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')