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 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 ICAConfoundsInputSpec(BaseInterfaceInputSpec): in_directory = Directory(mandatory=True, desc='directory where ICA derivatives are found') ignore_aroma_err = traits.Bool(False, usedefault=True, desc='ignore ICA-AROMA errors')
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 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')