[Eeglablist] Help with LIMO ANCOVA/Regression and STUDY cluster analysis

deniz doruk drdenizdoruk at gmail.com
Sat Feb 6 12:24:37 PST 2021

Hello Cyril, 

Thank you very much for your clarifications. This is very helpful. Just a few follow questions:

> the 'best' thing to do would be to compute contrasts, i.e. [1 -1 0] for each subject which is your main effect, then ANCOVA 2 gp and covariates

> [...] What I tried was (after precomputing channel measures for ERPs, power spectrum and ERP-image):
>> 1)First level analysis: Estimate model parameters (beta files), with interaction term, OLS, and selected timeframe.
> --> no interaction - you do group statistics (anyway there should be any to compute given 2 conditions only ie your design should have 3 columns, if so no need to recompute)
>> 2)Second level analysis:
>> Choose channel file, and work folder
>> Run ANCOVA—> Full scalp analysis —> How many independent group?—>enter 2—>Load beta or con files? —> load beta files for each group separately (gp1 and gp2)_—> Which parameters to test?—> Enter [1 2] for my repeated conditions (n=2) —> Here I see the error:
> yes my bad -- there should a message preventing you to do that ; you cannot do rep. measures here (will include in the next patch)
> as explained above, use contrasts from 1st level instead.

-When I run the first level analysis it only creates 2 beta files, one for each group, but there are not any con files created automatically.
Here do you mean, following the first level analysis, I should create contrast files using contrast manager, separately for each independent group, using one-sample t-test and then use these con files in ANCOVA (define contrast [1 -1 0], then run Contrast Manager—> LIMO files for the group —> contrast.mat file —> second level—>one-sample t-test?)

-From what I understand, if I wanted to test the relation between my covariate and  each condition (for each different repeated measure), then I have to create different study designs for each condition (one condition x 2 groups) since I can not include repeated measure in ANCOVA? 

>> 2)Regression-LIMO
>> I also thought that if ANCOVA did not work, I could run a regression model separately for each independent group.
>> In the tutorial it gives an example of creating a first level contrast for each subject, and then run a-sample t-test to create the con files which would be used in the regression model along with the regressor variable. I was wondering if there is a way to use parameters from the repeated measure ANOVA model as they would account for the noise better, or maybe it would not differ much since I used OLS?
> well see above -- if you split the ANCOVA covariates (ie use XXXXXX000000 and 00000XXXXX with values) say for age, then you model separately the effect of age for each group - which allws you to test [1 -1] if group differ, [0 0 1 -1] if the effect of age differ, [0 0 1 1] the common effect of age

-Here are you referring to post-hoc contrast analysis following ANCOVA? So for the covariate file should I have 2 columns (000XXX  and XXX000) with each column representing values from from one group? 

Sorry for all the questions, I just wanted to make sure I am doing the right thing! We are getting some excited results with LIMO, so I really hope to be able to finalize my analysis using LIMO, but  at the same time I want to be  confident about the stats and what they mean for when it gets published!

Thank you very much!!

> -
> Dr Cyril Pernet,
> Centre for Clinical Brain Sciences (CCBS)
> Neuroimaging Sciences
> wamcyril at gmail.com
> https://urldefense.com/v3/__https://cpernet.github.io/__;!!Mih3wA!XvwCdIMmKCt9C9LdzqTML_KC-G6quFcFj2Ex_fKfNCo0WXt0_GGKr4eW4t9sBGFyxtNbaQ$ 

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