Discarding dummy scans of preprocessed functional data by fMRIPrep

Hello. I have a question about fMRIPrep.
I ran fMRIPrep with the -- dummy -scans N and I understand that the N scans are not really discarded and just treated as dummy scans. However, I did not include the dummy scans into onset timing so I would like to discard N dummy scans before runnning the first level GLM with SPM12.

Now, I’m planning to discard the N scans of preprocessed functional data and the corresponding rows of confound timeseries before the first level analysis. Is this correct way?

Thanks, in advance.


The two things you can do are either 1) move timings forward in your events file to account for the dummy scans, or as you suggested 2) discard the dummy scans in the confounds and BOLD image. The results you get with either method should be the same, but I would suggest doing the first method instead. It is good practice in general not to throw away data unless you are absolutely sure you will not need it.


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