class SplitDWIsOutputSpec(TraitedSpec): dwi_files = OutputMultiObject(File(exists=True), desc='single volume dwis') bvec_files = OutputMultiObject(File(exists=True), desc='single volume bvecs') bval_files = OutputMultiObject(File(exists=True), desc='single volume bvals') b0_images = OutputMultiObject(File(exists=True), desc='just the b0s') b0_indices = traits.List(desc='list of original indices for each b0 image') original_files = OutputMultiObject(File(exists=True))
class _DerivativesDataSinkOutputSpec(TraitedSpec): out_file = OutputMultiObject(File(exists=True, desc='written file path')) out_meta = OutputMultiObject(File(exists=True, desc='written JSON sidecar path')) compression = OutputMultiObject( traits.Bool, desc='whether ``in_file`` was compressed/uncompressed ' 'or `it was copied directly.') fixed_hdr = traits.List(traits.Bool, desc='whether derivative header was fixed')
class ComposeTransformsOutputSpec(TraitedSpec): out_warps = OutputMultiObject(File(exists=True), desc='composed all transforms to output_grid') out_affines = OutputMultiObject(File(exists=True), desc='composed affine-only transforms to output_grid') transform_lists = OutputMultiObject(traits.List(File(exists=True)), desc='lists of transforms for each image') log_cmdline = File(desc='a list of command lines used to apply transforms')
class ConcatRPESplitsOutputSpec(TraitedSpec): dwi_files = OutputMultiObject(File(exists=True), desc='single volume dwis') bvec_files = OutputMultiObject(File(exists=True), desc='single volume bvecs') bval_files = OutputMultiObject(File(exists=True), desc='single volume bvals') b0_images = OutputMultiObject(File(exists=True), desc='just the b0s') b0_indices = traits.List(desc='list of indices for each b0 image') original_files = traits.List(desc='list of source series for each dwi') sdc_method = traits.Str("PEB/PEPOLAR Series (phase-encoding based / PE-POLARity)")
class _FlattenOutputSpec(TraitedSpec): out_list = OutputMultiObject( traits.Tuple( File(exists=True), traits.DictStrAny, ), desc="list of output files", ) out_data = OutputMultiObject(File(exists=True)) out_meta = OutputMultiObject(traits.DictStrAny)
class _DerivativesDataSinkOutputSpec(TraitedSpec): out_file = OutputMultiObject(File(exists=True, desc="written file path")) out_meta = OutputMultiObject( File(exists=True, desc="written JSON sidecar path")) compression = OutputMultiObject( traits.Either(None, traits.Bool), desc= "whether ``in_file`` should be compressed (True), uncompressed (False) " "or left unmodified (None).", ) fixed_hdr = traits.List(traits.Bool, desc="whether derivative header was fixed")
class _BIDSDataGrabberOutputSpec(TraitedSpec): out_dict = traits.Dict(desc="output data structure") fmap = OutputMultiObject(desc="output fieldmaps") bold = OutputMultiObject(desc="output functional images") sbref = OutputMultiObject(desc="output sbrefs") t1w = OutputMultiObject(desc="output T1w images") roi = OutputMultiObject(desc="output ROI images") t2w = OutputMultiObject(desc="output T2w images") flair = OutputMultiObject(desc="output FLAIR images") asl = OutputMultiObject(desc='output ASL images') m0z = OutputMultiObject(desc='output MZeros images') cbf = OutputMultiObject(desc='output CBF images')
class BIDSGrabOutputSpec(TraitedSpec): fmri_prep = OutputMultiPath(ImageFile) fmri_prep_aroma = OutputMultiPath(ImageFile) conf_raw = OutputMultiPath(File) conf_json = OutputMultiPath(File) # TODO: Kamil check entities = OutputMultiObject(traits.Dict) tr_dict = traits.Dict()
class GroupImagesOutputSpec(TraitedSpec): plus_dwi_files = OutputMultiObject(File(exists=True)) plus_bval_files = OutputMultiObject(File(exists=True)) plus_bvec_files = OutputMultiObject(File(exists=True)) plus_original_files = OutputMultiObject(File(exists=True)) minus_dwi_files = OutputMultiObject(File(exists=True)) minus_bval_files = OutputMultiObject(File(exists=True)) minus_bvec_files = OutputMultiObject(File(exists=True)) minus_original_files = OutputMultiObject(File(exists=True))
class _RobustAverageOutputSpec(TraitedSpec): out_file = File(exists=True, desc="the averaged image") out_volumes = File(exists=True, desc="the volumes selected that have been averaged") out_drift = traits.List( traits.Float, desc="the ratio to the grand mean or global signal drift") out_hmc = OutputMultiObject(File(exists=True), desc="head-motion correction matrices")
