ds000238-mriqc: "Exception raised while executing Node motion_correct"

[jbwexler]

This just occurred for one subject. Rerunning didn't solve it.

Node: mriqc_wf.funcMRIQC.fMRI_HMC.motion_correct Working directory: /scratch1/03201/jbwexler/work_dir/mriqc/ds000238_sub-22/mriqc_wf/funcMRIQC/fMRI_HMC/_infile..scratch1..03201..jbwexler..openneuro_derivatives..derivatives..mriqc..ds000238-mriqc..sourcedata..raw..sub-22..func..sub-22_task-slow12_run-1_bold.nii.gz/motion_correct

Node inputs:

args = -Fourier -twopass basefile = copyorigin = environ = {} in_file = in_weight_volume = interp = md1d_file = num_threads = 1 oned_file = oned_matrix_save = out_file = outputtype = NIFTI_GZ timeshift = verbose = zpad = 4

Traceback (most recent call last): File "/opt/conda/lib/python3.9/site-packages/mriqc/engine/plugin.py", line 60, in run_node result["result"] = node.run(updatehash=updatehash) File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 524, in run result = self._run_interface(execute=True) File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 642, in _run_interface return self._run_command(execute) File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 750, in _run_command raise NodeExecutionError( nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node motion_correct.

Traceback (most recent call last): File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 454, in aggregate_outputs setattr(outputs, key, val) File "/opt/conda/lib/python3.9/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/lib/python3.9/site-packages/nipype/interfaces/base/traits_extension.py", line 135, in validate self.error(objekt, name, str(value)) File "/opt/conda/lib/python3.9/site-packages/traits/base_trait_handler.py", line 74, in error raise TraitError( traits.trait_errors.TraitError: The 'oned_file' trait of a VolregOutputSpec instance must be a pathlike object or string representing an existing file, but a value of '/scratch1/03201/jbwexler/work_dir/mriqc/ds000238_sub-22/mriqc_wf/funcMRIQC/fMRI_HMC/_infile..scratch1..03201..jbwexler..openneuro_derivatives..derivatives..mriqc..ds000238-mriqc..sourcedata..raw..sub-22..func..sub-22_task-slow12_run-1_bold.nii.gz/motion_correct/sub-22_task-slow12_run-1_bold.1D' <class 'str'> was specified.

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 401, in run outputs = self.aggregate_outputs(runtime) File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 461, in aggregate_outputs raise FileNotFoundError(msg) FileNotFoundError: No such file or directory '/scratch1/03201/jbwexler/work_dir/mriqc/ds000238_sub-22/mriqc_wf/funcMRIQC/fMRI_HMC/_infile..scratch1..03201..jbwexler..openneuro_derivatives..derivatives..mriqc..ds000238-mriqc..sourcedata..raw..sub-22..func..sub-22_task-slow12_run-1_bold.nii.gz/motion_correct/sub-22_task-slow12_run-1_bold.1D' for output 'oned_file' of a Volreg interface

[jbwexler]

Same error for one subject in ds000149-mriqc

[jbwexler]

Similar error for sub-09 in ds000011. Turns out due to a corrupted bold file.