Dear Mr. Greve

Thanks for your suggestions.

However I'm still a bit puzzled about how to contrast two runs corresponding to different stimulations (StimA: runA and StimB:runB) from one subject.

I have two runs each containing a paradigm file corresponding to one of the two stimulations.

How is it possible to contrast those two stimulation conditions acquired in two different runs since one run and thus also the paradigm file does not contain both stimulation conditions?

Seemingly both stimulation conditions must be in one paradigm file set to different onset timings to perform mkcontrast-sess

My folder Structure is as follows

Project Name

Session = Subject

Runs (001, 002) = Stimulation A and Stimulation B, each with a separate paradigm file

I know that I do not have to model the no-stimulation periods explicitely

Best wishes

Chris

Von: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> im Auftrag von Douglas N. Greve <dgreve@mgh.harvard.edu>
Gesendet: Freitag, 6. März 2020 17:54:16
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] within-subject contrast between runs

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Dear Freesurfer Experts,

I have a very basic questions about creating subject-wise contrasts between runs

 

Background

Study with two runs per subject where each run corresponds two a different condition (i.e. Stimulation A (on - off) and Stimulation B (on - off).

I performed the preprocessing and 1st levels stats in the native subjects space

Questions

• How can I obtain a within-subjects contrast between two runs (the Stimulation A vs. Stimulation B )  obtained in two runs within one session?

The easiest way is to code the conditions differently in the paradigm file (eg, instead of two conditions, you'd have 4, ARun1, BRun1, ARun2, BRun2), then just create contrasts as normal

• Can I obtain this within-subject contrast by staying in the native subject space?

It can be done in fsaverage or the native subject surface space, it is not related.

• Do I have to concatenate both runs and create a new parradigm file?

No, see above

Thanks for your support

Sincerely

Chris

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