t1-volume pipeline

[JiWon Youn]

Dear clinicaTeam,  

I am currently running the t1-volume pipeline in Clinica version 0.7.5, but I have encountered an error.
Could you please guide me on how to resolve this error?

Best regards,
JiWonYoun


2023-07-11 11:08:05,810:INFO:The t1-volume pipeline is divided into 4 parts:
        t1-volume-tissue-segmentation pipeline: Tissue segmentation, bias correction and spatial normalization to MNI space
        t1-volume-create-dartel pipeline: Inter-subject registration with the creation of a new DARTEL template
        t1-volume-dartel2mni pipeline: DARTEL template to MNI
        t1-volume-parcellation pipeline: Atlas statistics
2023-07-11 11:08:05,810:INFO:Part 1/4: Running t1-volume-segmentation pipeline.
2023-07-11 11:08:06,492:INFO:The pipeline will be run on the following 2 image(s):
2023-07-11 11:08:06,492:INFO:   sub-0004 | ses-1, ses-2,
2023-07-11 11:08:06,493:INFO:The pipeline will last approximately 10 minutes per image.
Traceback (most recent call last):
  File "/usr/local/bin/clinica", line 8, in <module>
    sys.exit(main())
  File "/usr/local/lib/python3.8/dist-packages/clinica/cmdline.py", line 92, in main
    cli()
  File "/usr/local/lib/python3.8/dist-packages/click/core.py", line 1130, in __call__
    return self.main(*args, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/click/core.py", line 1055, in main
    rv = self.invoke(ctx)
  File "/usr/local/lib/python3.8/dist-packages/click/core.py", line 1657, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/usr/local/lib/python3.8/dist-packages/click/core.py", line 1657, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/usr/local/lib/python3.8/dist-packages/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/usr/local/lib/python3.8/dist-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/click/decorators.py", line 26, in new_func
    return f(get_current_context(), *args, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/clinica/pipelines/t1_volume/t1_volume_cli.py", line 93, in cli
    ctx.invoke(
  File "/usr/local/lib/python3.8/dist-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/clinica/pipelines/t1_volume_tissue_segmentation/t1_volume_tissue_segmentation_               cli.py", line 68, in cli
    pipeline.run(plugin="MultiProc", plugin_args={"n_procs": n_procs})
  File "/usr/local/lib/python3.8/dist-packages/clinica/pipelines/engine.py", line 353, in run
    raise e
  File "/usr/local/lib/python3.8/dist-packages/clinica/pipelines/engine.py", line 334, in run
    exec_graph = Workflow.run(self, plugin, plugin_args, update_hash)
  File "/usr/local/lib/python3.8/dist-packages/nipype/pipeline/engine/workflows.py", line 638, in run
    runner.run(execgraph, updatehash=updatehash, config=self.config)
  File "/usr/local/lib/python3.8/dist-packages/nipype/pipeline/plugins/base.py", line 166, in run
    self._clean_queue(jobid, graph, result=result)
  File "/usr/local/lib/python3.8/dist-packages/nipype/pipeline/plugins/base.py", line 244, in _clean_queue
    raise RuntimeError("".join(result["traceback"]))
RuntimeError: Traceback (most recent call last):
  File "/usr/local/lib/python3.8/dist-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/usr/local/lib/python3.8/dist-packages/nipype/pipeline/engine/nodes.py", line 524, in run
    result = self._run_interface(execute=True)
  File "/usr/local/lib/python3.8/dist-packages/nipype/pipeline/engine/nodes.py", line 642, in _run_interface
    return self._run_command(execute)
  File "/usr/local/lib/python3.8/dist-packages/nipype/pipeline/engine/nodes.py", line 750, in _run_command
    raise NodeExecutionError(
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node 2-SpmSegmentation.

Traceback (most recent call last):
  File "/usr/local/lib/python3.8/dist-packages/nipype/interfaces/base/core.py", line 454, in aggregate_outputs
    setattr(outputs, key, val)
  File "/usr/local/lib/python3.8/dist-packages/nipype/interfaces/base/traits_extension.py", line 425, in validate
    value = super(MultiObject, self).validate(objekt, name, newvalue)
  File "/usr/local/lib/python3.8/dist-packages/traits/trait_types.py", line 2699, in validate
    return TraitListObject(self, object, name, value)
  File "/usr/local/lib/python3.8/dist-packages/traits/trait_list_object.py", line 582, in __init__
    super().__init__(
  File "/usr/local/lib/python3.8/dist-packages/traits/trait_list_object.py", line 213, in __init__
    super().__init__(self.item_validator(item) for item in iterable)
  File "/usr/local/lib/python3.8/dist-packages/traits/trait_list_object.py", line 213, in <genexpr>
    super().__init__(self.item_validator(item) for item in iterable)
  File "/usr/local/lib/python3.8/dist-packages/traits/trait_list_object.py", line 865, in _item_validator
    return trait_validator(object, self.name, value)
  File "/usr/local/lib/python3.8/dist-packages/nipype/interfaces/base/traits_extension.py", line 330, in validate
    value = super(File, self).validate(objekt, name, value, return_pathlike=True)
  File "/usr/local/lib/python3.8/dist-packages/nipype/interfaces/base/traits_extension.py", line 135, in validate
    self.error(objekt, name, str(value))
  File "/usr/local/lib/python3.8/dist-packages/traits/base_trait_handler.py", line 74, in error
    raise TraitError(
traits.trait_errors.TraitError: Each element of the 'transformation_mat' trait of a NewSegmentOutputSpec instance must be a p               athlike object or string representing an existing file, but a value of '/jwyoun/cmc-ad/p3-all/02-data/clinica/temp/t1-volume-               tissue-segmentation/b7d647b98ee2f6737fe2d54d0a0accf45fe44279/2-SpmSegmentation/sub-0004_ses-1_T1w_seg8.mat' <class 'str'> was                specified.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/lib/python3.8/dist-packages/nipype/interfaces/base/core.py", line 401, in run
    outputs = self.aggregate_outputs(runtime)
  File "/usr/local/lib/python3.8/dist-packages/nipype/interfaces/base/core.py", line 461, in aggregate_outputs
    raise FileNotFoundError(msg)
FileNotFoundError: No such file or directory '['/jwyoun/cmc-ad/p3-all/02-data/clinica/temp/t1-volume-tissue-segmentation/b7d6               47b98ee2f6737fe2d54d0a0accf45fe44279/2-SpmSegmentation/sub-0004_ses-1_T1w_seg8.mat']' for output 'transformation_mat' of a Ne               wSegment interface

[Ghislain Vaillant]

Hi JiWonYoun,

Thank you for reaching out to the Clinica community.

Could you provide us with more details regarding your SPM setup?

Are you using it through MATLAB or using the SPM standalone version?

Cheers,

Ghis