Hi @elaurent,
Can you describe how it went wrong? I know you said that you tried putting the skull stripped T1w as the raw with version 20.0.0 with the skip skull strip flag. Given that it looks like that flag was introduced after 20.0.0 (looks like it was 20.1.0rc1 Merge pull request #2039 from oesteban/enh/skip-anat-brain-extraction · nipreps/fmriprep@0482c23 · GitHub), that’s probably why it didn’t work. But I don’t know what precisely you’ve tried with the most recent version, which makes it difficult for me to provide specific support.
One issue I see is that the final anatomical derivative for the T1 isn’t just skull stripped, but entirely preprocessed (i.e. with additional steps like intensity normalization). If you want the have fmriprep use it as a precomputed derivative, it should be entirely preprocessed in RAS space and named accordingly, like the usual fmriprep anatomical output.
Best,
Steven