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')