def create_parser():
parser = NiArgumentParser(fromfile_prefix_chars='@', argument_default=argparse.SUPPRESS,
description="AFNI subject level statistical analysis")
parser._add_outputs = False
group = parser.add_argument_group('Required')
group.add_argument('-s', '--subjects', nargs="+", required=True)
group.add_argument('-c', '--config', action=store_input, check_file=True, required=True, metavar="FILE")
group = parser.add_argument_group('Optional')
group.add_argument('--var', action="append", type=append_var, dest="vars")
group.add_argument("--run", nargs="+", dest="run_keys")
group.add_argument("--decon", action="append_const", const="decon", dest="run_keys")
group.add_argument("--reml", action="append_const", const="reml", dest="run_keys")
group.add_argument("--beta-series", action="append_const", const="beta_series",
dest="run_keys")
group.add_argument("--register-beta-series", action="append_const",
const="register_beta_series", dest="run_keys")
group.add_argument("--correlate", action="append_const", const="correlate", dest="run_keys")
group.add_argument("--verbose", action="store_const", const=1, dest="verbosity", default=0)
group.add_argument("--debug", action="store_const", const=2, dest="verbosity", default=0)
group.add_argument("--dry-run", action="store_true", default=False)
group.add_argument("--log", type=store_filename, default=None, metavar="FILE")
return parser
def create_parser():
parser = NiArgumentParser(fromfile_prefix_chars='@',
description="GLM/REML analysis of subject level activations")
group = parser.add_argument_group('Required')
group.add_argument('-s', '--subjects', nargs="+", required=True)
group.add_argument('-c', '--config', type=argparse.FileType('r'), required=True)
group = parser.add_argument_group('Optional')
group.add_argument("--interp", choices=["lin", "nn", "sinc", "spline"], default="lin")
group.add_argument("--dry-run", action="store_true", default=False)
group.add_argument("--cores", type=int, default=1)
group.add_argument("--verbose", action="store_const", const=1, dest="verbosity", default=0)
group.add_argument("--debug", action="store_const", const=2, dest="verbosity", default=0)
group.add_argument("--force", action="store_true", default=False, help="doesn't work")
return parser
def create_parser():
parser = NiArgumentParser(fromfile_prefix_chars='@', argument_default=argparse.SUPPRESS,
description="FSL group level statistical analysis (creates model)")
parser._add_outputs = False
group = parser.add_argument_group('Required')
group.add_argument('-c', '--config', action=store_input, check_file=True, required=True)
group.add_argument('--var', action="append", type=append_var, dest="vars")
group = parser.add_argument_group('Optional')
group.add_argument('--iterable', nargs="+")
group.add_argument("--run", nargs="+", dest="run_keys")
group.add_argument("--fsf", action="append_const", const="fsf", dest="run_keys")
group.add_argument("--feat", action="append_const", const="feat", dest="run_keys")
group.add_argument("--verbose", action="store_const", const=1, dest="verbosity", default=0)
group.add_argument("--debug", action="store_const", const=2, dest="verbosity", default=0)
group.add_argument("--dry-run", action="store_true", default=False)
group.add_argument("--log", type=store_filename, default=None, metavar="FILE")
return parser
def create_parser():
parser = NiArgumentParser(fromfile_prefix_chars='@', argument_default=argparse.SUPPRESS,
description="Find peak coordinate for each subject that is closest to a given" \
" reference coordinate")
parser._add_inputs = False
parser._add_outputs = False
group = parser.add_argument_group('Required')
group.add_argument('-i', '--input', required=True, metavar="FILE")
group.add_argument('-m', '--mask', required=True, metavar="FILE")
group.add_argument('-o', '--prefix', required=True, metavar="FILE PREFIX")
group.add_argument('-c', '--coord', nargs=3, type=int, required=True, metavar=('x','y','z'))
group = parser.add_argument_group('Command Options')
group.add_argument("-t", "--thresh", type=float, default=2.3, metavar="THRESHOLD", help="default: %(default)s")
group.add_argument('--std', default=standard_image("MNI152_T1_2mm_brain.nii.gz"), metavar="FILE", help="default: %(default)s")
group.add_argument("--orient", default="LPI", metavar="XXX", help="default: %(default)s")
group.add_argument('-r', "--radius", type=int, default=1, metavar="mm", help="default: %(default)s")
group = parser.add_argument_group('I/O Options')
group.add_argument('--roi', action="store_true", default=False, help="create ROI")
group.add_argument('--pic', action="store_true", default=False, help="create picture")
group.add_argument('-s', '--subjects', nargs="+", metavar="ID")
group.add_argument('--var', action="append", type=append_var, dest="vars")
group.add_argument('--overwrite', action="store_true", default=False, help="default: %(default)s")
group.add_argument("--verbose", action="store_const", const=1, dest="verbosity", default=0)
group.add_argument("--debug", action="store_const", const=2, dest="verbosity", default=0)
group.add_argument("--dry-run", action="store_true", default=False, help="default: %(default)s")
group.add_argument("--log", type=store_filename, default=None, metavar="FILE", help="default: %(default)s")
return parser
def create_parser():
parser = NiArgumentParser(fromfile_prefix_chars="@",
argument_default=argparse.SUPPRESS,
description="""Create motion report""")
parser._add_inputs = False
parser._add_outputs = False
group = parser.add_argument_group('Required "Options"')
group.add_argument('-s', '--subjects', nargs="+", required=True)
group.add_argument('-a', '--anatdirs', nargs="+", action=store_special, required=True)
group.add_argument('-r', '--regdirs', nargs="+", action=store_special, default=None)
group.add_argument('-f', '--funcdirs', nargs="+", action=store_special, default=None)
group.add_argument('-e', '--segdirs', nargs="+", action=store_special, default=None)
group.add_argument('-n', '--nuidirs', nargs="+", action=store_special, default=None)
group.add_argument('-o', '--outdir', required=True)
group = parser.add_argument_group('Optional "Options"')
group.add_argument("--overwrite", action="store_true", default=False)
group.add_argument("--verbose", action="store_const", const=1, dest="verbosity", default=0)
group.add_argument("--debug", action="store_const", const=2, dest="verbosity", default=0)
return parser
