0.000 1.000; 1.000 1.000 0.000 75.300 1.000 0.000; 1.000 1.000 0.000 65.600 0.000 1.000; 1.000 1.000 0.000 62.400 0.000 1.000; 1.000 1.000 0.000 77.200 1.000 0.000; 1.000 1.000 0.000 70.700 1.000 0.000; 1.000 1.000 0.000 70.100 1.000 0.000; 1.000 1.000 0.000 82.600 1.000 0.000; 1.000 1.000 0.000 80.200 1.000 0.000; 1.000 1.000 0.000 65.900 1.000 0.000; 1.000 1.000 0.000 59.700 1.000 0.000; 1.000 1.000 0.000 71.800 0.000 1.000; 1.000 1.000 0.000 72.400 1.000 0.000; 1.000 1.000 0.000 80.500 1.000 0.000; 1.000 1.000 0.000 62.900 0.000 1.000; 1.000 1.000 0.000 67.400 0.000 1.000; 1.000 1.000 0.000 80.200 1.000 0.000; 1.000 1.000 0.000 85.500 0.000 1.000; 1.000 1.000 0.000 65.900 0.000 1.000; 1.000 1.000 0.000 89.100 1.000 0.000; 1.000 1.000 0.000 56.400 0.000 1.000; 1.000 1.000 0.000 82.700 0.000 1.000; 1.000 1.000 0.000 68.300 0.000 1.000; 1.000 1.000 0.000 74.000 0.000 1.000;
and my contrast is: -1 1 0 0 0,
So I think right now you should understand what I mean, sorry for the mess!
In SurfStat, they treat these variables as main effect, and gender*group as interaction, so my question is in FS, do we have a way to do this like main effect for the categorized factor?
Hope to hear from you soon!
*De :* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Hao wen hao.freesurfer@hotmail.com *Envoyé :* mardi 14 juin 2016 12:10:38 *À :* Freesurfer support list *Objet :* Re: [Freesurfer] Define the design matrix by myself
Hello:
To make it more clear!
I thought from FSGD file in mris_preproc, it will regard the group and gender as class, so in the X.dat will be gender*group; will not be possible to have the seperate columns for gender and group? do I understand it correctly?
Or the FSGD file used in mris-preproc has nothing to do with the design matrix? It is used just to gather the thickness info from all the subjects?
Thank you
*De :* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Hao wen hao.freesurfer@hotmail.com *Envoyé :* mardi 14 juin 2016 09:25:06 *À :* Freesurfer support list *Objet :* Re: [Freesurfer] Define the design matrix by myself Yes, actually, I just want to know what does that mean when we use *, for example Gender*Group, does this mean group and gender has a interaction? So what i want to know, if we can create design matrix like this: X = 1 + age + gender + group, I dont want the interact between group and gender
Hope to hear from you soon! Merci Hao
*De :* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Douglas Greve greve@nmr.mgh.harvard.edu *Envoyé :* mardi 14 juin 2016 04:20:18 *À :* freesurfer@nmr.mgh.harvard.edu *Objet :* Re: [Freesurfer] Define the design matrix by myself 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:
- 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 contrastshould 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:
- 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!
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
When passed to mris_preproc, the fsgd file is only to specify the subjects. Using the fsgd file for both mris_preproc and mri_glmfit assure that the order of the subjects is the same
On 6/14/16 6:10 AM, Hao wen wrote:
Hello:
To make it more clear!
I thought from FSGD file in mris_preproc, it will regard the group and gender as class, so in the X.dat will be gender*group; will not be possible to have the seperate columns for gender and group? do I understand it correctly?
Or the FSGD file used in mris-preproc has nothing to do with the design matrix? It is used just to gather the thickness info from all the subjects?
