External Email - Use Caution
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
Yes, exactly on both questions
On 4/22/2021 8:23 AM, Marilena Wilding wrote:
External Email - Use Caution
External Email - Use Caution
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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Douglas N. Greve -
Marilena Wilding