fMRIprep BOLD brain mask issue

Software Support
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Dear @jsein,

thanks a lot for your response! Could you elaborate a little on how you would do that practically? I believe, for “resampling” the anatomical and functional images would have to be aligned already, just not in the same space, right? Do you mean something like:

  1. registering the anatomical brain mask to the raw EPI space, using e.g. FLIRT
  2. apply brain masks to raw EPIs
  3. rerun fmriprep and skip skull stripping as you mentioned here: Using fmriprep with brain-extracted raw data - Neuro Questions - Neurostars?

I’m nor 100% sure what --skull-strip-t1w skip really does? Does it only skip T1 brain extraction or also change behavior on functional processing?

Many thanks for your opinion!

Best,
Martin