Hi @YukunQu,
Yes, please make your own recon spec json that is a copy of the json file (https://github.com/PennLINC/qsiprep/blob/master/qsiprep/data/pipelines/mrtrix_multishell_msmt_ACT-hsvs.json) but with your atlas in the atlases field. Then pass that modified json into the —recon-spec argument.
Best,
Steven