Remove the first four scans of fMRI sequence BEFORE/DURING fMRI prep

Hi there,

This is a pretty simple question (newbie here).

I want to exclude the first four dicom acquisitions of my fMRI sequences from my NIFTI conversions that I put into fMRIprep. Is there a way to do this in Dcm2niix or Dcm2Bids? or does fMRIprep somehow automatically do this?

Thanks,

Jen

Hi Jen,

I believe you can just set the number of —dummy-scans to be 4 in your fmriprep command. If not, I think FSL’s fslroi can do something similar to your nifti files. Alternatively you can process as normal and use one-hot encoded vectors in your design matrices to exclude the first four volumes from further analysis (similar to how motion outliers are treated).

Hope this helps,
Steven