Larmarbar

Thanks for pointing that out, that makes a lot of sense! It appears my issue is that when running with --recon-only, the --bids-filter-file seems to be ignored? Is this by...

It appeared to still run reconstruction on both sessions for a given subject rather than just the one specified in the filter file when using --recon-only. When I am running...

That's good to know! I think noting this in the documentation for the bids-filter flag would already be very helpful!