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Dear Freesurfers,

 

I’m currently doing 2nd level analysis on a FIR model.

I first concatenated my data with this command:

 

isxconcat-sess -sf sessidlist -analysis FIR_group.lh -contrast global-v-local -no-hrf -hemi lh -o group_analysis

 

I got 29 timepoints and their corresponding 29 ces.nii and cesvar.nii files.

 

Then I ran glmfit (for each timepoint):

 

mri_glmfit \

--y ces.000.nii \

--wls cesvar.000.nii.gz \

--surface fsaverage lh \

--glmdir group_GLM_lh_000.wls \

--osgm \

--nii.gz

 

In my paradigm I’m showing a stimulus that can be seen in two ways. In my analysis I separate the runs, depending on what the participant indicated to have seen (1 or 2) and compute the contrast in activation between these two percepts. I was now wondering if the command above is correct with the ‘osgm’-flag? Since I’m only interested in the difference between the two conditions from the paradigm and not different groups of participants (e.g. patients vs. healthy people) I don’t have to specify a fsgd file, correct? And if I wanted to specify covariates I’d just make such a file but without groups and only variables?

 

Thank you very much for your help!

 

Best,

Mara

 

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