fmriprep: traits.trait_errors.TraitError: The 'output_image' trait of a _FixN4BiasFieldCorrectionOutputSpec instance must be a pathlike object or string representing an existing file

What happened?

hi i was trying to run fMRIprep uisng the code below

fmriprep /inputfolder/ /output/ participant --participant-label sub-Bxxxx --fs-license-file /pathtolicense/license.txt --nthreads 5 --omp-nthreads 5 --mem-mb 15G --use-aroma --ignore slicetiming --ignore t2w

( i have used xxxx to anomymize the info )

this code was proven to be functional on another participant; but it returned the error below after running for 7 hours on this participant;

error:

traits.trait_errors.TraitError: The ‘output_image’ trait of a _FixN4BiasFieldCorrectionOutputSpec instance must be a pathlike object or string representing an existing file, but a value of ‘/work/fmriprep_23_0_wf/single_subject_Bxxxx_wf/func_preproc_ses_xxxx_task_rest24mm490scansms8_run_1_echo_1_wf/initial_boldref_wf/enhance_and_skullstrip_bold_wf/n4_correct/sub-Bxxxx_ses-xxxx_task-rest24mm490scansms8_run-1_echo-1_bold_average_corrected.nii.gz’ <class ‘str’> was specified.

the parameters used was 8 cpu, 32G RAM, 100G disk space; our data has 490 volumes, with TR=0.735, TE being 0.035, dimension being 929264*490

What command did you use?

fmriprep /inputfolder/ /output/ participant --participant-label sub-Bxxxx --fs-license-file /pathtolicense/license.txt --nthreads 5 --omp-nthreads 5 --mem-mb 15G --use-aroma --ignore slicetiming --ignore t2w

What version of fMRIPrep are you running?

the latest version in dockerhub is pulled and used

How are you running fMRIPrep?

Docker

Is your data BIDS valid?

Yes

Are you reusing any previously computed results?

No

Please copy and paste any relevant log output.

�2023-05-12T10:30:18.271679031Z    File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface

F2023-05-12T10:30:18.271682869Z      return self._run_command(execute)

�2023-05-12T10:30:18.271686160Z    File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command

B2023-05-12T10:30:18.271697312Z      raise NodeExecutionError(msg)

�2023-05-12T10:30:18.271700553Z  nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node n4_correct.

!2023-05-12T10:30:18.271703711Z  

)2023-05-12T10:30:18.271708212Z  Cmdline:


2023-05-12T10:30:18.271711698Z  	N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /work/fmriprep_23_0_wf/single_subject_B10203_wf/func_preproc_ses_WQZHEADFMRI20230317133821278000_task_rest24mm490scansms8_run_1_echo_1_wf/initial_boldref_wf/gen_avg/sub-B10203_ses-WQZHEADFMRI20230317133821278000_task-rest24mm490scansms8_run-1_echo-1_bold_average.nii.gz --output sub-B10203_ses-WQZHEADFMRI20230317133821278000_task-rest24mm490scansms8_run-1_echo-1_bold_average_corrected.nii.gz -r --weight-image /work/fmriprep_23_0_wf/single_subject_B10203_wf/func_preproc_ses_WQZHEADFMRI20230317133821278000_task_rest24mm490scansms8_run_1_echo_1_wf/initial_boldref_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_res-01_label-brain_probseg_trans_hdr.nii.gz

(2023-05-12T10:30:18.271716073Z  Stdout:

!2023-05-12T10:30:18.271718858Z  

(2023-05-12T10:30:18.271721571Z  Stderr:

!2023-05-12T10:30:18.271724433Z  

+2023-05-12T10:30:18.271727169Z  Traceback:

D2023-05-12T10:30:18.271730030Z  	Traceback (most recent call last):

�2023-05-12T10:30:18.271732939Z  	  File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 453, in aggregate_outputs

@2023-05-12T10:30:18.271736107Z  	    setattr(outputs, key, val)

�2023-05-12T10:30:18.271738939Z  	  File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/traits_extension.py", line 330, in validate

s2023-05-12T10:30:18.271742018Z  	    value = super(File, self).validate(objekt, name, value, return_pathlike=True)

�2023-05-12T10:30:18.271745617Z  	  File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/traits_extension.py", line 135, in validate

J2023-05-12T10:30:18.271748797Z  	    self.error(objekt, name, str(value))

�2023-05-12T10:30:18.271751840Z  	  File "/opt/conda/lib/python3.9/site-packages/traits/base_trait_handler.py", line 74, in error

72023-05-12T10:30:18.271754858Z  	    raise TraitError(

72023-05-12T10:30:18.271757734Z  	traits.trait_errors.TraitError: The 'output_image' trait of a _FixN4BiasFieldCorrectionOutputSpec instance must be a pathlike object or string representing an existing file, but a value of '/work/fmriprep_23_0_wf/single_subject_Bxxxx_wf/func_preproc_ses_xxxx_task_rest24mm490scansms8_run_1_echo_1_wf/initial_boldref_wf/enhance_and_skullstrip_bold_wf/n4_correct/sub-Bxxxx_ses-xxxx_task-rest24mm490scansms8_run-1_echo-1_bold_average_corrected.nii.gz' <class 'str'> was specified.

!2023-05-12T10:30:18.271761555Z  

e2023-05-12T10:30:18.271764300Z  	During handling of the above exception, another exception occurred:

!2023-05-12T10:30:18.271767368Z  

D2023-05-12T10:30:18.271770152Z  	Traceback (most recent call last):

�2023-05-12T10:30:18.271775258Z  	  File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 398, in run

L2023-05-12T10:30:18.271781446Z  	    runtime = self._post_run_hook(runtime)

�2023-05-12T10:30:18.271784457Z  	  File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/mixins/fixheader.py", line 127, in _post_run_hook

h2023-05-12T10:30:18.271787504Z  	    outputs = self.aggregate_outputs(runtime=runtime).get_traitsfree()

�2023-05-12T10:30:18.271790496Z  	  File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 460, in aggregate_outputs

B2023-05-12T10:30:18.271793509Z  	    raise FileNotFoundError(msg)


�2023-05-12T10:30:18.271796578Z  	FileNotFoundError: No such file or directory '/work/fmriprep_23_0_wf/single_subject_Bxxxx_wf/func_preproc_ses_xxxx_task_rest24mm490scansms8_run_1_echo_1_wf/initial_boldref_wf/enhance_and_skullstrip_bold_wf/n4_correct/sub-Bxxxx_ses-xxxx_task-rest24mm490scansms8_run-1_echo-1_bold_average_corrected.nii.gz' for output 'output_image' of a FixN4BiasFieldCorrection interface

!2023-05-12T10:30:18.271800138Z  

!2023-05-12T10:30:18.271802871Z  

?2023-05-12T10:30:24.407066899Z  230512-10:30:24,406 cli ERROR:

�2023-05-12T10:30:24.407098798Z  	 Preprocessing did not finish successfully. Errors occurred while processing data from participants: B10203 (1). Check the HTML reports for details.

?2023-05-12T10:30:24.407104198Z  230512-10:30:24,406 cli ERROR:

�2023-05-12T10:30:24.407110928Z  	 Preprocessing did not finish successfully. Errors occurred while processing data from participants: B10203 (1). Check the HTML reports for details.
V2023-05-12T10:30:27.879656462Z  Sentry is attempting to send 5 pending error messages
82023-05-12T10:30:27.879693497Z  Waiting up to 2 seconds
52023-05-12T10:30:27.879698598Z  Press Ctrl-C to quit

Additional information / screenshots

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