Hello ppl,
I use fmriprep 20.0.6 in singularity generally without problems. In a specific dataset, which it passes the online bids validator, I come across an error which I have difficulties to decode. So, when I run fmriprep with –anat-only, --fs-no-reconall, --skull-strip-fixed-seed but without the –skip_bids_validation param I receive:
You are using fMRIPrep-20.0.6, and a newer version of fMRIPrep is available: 20.1.1.
Please check out our documentation about how and when to upgrade:
https://fmriprep.readthedocs.io/en/latest/faq.html#upgrading
Traceback (most recent call last):
File “/usr/local/miniconda/bin/fmriprep”, line 10, in
sys.exit(main())
File “/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/run.py”, line 319, in main
validate_input_dir(exec_env, opts.bids_dir, opts.participant_label)
File “/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/utils/bids.py”, line 146, in validate_input_dir
subprocess.check_call([‘bids-validator’, bids_dir, ‘-c’, temp.name])
File “/usr/local/miniconda/lib/python3.7/subprocess.py”, line 341, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command ‘[‘bids-validator’, PosixPath(’/data/project/age_prediction/datasets/datasets_repo/original/ixi/bids/GUYS’), ‘-c’, ‘/tmp/tmpy0qjczca’]’ returned non-zero exit status 3.
Sentry is attempting to send 0 pending error messages
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If I add the –skip_bids_validation then the error changes to the following poem:
You are using fMRIPrep-20.0.6, and a newer version of fMRIPrep is available: 20.1.1.
Please check out our documentation about how and when to upgrade:
https://fmriprep.readthedocs.io/en/latest/faq.html#upgrading
exception calling callback for <Future at 0x7fbd741b54a8 state=finished raised FileNotFoundError>
concurrent.futures.process._RemoteTraceback:
“”"
Traceback (most recent call last):
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py”, line 67, in run_node
result[“result”] = node.run(updatehash=updatehash)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 486, in run
self._get_hashval()
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 538, in _get_hashval
self._get_inputs()
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 609, in _get_inputs
self.set_input(key, deepcopy(output_value))
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 302, in set_input
setattr(self.inputs, parameter, deepcopy(val))
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/traits_extension.py”, line 425, in validate
value = super(MultiObject, self).validate(objekt, name, newvalue)
File “/usr/local/miniconda/lib/python3.7/site-packages/traits/trait_types.py”, line 2336, in validate
return TraitListObject( self, object, name, value )
File “/usr/local/miniconda/lib/python3.7/site-packages/traits/trait_handlers.py”, line 2313, in init
raise excp
File “/usr/local/miniconda/lib/python3.7/site-packages/traits/trait_handlers.py”, line 2305, in init
value = [ validate( object, name, val ) for val in value ]
File “/usr/local/miniconda/lib/python3.7/site-packages/traits/trait_handlers.py”, line 2305, in
value = [ validate( object, name, val ) for val in value ]
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/traits_extension.py”, line 329, in validate
value = super(File, self).validate(objekt, name, value, return_pathlike=True)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/traits_extension.py”, line 134, in validate
self.error(objekt, name, str(value))
File “/usr/local/miniconda/lib/python3.7/site-packages/traits/trait_handlers.py”, line 172, in error
value )
traits.trait_errors.TraitError: Each element of the ‘t1w_list’ trait of a _TemplateDimensionsInputSpec instance must be a pathlike object or string representing an existing file, but a value of ‘/data/project/age_prediction/datasets/datasets_repo/original/ixi/bids/GUYS/sub-IXI229/anat/sub-IXI229_T1w.nii.gz’ <class ‘str’> was specified.Error setting node input:
Node: t1w_ref_dimensions
input: t1w_list
results_file: /tmp/fmriprep_wf/single_subject_IXI229_wf/bidssrc/result_bidssrc.pklz
value: /data/project/age_prediction/datasets/datasets_repo/original/ixi/bids/GUYS/sub-IXI229/anat/sub-IXI229_T1w.nii.gzDuring handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “/usr/local/miniconda/lib/python3.7/concurrent/futures/process.py”, line 232, in process_worker
r = call_item.fn(*call_item.args, **call_item.kwargs)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py”, line 70, in run_node
result[“result”] = node.result
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 217, in result
op.join(self.output_dir(), "result%s.pklz" % self.name)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/utils.py”, line 291, in load_resultfile
raise FileNotFoundError(results_file)
FileNotFoundError: /tmp/fmriprep_wf/single_subject_IXI229_wf/anat_preproc_wf/anat_template_wf/t1w_ref_dimensions/result_t1w_ref_dimensions.pklz
“”"The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File “/usr/local/miniconda/lib/python3.7/concurrent/futures/_base.py”, line 324, in _invoke_callbacks
callback(self)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py”, line 159, in _async_callback
result = args.result()
File “/usr/local/miniconda/lib/python3.7/concurrent/futures/_base.py”, line 425, in result
return self.__get_result()
File “/usr/local/miniconda/lib/python3.7/concurrent/futures/_base.py”, line 384, in __get_result
raise self._exception
FileNotFoundError: /tmp/fmriprep_wf/single_subject_IXI229_wf/anat_preproc_wf/anat_template_wf/t1w_ref_dimensions/result_t1w_ref_dimensions.pklz
Any ideas of what is wrong there?
Thanks in advance for any help,
Georgios