Thank you
*De :* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Hao wen hao.freesurfer@hotmail.com *Envoyé :* mardi 14 juin 2016 09:25:06 *À :* Freesurfer support list *Objet :* Re: [Freesurfer] Define the design matrix by myself Yes, actually, I just want to know what does that mean when we use *, for example Gender*Group, does this mean group and gender has a interaction? So what i want to know, if we can create design matrix like this: X = 1 + age + gender + group, I dont want the interact between group and gender
Hope to hear from you soon! Merci Hao
*De :* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Douglas Greve greve@nmr.mgh.harvard.edu *Envoyé :* mardi 14 juin 2016 04:20:18 *À :* freesurfer@nmr.mgh.harvard.edu *Objet :* Re: [Freesurfer] Define the design matrix by myself 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:
- 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 contrastshould 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:
- 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!
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Glad to know the fsgd file explanation:)
I have deleted the first colum(constant column, I made a simple mistake), but it didnt work even without the constant column, I got the same error:
ERROR: matrix is ill-conditioned or badly scaled, condno = 1.07053e+07 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class.
here is the design matrix:
AD CN age male female
0.000 1.000 74.300 0.000 1.000; 0.000 1.000 73.700 0.000 1.000; 0.000 1.000 84.500 1.000 0.000; 0.000 1.000 78.500 1.000 0.000; 0.000 1.000 80.800 0.000 1.000; 0.000 1.000 65.400 0.000 1.000; 0.000 1.000 73.100 1.000 0.000; 0.000 1.000 72.600 1.000 0.000; 0.000 1.000 63.200 0.000 1.000; 0.000 1.000 71.700 0.000 1.000; 0.000 1.000 77.700 1.000 0.000; 0.000 1.000 76.900 0.000 1.000; 0.000 1.000 73.200 0.000 1.000; 0.000 1.000 76.200 0.000 1.000; 0.000 1.000 84.700 0.000 1.000; 0.000 1.000 69.600 1.000 0.000; 0.000 1.000 70.100 0.000 1.000; 0.000 1.000 70.900 1.000 0.000; 0.000 1.000 77.000 1.000 0.000; 0.000 1.000 74.500 0.000 1.000; 0.000 1.000 74.400 1.000 0.000; 0.000 1.000 72.900 0.000 1.000; 0.000 1.000 74.000 0.000 1.000; 0.000 1.000 70.600 0.000 1.000; 0.000 1.000 78.200 0.000 1.000; 0.000 1.000 70.600 0.000 1.000; 0.000 1.000 80.300 1.000 0.000; 0.000 1.000 65.100 0.000 1.000; 0.000 1.000 69.800 0.000 1.000; 0.000 1.000 71.100 0.000 1.000; 1.000 0.000 81.300 0.000 1.000; 1.000 0.000 75.400 0.000 1.000; 1.000 0.000 73.900 1.000 0.000; 1.000 0.000 64.100 0.000 1.000; 1.000 0.000 80.100 0.000 1.000; 1.000 0.000 78.300 0.000 1.000; 1.000 0.000 73.200 0.000 1.000; 1.000 0.000 75.300 1.000 0.000; 1.000 0.000 65.600 0.000 1.000; 1.000 0.000 62.400 0.000 1.000; 1.000 0.000 77.200 1.000 0.000; 1.000 0.000 70.700 1.000 0.000; 1.000 0.000 70.100 1.000 0.000; 1.000 0.000 82.600 1.000 0.000; 1.000 0.000 80.200 1.000 0.000; 1.000 0.000 65.900 1.000 0.000; 1.000 0.000 59.700 1.000 0.000; 1.000 0.000 71.800 0.000 1.000; 1.000 0.000 72.400 1.000 0.000; 1.000 0.000 80.500 1.000 0.000; 1.000 0.000 62.900 0.000 1.000; 1.000 0.000 67.400 0.000 1.000; 1.000 0.000 80.200 1.000 0.000; 1.000 0.000 85.500 0.000 1.000; 1.000 0.000 65.900 0.000 1.000; 1.000 0.000 89.100 1.000 0.000; 1.000 0.000 56.400 0.000 1.000; 1.000 0.000 82.700 0.000 1.000; 1.000 0.000 68.300 0.000 1.000; 1.000 0.000 74.000 0.000 1.000;
here is my contraix matrix:
-1 1 0 0 0
I dont know why? It is because of the column male and female that we can not treat them like this?
