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ds002320-mriqc: "IndexError: cannot do a non-empty take from an empty axes." #65

Open jbwexler opened 1 year ago

jbwexler commented 1 year ago

Just for a few subjects. Looks like this was supposed to be fixed in the last release: https://github.com/nipreps/mriqc/issues/1048

Node: mriqc_wf.anatMRIQC.synthstrip_wf.pre_clip Working directory: /scratch1/03201/jbwexler/work_dir/mriqc/ds002320_sub-47/mriqc_wf/anatMRIQC/synthstrip_wf/_infile..scratch1..03201..jbwexler..openneuro_derivatives..derivatives..mriqc..ds002320-mriqc..sourcedata..raw..sub-47..anat..sub-47_T1w.nii.gz/pre_clip

Node inputs:

dtype = int16 in_file = invert = False nonnegative = True p_max = 99.9 p_min = 10.0

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 527, in run result = self._run_interface(execute=True) File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface return self._run_command(execute) File "/opt/conda/lib/python3.9/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 pre_clip.

Traceback: Traceback (most recent call last): File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 398, in run runtime = self._run_interface(runtime) File "/opt/conda/lib/python3.9/site-packages/niworkflows/interfaces/nibabel.py", line 467, in _run_interface self._results["out_file"] = _advanced_clip( File "/opt/conda/lib/python3.9/site-packages/niworkflows/interfaces/nibabel.py", line 705, in _advanced_clip a_min = np.percentile( File "<__array_function__ internals>", line 180, in percentile File "/opt/conda/lib/python3.9/site-packages/numpy/lib/function_base.py", line 4134, in percentile return _quantile_unchecked( File "/opt/conda/lib/python3.9/site-packages/numpy/lib/function_base.py", line 4383, in _quantile_unchecked r, k = _ureduce(a, File "/opt/conda/lib/python3.9/site-packages/numpy/lib/function_base.py", line 3702, in _ureduce r = func(a, *kwargs) File "/opt/conda/lib/python3.9/site-packages/numpy/lib/function_base.py", line 4552, in _quantile_ureduce_func result = _quantile(arr, File "/opt/conda/lib/python3.9/site-packages/numpy/lib/function_base.py", line 4658, in _quantile take(arr, indices=-1, axis=DATA_AXIS) File "<__array_function__ internals>", line 180, in take File "/opt/conda/lib/python3.9/site-packages/numpy/core/fromnumeric.py", line 190, in take return _wrapfunc(a, 'take', indices, axis=axis, out=out, mode=mode) File "/opt/conda/lib/python3.9/site-packages/numpy/core/fromnumeric.py", line 57, in _wrapfunc return bound(args, **kwds) IndexError: cannot do a non-empty take from an empty axes.