Open jbwexler opened 1 year ago
This seems to have been resolved in fmriprep (I'll test it with the next release)
I'm getting this error for all attempted subjects in ds004489 as well (with minimal mode).
Anything new in the traceback?
It looks pretty similar:
Traceback (most recent call last): , File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node result["result"] = node.run(updatehash=updatehash) , File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run result = self._run_interface(execute=True) , File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface return self._run_command(execute) , File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command raise NodeExecutionError(msg) ,nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node n4_correct.
Cmdline: N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /scratch1/03201/jbwexler/openneuro_derivatives/derivatives/fmriprep/ds004489-fmriprep/sourcedata/raw/sub-1014/ses-2/func/sub-1014_ses-2_task-FOV_run-6_sbref.nii.gz --output sub-1014_ses-2_task-FOV_run-6_sbref_corrected.nii.gz -r --weight-image /scratch1/03201/jbwexler/work_dir/fmriprep/ds004489_sub-1014/fmriprep_23_2_wf/fit_sub_1014_wf/func_preproc_ses_2_task_FOV_run_6_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_res-01_label-brain_probseg_trans_hdr.nii.gz Stdout:
Stderr:
Traceback: Traceback (most recent call last): File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 453, in aggregate_outputs setattr(outputs, key, val) File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/traits_extension.py", line 330, in validate value = super(File, self).validate(objekt, name, value, return_pathlike=True) File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/traits_extension.py", line 135, in validate self.error(objekt, name, str(value)) File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/traits/base_trait_handler.py", line 74, in error raise TraitError( 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 '/scratch1/03201/jbwexler/work_dir/fmriprep/ds004489_sub-1014/fmriprep_23_2_wf/fit_sub_1014_wf/func_preproc_ses_2_task_FOV_run_6_wf/enhance_and_skullstrip_bold_wf/n4_correct/sub-1014_ses-2_task-FOV_run-6_sbref_corrected.nii.gz' <class 'str'> was specified.
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 398, in run runtime = self._post_run_hook(runtime) File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/mixins/fixheader.py", line 127, in _post_run_hook outputs = self.aggregate_outputs(runtime=runtime).get_traitsfree() File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 460, in aggregate_outputs raise FileNotFoundError(msg) FileNotFoundError: No such file or directory '/scratch1/03201/jbwexler/work_dir/fmriprep/ds004489_sub-1014/fmriprep_23_2_wf/fit_sub_1014_wf/func_preproc_ses_2_task_FOV_run_6_wf/enhance_and_skullstrip_bold_wf/n4_correct/sub-1014_ses-2_task-FOV_run-6_sbref_corrected.nii.gz' for output 'output_image' of a FixN4BiasFieldCorrection interface
Previously ran into this error with this dataset https://github.com/poldracklab/tacc-openneuro/issues/61. Reran a sample of 4 subs with 23.0.2. No longer getting that error but 2/4 subjects failed with the following: