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()
