class MaskEPIInputSpec(BaseInterfaceInputSpec):
in_files = InputMultiPath(File(exists=True),
mandatory=True,
desc='input EPI or list of files')
lower_cutoff = traits.Float(0.2, usedefault=True)
upper_cutoff = traits.Float(0.85, usedefault=True)
connected = traits.Bool(True, usedefault=True)
opening = traits.Int(2, usedefault=True)
exclude_zeros = traits.Bool(False, usedefault=True)
ensure_finite = traits.Bool(True, usedefault=True)
target_affine = traits.File()
target_shape = traits.File()
class PlotContoursInputSpec(BaseInterfaceInputSpec):
in_file = File(exists=True, mandatory=True, desc='File to be plotted')
in_contours = File(exists=True,
mandatory=True,
desc='file to pick the contours from')
cut_coords = traits.Int(8, usedefault=True, desc='number of slices')
levels = traits.List([.5],
traits.Float,
usedefault=True,
desc='add a contour per level')
colors = traits.List(['r'],
traits.Str,
usedefault=True,
desc='colors to be used for contours')
display_mode = traits.Enum('ortho',
'x',
'y',
'z',
'yx',
'xz',
'yz',
usedefault=True,
desc='visualization mode')
saturate = traits.Bool(False, usedefault=True, desc='saturate background')
out_file = traits.File(exists=False, desc='output file name')
vmin = traits.Float(desc='minimum intensity')
vmax = traits.Float(desc='maximum intensity')
class MaskEPIInputSpec(BaseInterfaceInputSpec):
in_files = InputMultiPath(File(exists=True),
mandatory=True,
desc='input EPI or list of files')
lower_cutoff = traits.Float(0.2, usedefault=True)
upper_cutoff = traits.Float(0.85, usedefault=True)
connected = traits.Bool(True, usedefault=True)
enhance_t2 = traits.Bool(False,
usedefault=True,
desc='enhance T2 contrast on image')
opening = traits.Int(2, usedefault=True)
closing = traits.Bool(True, usedefault=True)
fill_holes = traits.Bool(True, usedefault=True)
exclude_zeros = traits.Bool(False, usedefault=True)
ensure_finite = traits.Bool(True, usedefault=True)
target_affine = traits.Either(None,
traits.File(exists=True),
default=None,
usedefault=True)
target_shape = traits.Either(None,
traits.File(exists=True),
default=None,
usedefault=True)
no_sanitize = traits.Bool(False, usedefault=True)