class PlotBaseInputSpec(BaseInterfaceInputSpec): in_file = File(exists=True, mandatory=True, desc='File to be plotted') title = traits.Str(desc='a title string for the plot') annotate = traits.Bool(True, usedefault=True, desc='annotate left/right') figsize = traits.Tuple((11.69, 8.27), traits.Float, traits.Float, usedefault=True, desc='Figure size') dpi = traits.Int(300, usedefault=True, desc='Desired DPI of figure') out_file = File('mosaic.svg', usedefault=True, desc='output file name') cmap = traits.Str('Greys_r', usedefault=True)
class FunctionalSummaryInputSpec(BaseInterfaceInputSpec): slice_timing = traits.Enum(False, True, 'TooShort', usedefault=True, desc='Slice timing correction used') distortion_correction = traits.Str( 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_file = File(exists=True, desc='Confounds file')
class FSDetectInputsOutputSpec(TraitedSpec): t2w = File(desc='reference T2w image') use_t2w = traits.Bool(desc='enable use of T2w downstream computation') flair = File(desc='reference FLAIR image') use_flair = traits.Bool(desc='enable use of FLAIR downstream computation') hires = traits.Bool(desc='enable hi-res processing') mris_inflate = traits.Str(desc='mris_inflate argument')
class DerivativesDataSinkInputSpec(BaseInterfaceInputSpec): base_directory = traits.Directory( desc='Path to the base directory for storing data.') in_file = InputMultiPath(File(exists=True), mandatory=True, desc='the object to be saved') source_file = File(exists=False, mandatory=True, desc='the input func file') suffix = traits.Str('', mandatory=True, desc='suffix appended to source_file') extra_values = traits.List(traits.Str)
class BIDSFreeSurferDirInputSpec(BaseInterfaceInputSpec): derivatives = Directory(exists=True, mandatory=True, desc='BIDS derivatives directory') freesurfer_home = Directory(exists=True, mandatory=True, desc='FreeSurfer installation directory') subjects_dir = traits.Str('freesurfer', usedefault=True, desc='Name of FreeSurfer subjects directory') spaces = traits.List(traits.Str, desc='Set of output spaces to prepare') overwrite_fsaverage = traits.Bool(False, usedefault=True, desc='Overwrite fsaverage directories, if present')
class BIDSInfoOutputSpec(TraitedSpec): subject_id = traits.Str() session_id = traits.Str() task_id = traits.Str() acq_id = traits.Str() rec_id = traits.Str() run_id = traits.Str()
class ReadSidecarJSONOutputSpec(TraitedSpec): subject_id = traits.Str() session_id = traits.Str() task_id = traits.Str() acq_id = traits.Str() rec_id = traits.Str() run_id = traits.Str() out_dict = traits.Dict()
class DerivativesDataSinkInputSpec(BaseInterfaceInputSpec): base_directory = traits.Directory( desc='Path to the base directory for storing data.') in_file = InputMultiPath(File(exists=True), mandatory=True, desc='the object to be saved') source_file = File(exists=False, mandatory=True, desc='the input func file') suffix = traits.Str('', mandatory=True, desc='suffix appended to source_file') extra_values = traits.List(traits.Str) compress = traits.Bool( desc="force compression (True) or uncompression (False)" " of the output file (default: same as input)")
class FSInjectBrainExtractedOutputSpec(TraitedSpec): subjects_dir = Directory(desc='FreeSurfer SUBJECTS_DIR') subject_id = traits.Str(desc='Subject ID')
class FSInjectBrainExtractedInputSpec(BaseInterfaceInputSpec): subjects_dir = Directory(mandatory=True, desc='FreeSurfer SUBJECTS_DIR') subject_id = traits.Str(mandatory=True, desc='Subject ID') in_brain = File(mandatory=True, exists=True, desc='input file, part of a BIDS tree')
class GiftiNameSourceOutputSpec(TraitedSpec): out_name = traits.Str( desc='(partial) filename formatted according to template')
class GiftiNameSourceInputSpec(BaseInterfaceInputSpec): in_file = File(mandatory=True, exists=True, desc='input GIFTI file') pattern = traits.Str( mandatory=True, desc='input file name pattern (must capture named group "LR")') template = traits.Str(mandatory=True, desc='output file name template')
class GenerateCiftiOutputSpec(TraitedSpec): out_file = File(exists=True, desc="generated CIFTI file") variant = traits.Str(desc="combination of target spaces label") variant_key = File(exists=True, desc='file storing variant space information')
class CiftiNameSourceInputSpec(BaseInterfaceInputSpec): variant = traits.Str(mandatory=True, desc=('unique label of spaces used in combination to' ' generate CIFTI file'))
class MedialNaNsInputSpec(BaseInterfaceInputSpec): in_file = File(exists=True, mandatory=True, desc='input surface file') target_subject = traits.Str(mandatory=True, desc='target subject ID') subjects_dir = Directory(mandatory=True, desc='FreeSurfer SUBJECTS_DIR')