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 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 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 StructuralQCInputSpec(BaseInterfaceInputSpec):
in_file = File(exists=True, mandatory=True, desc='file to be plotted')
in_noinu = File(exists=True,
mandatory=True,
desc='image after INU correction')
in_segm = File(exists=True,
mandatory=True,
desc='segmentation file from FSL FAST')
in_bias = File(exists=True, mandatory=True, desc='bias file')
head_msk = File(exists=True, mandatory=True, desc='head mask')
air_msk = File(exists=True, mandatory=True, desc='air mask')
rot_msk = File(exists=True, mandatory=True, desc='rotation mask')
artifact_msk = File(exists=True, mandatory=True, desc='air mask')
in_pvms = InputMultiPath(File(exists=True),
mandatory=True,
desc='partial volume maps from FSL FAST')
in_tpms = InputMultiPath(File(),
desc='tissue probability maps from FSL FAST')
mni_tpms = InputMultiPath(File(),
desc='tissue probability maps from FSL FAST')
in_fwhm = traits.List(traits.Float,
mandatory=True,
desc='smoothness estimated with AFNI')
class GatherConfoundsOutputSpec(TraitedSpec):
confounds_file = File(exists=True, desc='output confounds file')
confounds_list = traits.List(traits.Str, desc='list of headers')
class AddTSVHeaderInputSpec(BaseInterfaceInputSpec):
in_file = File(exists=True, mandatory=True, desc='input file')
columns = traits.List(traits.Str,
mandatory=True,
desc='header for columns')
class ReadSidecarJSONInputSpec(BaseInterfaceInputSpec):
in_file = File(exists=True, mandatory=True, desc='the input nifti file')
fields = traits.List(traits.Str, desc='get only certain fields')
class AddTPMsInputSpec(BaseInterfaceInputSpec):
in_files = InputMultiPath(File(exists=True), mandatory=True, desc='input list of ROIs')
indices = traits.List(traits.Int, desc='select specific maps')
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')