class BIDSDataGrabberOutputSpec(TraitedSpec): out_dict = traits.Dict(desc='output data structure') fmap = OutputMultiObject(desc='output fieldmaps') bold = OutputMultiObject(desc='output functional images') sbref = OutputMultiObject(desc='output sbrefs') t1w = OutputMultiObject(desc='output T1w images') roi = OutputMultiObject(desc='output ROI images') t2w = OutputMultiObject(desc='output T2w images') flair = OutputMultiObject(desc='output FLAIR images')
class _TemplateDimensionsOutputSpec(TraitedSpec): t1w_valid_list = OutputMultiObject(exists=True, desc="valid T1w images") target_zooms = traits.Tuple(traits.Float, traits.Float, traits.Float, desc="Target zoom information") target_shape = traits.Tuple(traits.Int, traits.Int, traits.Int, desc="Target shape information") out_report = File(exists=True, desc="conformation report")
class MultivariateTemplateConstruction2OutputSpec(TraitedSpec): templates = OutputMultiObject(File(exists=True), mandatory=True) forward_transforms = OutputMultiObject(OutputMultiObject( File(exists=True)), mandatory=True) reverse_transforms = OutputMultiObject(OutputMultiObject( File(exists=True)), mandatory=True) iteration_templates = OutputMultiObject(File(exists=True))
class _BSplineApproxOutputSpec(TraitedSpec): out_field = File(exists=True) out_coeff = OutputMultiObject(File(exists=True)) out_error = File(exists=True) out_extrapolated = File()
class DerivativesDataSinkOutputSpec(TraitedSpec): out_file = OutputMultiObject(File(exists=True, desc='written file path')) compression = OutputMultiPath( traits.Bool, desc='whether ``in_file`` was compressed/uncompressed ' 'or `it was copied directly.')
class _TransformCoefficientsOutputSpec(TraitedSpec): out_coeff = OutputMultiObject(File(exists=True), desc="moved coefficients")
class _TOPUPCoeffReorientOutputSpec(TraitedSpec): out_coeff = OutputMultiObject(File(exists=True), desc="patched coefficients")
class _aCompCorMasksOutputSpec(TraitedSpec): out_masks = OutputMultiObject( File(exists=True), desc="CSF, WM and combined masks, respectively")
class _ApplyCoeffsFieldOutputSpec(TraitedSpec): out_corrected = OutputMultiObject(File(exists=True)) out_field = OutputMultiObject(File(exists=True)) out_warp = OutputMultiObject(File(exists=True))
class SplitIntramodalTransformOutputSpec(TraitedSpec): transform_files = OutputMultiObject(File(exists=True))
class ReorderOutputsOutputSpec(TraitedSpec): full_transforms = OutputMultiObject(traits.List()) full_predicted_dwi_series = OutputMultiObject(File(exists=True)) hmc_warped_images = OutputMultiObject(File(exists=True))
class _SplitSeriesOutputSpec(TraitedSpec): out_files = OutputMultiObject(File(exists=True), desc="output list of 3d images")
class MatchTransformsOutputSpec(TraitedSpec): transforms = OutputMultiObject(File(exists=True), mandatory=True)
class DisassembleTransformOutputSpec(TraitedSpec): out_transforms = OutputMultiObject(File(exists=True))
class BIDSDataGrabberOutputSpec(_BIDSDataGrabberOutputSpec): dwi = OutputMultiObject(desc="output DWI images")
class _ANTsBBROutputSpec(TraitedSpec): forward_transforms = OutputMultiObject(File())
class B0RPEFieldmapOutputSpec(TraitedSpec): fmap_file = OutputMultiObject(File(exists=True)) fmap_info = OutputMultiObject(File(exists=True))
class IntraModalMergeOutputSpec(TraitedSpec): out_file = File(exists=True, desc='merged image') out_avg = File(exists=True, desc='average image') out_mats = OutputMultiObject(File(exists=True), desc='output matrices') out_movpar = OutputMultiObject(File(exists=True), desc='output movement parameters')
class SliceQCOutputSpec(TraitedSpec): imputed_images = OutputMultiObject(File(exists=True), desc='dwi files with imputed slices') slice_stats = File(exists=True, desc='npy file with the slice-by-TR error matrix')
class ExtractDWISForModelOutputSpec(TraitedSpec): model_dwi_files = OutputMultiObject(File(exists=True)) model_bvals = OutputMultiObject(File(exists=True)) model_bvecs = OutputMultiObject(File(exists=True)) transforms = InputMultiObject()