class FunctionalSummaryInputSpec(BaseInterfaceInputSpec):
slice_timing = traits.Enum(False,
True,
'TooShort',
usedefault=True,
desc='Slice timing correction used')
distortion_correction = traits.Enum(
'epi',
'fieldmap',
'phasediff',
'SyN',
'None',
desc='Susceptibility distortion correction method',
mandatory=True)
pe_direction = traits.Enum(None,
'i',
'i-',
'j',
'j-',
mandatory=True,
desc='Phase-encoding direction detected')
registration = traits.Enum(
'FSL',
'FreeSurfer',
mandatory=True,
desc='Functional/anatomical registration method')
fallback = traits.Bool(desc='Boundary-based registration rejected')
registration_dof = traits.Enum(6,
9,
12,
desc='Registration degrees of freedom',
mandatory=True)
output_spaces = traits.List(desc='Target spaces')
confounds = traits.List(desc='Confounds collected')
class FilledImageLikeInputSpec(BaseInterfaceInputSpec):
in_file = File(exists=True, mandatory=True, desc='image to be demeaned')
fill_value = traits.Float(1.0, usedefault=True, desc='value to fill')
dtype = traits.Enum('float32',
'uint8',
usedefault=True,
desc='force output data type')
class FunctionalQCInputSpec(BaseInterfaceInputSpec):
in_epi = File(exists=True, mandatory=True, desc='input EPI file')
in_hmc = File(exists=True,
mandatory=True,
desc='input motion corrected file')
in_tsnr = File(exists=True, mandatory=True, desc='input tSNR volume')
in_mask = File(exists=True, mandatory=True, desc='input mask')
direction = traits.Enum('all',
'x',
'y',
'-x',
'-y',
usedefault=True,
desc='direction for GSR computation')
in_fd = File(exists=True,
mandatory=True,
desc='motion parameters for FD computation')
fd_thres = traits.Float(0.2,
usedefault=True,
desc='motion threshold for FD computation')
in_dvars = File(exists=True,
mandatory=True,
desc='input file containing DVARS')
in_fwhm = traits.List(traits.Float,
mandatory=True,
desc='smoothness estimated with AFNI')
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 SubjectSummaryInputSpec(BaseInterfaceInputSpec):
t1w = InputMultiPath(File(exists=True), desc='T1w structural images')
t2w = InputMultiPath(File(exists=True), desc='T2w structural images')
subjects_dir = Directory(desc='FreeSurfer subjects directory')
subject_id = Str(desc='Subject ID')
bold = traits.List(desc='BOLD functional series')
output_spaces = traits.List(desc='Target spaces')
template = traits.Enum('MNI152NLin2009cAsym', desc='Template space')
class GenerateCiftiInputSpec(BaseInterfaceInputSpec):
bold_file = File(mandatory=True, exists=True, desc="input BOLD file")
volume_target = traits.Enum("MNI152NLin2009cAsym",
mandatory=True,
usedefault=True,
desc="CIFTI volumetric output space")
surface_target = traits.Enum("fsaverage5",
"fsaverage6",
mandatory=True,
usedefault=True,
desc="CIFTI surface target space")
subjects_dir = Directory(mandatory=True, desc="FreeSurfer SUBJECTS_DIR")
TR = traits.Float(mandatory=True, desc="repetition time")
gifti_files = traits.List(
File(exists=True),
mandatory=True,
desc="list of surface geometry files (length 2 with order [L,R])")
class FunctionalSummaryInputSpec(BaseInterfaceInputSpec):
slice_timing = traits.Bool(False,
usedefault=True,
desc='Slice timing correction used')
distortion_correction = traits.Enum(
'epi',
'fieldmap',
'phasediff',
'SyN',
'None',
desc='Susceptibility distortion correction method',
mandatory=True)
registration = traits.Enum(
'FLIRT',
'bbregister',
mandatory=True,
desc='Functional/anatomical registration method')
output_spaces = traits.List(desc='Target spaces')
confounds = traits.List(desc='Confounds collected')
class FUGUEvsm2ANTSwarpInputSpec(BaseInterfaceInputSpec):
in_file = File(exists=True,
mandatory=True,
desc='input displacements field map')
pe_dir = traits.Enum('i',
'i-',
'j',
'j-',
'k',
'k-',
desc='phase-encoding axis')
class MergeInputSpec(BaseInterfaceInputSpec):
in_files = InputMultiPath(File(exists=True),
mandatory=True,
desc='input list of files to merge')
dtype = traits.Enum('f4',
'f8',
'u1',
'u2',
'u4',
'i2',
'i4',
usedefault=True,
desc='numpy dtype of output image')
header_source = File(
exists=True,
desc='a Nifti file from which the header should be copied')
class JoinTSVColumnsInputSpec(BaseInterfaceInputSpec):
in_file = File(exists=True, mandatory=True, desc='input file')
join_file = File(exists=True, mandatory=True, desc='file to be adjoined')
side = traits.Enum('right', 'left', usedefault=True, desc='where to join')
columns = traits.List(traits.Str, desc='header for columns')
