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')