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ds001105-mriqc: "the 'tissue_class_map' trait of a FASTOutputSpec instance must be a pathlike object" #47

Open jbwexler opened 1 year ago

jbwexler commented 1 year ago

For all subjects:

Node: mriqc_wf.anatMRIQC.segmentation Working directory: /scratch1/03201/jbwexler/work_dir/mriqc/ds001105_sub-007/mriqc_wf/anatMRIQC/_infile ..scratch1..03201..jbwexler..openneuro_derivatives..derivatives..mriqc..ds001105-mriqc..sourcedata..ra w..sub-007..anat..sub-007_T1w.nii.gz/segmentation

Node inputs:

args = bias_iters = bias_lowpass = environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'} hyper = img_type = in_files = init_seg_smooth = init_transform = iters_afterbias = manual_seg = mixel_smooth = no_bias = no_pve = number_classes = other_priors = out_basename = segment output_biascorrected = output_biasfield = output_type = NIFTI_GZ probability_maps = segment_iters = segments = True use_priors = verbose =

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_comm and raise NodeExecutionError( nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node segmentation.

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 'tissue_class_map' trait of a FASTOutputSpec instance must be a pathlike object or string representing an existing file, but a value of '/scratch1/03201/jbwexler/work_dir/mriqc/ds001105_sub-007/mriqc_wf/anatMRIQC/_infile..scratch1..03201..jbwexler..openneuro_derivatives..derivatives..mriqc..ds001105-mriqc..sourcedata..raw..sub-007..anat..sub-007_T1w.nii.gz/segmentation/segment_seg.nii.gz' <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/ds001105_sub-007/mriqc_wf/anatMRIQC/_infile..scratch1..03201..jbwexler..openneuro_derivatives..derivatives..mriqc..ds001105-mriqc..sourcedata..raw..sub-007..anat..sub-007_T1w.nii.gz/segmentation/segment_seg.nii.gz' for output 'tissue_class_map' of a FAST interface