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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> de la part de Hao wen
<hao.freesur...@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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> de la part de Hao wen
<hao.freesur...@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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> de la part de Douglas Greve
<gr...@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 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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> de la part de Hao wen
<hao.freesur...@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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