Hope to hear from you soon
Merci!
________________________________ De : freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Douglas Greve greve@nmr.mgh.harvard.edu Envoyé : mardi 14 juin 2016 17:23:08 À : Freesurfer support list Objet : Re: [Freesurfer] Define the design matrix by myself
When passed to mris_preproc, the fsgd file is only to specify the subjects. Using the fsgd file for both mris_preproc and mri_glmfit assure that the order of the subjects is the same
On 6/14/16 6:10 AM, Hao wen wrote:
Hello:
To make it more clear!
I thought from FSGD file in mris_preproc, it will regard the group and gender as class, so in the X.dat will be gender*group; will not be possible to have the seperate columns for gender and group? do I understand it correctly?
Or the FSGD file used in mris-preproc has nothing to do with the design matrix? It is used just to gather the thickness info from all the subjects?
Thank you
________________________________ De : freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu de la part de Hao wen hao.freesurfer@hotmail.commailto:hao.freesurfer@hotmail.com Envoyé : mardi 14 juin 2016 09:25:06 À : Freesurfer support list Objet : Re: [Freesurfer] Define the design matrix by myself
Yes, actually, I just want to know what does that mean when we use *, for example Gender*Group, does this mean group and gender has a interaction? So what i want to know, if we can create design matrix like this: X = 1 + age + gender + group, I dont want the interact between group and gender
Hope to hear from you soon! Merci Hao ________________________________ De : freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu de la part de Douglas Greve greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu Envoyé : mardi 14 juin 2016 04:20:18 À : freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Objet : Re: [Freesurfer] Define the design matrix by myself
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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu de la part de Hao wen hao.freesurfer@hotmail.commailto:hao.freesurfer@hotmail.com Envoyé : vendredi 10 juin 2016 11:10:37 À : freesurfer@nmr.mgh.harvard.edumailto: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!
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The 1st and 2nd column add up to the 3rd and 4th column. To do this type of model, you'll have to have 1. A column of 1s (like you had before) 2. Get rid of columns 2 and 5.
This makes the 1st column of all 1s represent a CN-female. the (new) 2nd column is the additive effect of AD. You'll basically be fitting this equation
thickness = offset + beta1*AD + beta2*Age + beta3*male
On 6/15/16 9:44 AM, Hao wen wrote:
Glad to know the fsgd file explanation:)
I have deleted the first colum(constant column, I made a simple mistake), but it didnt work even without the constant column, I got the same error:
ERROR: matrix is ill-conditioned or badly scaled, condno = 1.07053e+07
Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class.
