def bin_paths(ops, raw):
    """ set which binary is being aligned to """
    raw_file_align = []
    raw_file_alt = []
    reg_file_align = []
    reg_file_alt = []
    if raw:
        if ops['nchannels'] > 1:
            if ops['functional_chan'] == ops['align_by_chan']:
                raw_file_align = ops['raw_file']
                raw_file_alt = ops['raw_file_chan2']
                reg_file_align = ops['reg_file']
                reg_file_alt = ops['reg_file_chan2']
            else:
                raw_file_align = ops['raw_file_chan2']
                raw_file_alt = ops['raw_file']
                reg_file_align = ops['reg_file_chan2']
                reg_file_alt = ops['reg_file']
        else:
            raw_file_align = ops['raw_file']
            reg_file_align = ops['reg_file']
    elif ops['nchannels'] > 1:
        if ops['functional_chan'] == ops['align_by_chan']:
            reg_file_align = ops['reg_file']
            reg_file_alt = ops['reg_file_chan2']
        else:
            reg_file_align = ops['reg_file_chan2']
            reg_file_alt = ops['reg_file']
    else:
        reg_file_align = ops['reg_file']
    return reg_file_align, reg_file_alt, raw_file_align, raw_file_alt
