Re: [Freesurfer] Contrast files - 2 groups, 4 covariates

[Douglas N. Greve]

If it is only one subject and you have no continuous variables, you can 
do it that way. If you have continuous variables, you will need to use 
DOSS (different-offset same slope) to force the slopes to be the same 
across classes (because you can't compute a slope from a single data point)


On 5/10/2024 12:46 PM, Liliana Wu wrote:


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Thank you Douglas. That’s much clearer. I do however,  have a subject 
without a gender disclosure. Would I set up my class and contrasts as:


5 classes: PatentientsMale, PatientsFemale, HCMale, HCFemale, HCNa

then use contrast [0.5 0.5 -0.33 -0.33 -0.33 0 0 0 0 0 ...]?

Best,

Liliana


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Re: [Freesurfer] Contrast files - 2 groups, 4 covariates

[Liliana Wu]

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Thank you Douglas. That’s much clearer. I do however,  have a subject without a 
gender disclosure. Would I set up my class and contrasts as:

5 classes: PatentientsMale, PatientsFemale, HCMale, HCFemale, HCNa


then use contrast [0.5 0.5 -0.33 -0.33 -0.33 0 0 0 0 0 ...]?



Best,
Liliana

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Re: [Freesurfer] Contrast files - 2 groups, 4 covariates

[Douglas N. Greve]

The first one will test for a difference between group offset/intercept 
accounting for age, gender, episodes, and residuals. By setting a 
regressor contrast element to 0, one accounts for that variable because 
the variable appears in the model that is fit to the data (and so its 
effects already removed from other variables). One more thing: I would 
recommend incorporating gender in the class structure not as a 
continuous variable. So you would have 4 classes: PatentientsMale, 
PatientsFemale, HCMale, HCFemale then use contrast [0.5 0.5 -0.5 -0.5 0 
0 0 0 0 ...]


On 5/9/2024 3:26 PM, Liliana Wu wrote:


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Hello!

I am having trouble with creating my contrast files. I did go over 
FsfdExamples (*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples 
). 
However, I am unsure how should I create my contrast files if I want 
do a 2 group comparison while controlling 4 covariates:


Class:

Patients, healthy control

variables are:

Age,gender,episodes,residuals,

Here is how I set up my contrast files:

1 -1 0 0 0 0 0 0 0 0  - Contrast1 (measure group differences)

1 -1 0.125 0.125 0.125 0.125 0.125 0.125 0.125 0.125 – Contrast 2 
(measure group differences while accounting for covariates)


For some reason I think I am setting up those contrast files wrong… 
Any help is appreciated.


Best,

Liliana


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[Freesurfer] Contrast files - 2 groups, 4 covariates

[Liliana Wu]

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Hello!

I am having trouble with creating my contrast files. I did go over FsfdExamples 
(https://secure-web.cisco.com/1ezcK_pFVwJfmWpdVsJeZORU_8kaDi3SfZnw3BO98zpMkJch-p_v87YwJzoqtiefk_hIobUKYja2omqZRjod-i1GdU-HkzipUmBlo5LVsklOHdteQtjAi1L5l1J_T5iRzcE-h_C2xiFxUcjQxPmDrQFVFDP-mFdgiDx4hibkUidw4NEsFW1XHiR7roksIT1GrgvmbILffvuecnvDO6Z8oTqSldk1jddeE0vQYO5WHK19PUmdcg_uW0gtN1EgAhq3AxmE2NcKh2djkfca5f3nqamoDBZ84nG1kz_J43CQgPHPe_lX5eVqUfcsPGuqiMUbpt15_ZNoCDBTS88hFbjyFVA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsgdExamples).
 However, I am unsure how should I create my contrast files if I want do a 2 
group comparison while controlling 4 covariates:

Class:
Patients, healthy control

variables are:
Age,gender,episodes,residuals,


Here is how I set up my contrast files:

1 -1 0 0 0 0 0 0 0 0  - Contrast1 (measure group differences)
1 -1 0.125 0.125 0.125 0.125 0.125 0.125 0.125 0.125 – Contrast 2 (measure 
group differences while accounting for covariates)



For some reason I think I am setting up those contrast files wrong… Any help is 
appreciated.

Best,
Liliana

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