here is the design matrix:
AD CN age male female
0.000 1.000 74.300 0.000 1.000; 0.000 1.000 73.700 0.000 1.000; 0.000 1.000 84.500 1.000 0.000; 0.000 1.000 78.500 1.000 0.000; 0.000 1.000 80.800 0.000 1.000; 0.000 1.000 65.400 0.000 1.000; 0.000 1.000 73.100 1.000 0.000; 0.000 1.000 72.600 1.000 0.000; 0.000 1.000 63.200 0.000 1.000; 0.000 1.000 71.700 0.000 1.000; 0.000 1.000 77.700 1.000 0.000; 0.000 1.000 76.900 0.000 1.000; 0.000 1.000 73.200 0.000 1.000; 0.000 1.000 76.200 0.000 1.000; 0.000 1.000 84.700 0.000 1.000; 0.000 1.000 69.600 1.000 0.000; 0.000 1.000 70.100 0.000 1.000; 0.000 1.000 70.900 1.000 0.000; 0.000 1.000 77.000 1.000 0.000; 0.000 1.000 74.500 0.000 1.000; 0.000 1.000 74.400 1.000 0.000; 0.000 1.000 72.900 0.000 1.000; 0.000 1.000 74.000 0.000 1.000; 0.000 1.000 70.600 0.000 1.000; 0.000 1.000 78.200 0.000 1.000; 0.000 1.000 70.600 0.000 1.000; 0.000 1.000 80.300 1.000 0.000; 0.000 1.000 65.100 0.000 1.000; 0.000 1.000 69.800 0.000 1.000; 0.000 1.000 71.100 0.000 1.000; 1.000 0.000 81.300 0.000 1.000; 1.000 0.000 75.400 0.000 1.000; 1.000 0.000 73.900 1.000 0.000; 1.000 0.000 64.100 0.000 1.000; 1.000 0.000 80.100 0.000 1.000; 1.000 0.000 78.300 0.000 1.000; 1.000 0.000 73.200 0.000 1.000; 1.000 0.000 75.300 1.000 0.000; 1.000 0.000 65.600 0.000 1.000; 1.000 0.000 62.400 0.000 1.000; 1.000 0.000 77.200 1.000 0.000; 1.000 0.000 70.700 1.000 0.000; 1.000 0.000 70.100 1.000 0.000; 1.000 0.000 82.600 1.000 0.000; 1.000 0.000 80.200 1.000 0.000; 1.000 0.000 65.900 1.000 0.000; 1.000 0.000 59.700 1.000 0.000; 1.000 0.000 71.800 0.000 1.000; 1.000 0.000 72.400 1.000 0.000; 1.000 0.000 80.500 1.000 0.000; 1.000 0.000 62.900 0.000 1.000; 1.000 0.000 67.400 0.000 1.000; 1.000 0.000 80.200 1.000 0.000; 1.000 0.000 85.500 0.000 1.000; 1.000 0.000 65.900 0.000 1.000; 1.000 0.000 89.100 1.000 0.000; 1.000 0.000 56.400 0.000 1.000; 1.000 0.000 82.700 0.000 1.000; 1.000 0.000 68.300 0.000 1.000; 1.000 0.000 74.000 0.000 1.000;
here is my contraix matrix:
-1 1 0 0 0
I dont know why? It is because of the column male and female that we can not treat them like this?
Hope to hear from you soon
Merci!
*De :* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Douglas Greve greve@nmr.mgh.harvard.edu *Envoyé :* mardi 14 juin 2016 17:23:08 *À :* Freesurfer support list *Objet :* Re: [Freesurfer] Define the design matrix by myself When passed to mris_preproc, the fsgd file is only to specify the subjects. Using the fsgd file for both mris_preproc and mri_glmfit assure that the order of the subjects is the same
On 6/14/16 6:10 AM, Hao wen wrote:
Hello:
To make it more clear!
I thought from FSGD file in mris_preproc, it will regard the group and gender as class, so in the X.dat will be gender*group; will not be possible to have the seperate columns for gender and group? do I understand it correctly?
Or the FSGD file used in mris-preproc has nothing to do with the design matrix? It is used just to gather the thickness info from all the subjects?
Thank you
*De :* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Hao wen hao.freesurfer@hotmail.com *Envoyé :* mardi 14 juin 2016 09:25:06 *À :* Freesurfer support list *Objet :* Re: [Freesurfer] Define the design matrix by myself Yes, actually, I just want to know what does that mean when we use *, for example Gender*Group, does this mean group and gender has a interaction? So what i want to know, if we can create design matrix like this: X = 1 + age + gender + group, I dont want the interact between group and gender
Hope to hear from you soon! Merci Hao
*De :* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Douglas Greve greve@nmr.mgh.harvard.edu *Envoyé :* mardi 14 juin 2016 04:20:18 *À :* freesurfer@nmr.mgh.harvard.edu *Objet :* Re: [Freesurfer] Define the design matrix by myself 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:
- 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 contrastshould 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:
- 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!
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas Greve -
Hao wen