Hello NeuroStars Community,
I am trying to run niworkflows.interfaces.norm.SpatialNormalization in my local machine.
In fMRIPrep after Brain extraction and brain tissue segmentation, Spatial Normalization is performed. I was able to do Brain Extraction and Brain tissue Segmentation using ANT’s BrainExtraction module and FSL FAST module respectively in my local machine. Now I want to perform Spatial Normalization the way fMRIPrep is doing it. Based on the documentation all the structural preprocessing is being handled by init_anat_preproc_wf which is sMRIPrep pipeline. When I ran this niworkflows spatial normalization module it threw me this error. The outputs from BrainSegementation and BrainExtraction will be used as inputs for Spatial Normalization. It would be great learning experience for me is anyone can guide me thank you
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TraitError Traceback (most recent call last)
/tmp/ipykernel_159/2883818317.py in <module>
1 registration = SpatialNormalization(float=True, flavor="precise", moving_mask = moving_mask, template=template, template_spec=template_spec, moving_image = moving_image)
----> 2 registration.run()
~/anaconda3/lib/python3.9/site-packages/nipype/interfaces/base/core.py in run(self, cwd, ignore_exception, **inputs)
396 # Run interface
397 runtime = self._pre_run_hook(runtime)
--> 398 runtime = self._run_interface(runtime)
399 runtime = self._post_run_hook(runtime)
400 # Collect outputs
~/anaconda3/lib/python3.9/site-packages/niworkflows/interfaces/norm.py in _run_interface(self, runtime)
208 NIWORKFLOWS_LOG.info("Loading settings from file %s.", ants_settings)
209 # Configure an ANTs run based on these settings.
--> 210 self.norm = Registration(from_file=ants_settings, **ants_args)
211 self.norm.resource_monitor = False
212 self.norm.terminal_output = self.terminal_output
~/anaconda3/lib/python3.9/site-packages/nipype/interfaces/ants/registration.py in __init__(self, **inputs)
1013
1014 def __init__(self, **inputs):
-> 1015 super(Registration, self).__init__(**inputs)
1016 self._elapsed_time = None
1017 self._metric_value = None
~/anaconda3/lib/python3.9/site-packages/nipype/interfaces/ants/base.py in __init__(self, **inputs)
75
76 def __init__(self, **inputs):
---> 77 super(ANTSCommand, self).__init__(**inputs)
78 self.inputs.on_trait_change(self._num_threads_update, "num_threads")
79
~/anaconda3/lib/python3.9/site-packages/nipype/interfaces/base/core.py in __init__(self, command, terminal_output, write_cmdline, **inputs)
628 self, command=None, terminal_output=None, write_cmdline=False, **inputs
629 ):
--> 630 super(CommandLine, self).__init__(**inputs)
631 self._environ = None
632 # Set command. Input argument takes precedence
~/anaconda3/lib/python3.9/site-packages/nipype/interfaces/base/core.py in __init__(self, from_file, resource_monitor, ignore_exception, **inputs)
208
209 if from_file is not None:
--> 210 self.load_inputs_from_json(from_file, overwrite=True)
211
212 for name, value in list(inputs.items()):
~/anaconda3/lib/python3.9/site-packages/nipype/interfaces/base/core.py in load_inputs_from_json(self, json_file, overwrite)
487 for key in new_inputs:
488 if hasattr(self.inputs, key):
--> 489 setattr(self.inputs, key, inputs_dict[key])
490
491 def save_inputs_to_json(self, json_file):
~/anaconda3/lib/python3.9/site-packages/traits/trait_types.py in validate(self, object, name, value)
2693 return value
2694
-> 2695 return TraitListObject(self, object, name, value)
2696
2697 self.error(object, name, value)
~/anaconda3/lib/python3.9/site-packages/traits/trait_list_object.py in __init__(self, trait, object, name, value)
582 self._validate_length(len(value))
583
--> 584 super().__init__(
585 value,
586 item_validator=self._item_validator,
~/anaconda3/lib/python3.9/site-packages/traits/trait_list_object.py in __init__(self, iterable, item_validator, notifiers)
211 if item_validator is not None:
212 self.item_validator = item_validator
--> 213 super().__init__(self.item_validator(item) for item in iterable)
214 if notifiers is not None:
215 self.notifiers = list(notifiers)
~/anaconda3/lib/python3.9/site-packages/traits/trait_list_object.py in <genexpr>(.0)
211 if item_validator is not None:
212 self.item_validator = item_validator
--> 213 super().__init__(self.item_validator(item) for item in iterable)
214 if notifiers is not None:
215 self.notifiers = list(notifiers)
~/anaconda3/lib/python3.9/site-packages/traits/trait_list_object.py in _item_validator(self, value)
865
866 try:
--> 867 return trait_validator(object, self.name, value)
868 except TraitError as excp:
869 excp.set_prefix("Each element of the")
~/anaconda3/lib/python3.9/site-packages/traits/base_trait_handler.py in error(self, object, name, value)
72 The proposed new value for the attribute.
73 """
---> 74 raise TraitError(
75 object, name, self.full_info(object, name, value), value
76 )
TraitError: Each element of the 'transform_parameters' trait of a _FixHeaderRegistrationInputSpec instance must be a tuple of the form: (a float) or a tuple of the form: (a float, a float, a float) or a tuple of the form: (a float, an integer, an integer, an integer) or a tuple of the form: (a float, an integer, a float, a float, a float, a float) or a tuple of the form: (a float, a float, a float, an integer) or a tuple of the form: (a float, an integer, an integer, an integer, an integer), but a value of [0.05] <class 'list'> was specified.