"cannot do a non-empty take from an empty axes"
f4b
docker run -it --rm -v \
$bids_dir:/data:ro \
-v $out_dir:/out poldracklab/mriqc:latest \
/data /out participant --participant_label sub-103818
The use of ``template_resolution`` is deprecated
The use of ``template_resolution`` is deprecated
The use of ``template_resolution`` is deprecated
200520-20:19:39,207 nipype.interface WARNING:
calculating summary stats of label "gm" in a very small mask (0 voxels)
200520-20:19:39,257 nipype.workflow WARNING:
Storing result file without outputs
200520-20:19:39,258 nipype.workflow WARNING:
[Node] Error on "mriqc_wf.anatMRIQC.ComputeIQMs.measures" (/tmp/work/mriqc_wf/anatMRIQC/ComputeIQMs/_in_file_..data..sub-103818..ses-2..anat..sub-103818_ses-2_T1w.nii/measures)
200520-20:19:40,586 nipype.workflow ERROR:
Node measures.a1 failed to run on host a10640617675.
200520-20:19:40,589 nipype.workflow ERROR:
Saving crash info to /out/logs/crash-20200520-201940-root-measures.a1-8df9c402-b619-4bb6-a4cf-e891e22e1e26.txt
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
return self._run_command(execute)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
result = self._interface.run(cwd=outdir)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 397, in run
runtime = self._run_interface(runtime)
File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/interfaces/anatomical.py", line 113, in _run_interface
stats = summary_stats(inudata, pvmdata, airdata, erode=erode)
File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/qc/anatomical.py", line 602, in summary_stats
"p95": float(np.percentile(img[mask == 1], 95)),
File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/function_base.py", line 3540, in percentile
a, q, axis, out, overwrite_input, interpolation, keepdims)
File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/function_base.py", line 3652, in _quantile_unchecked
interpolation=interpolation)
File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/function_base.py", line 3250, in _ureduce
r = func(a, **kwargs)
File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/function_base.py", line 3767, in _quantile_ureduce_func
x1 = take(ap, indices_below, axis=axis) * weights_below
File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/core/fromnumeric.py", line 181, in take
return _wrapfunc(a, 'take', indices, axis=axis, out=out, mode=mode)
File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/core/fromnumeric.py", line 51, in _wrapfunc
return getattr(obj, method)(*args, **kwds)
IndexError: cannot do a non-empty take from an empty axes.
Traceback (most recent call last):
File "/usr/local/miniconda/bin/mriqc", line 10, in <module>
sys.exit(main())
File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/cli/run.py", line 69, in main
mriqc_wf.run(**config.nipype.get_plugin())
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/workflows.py", line 632, in run
runner.run(execgraph, updatehash=updatehash, config=self.config)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/base.py", line 164, in run
self._clean_queue(jobid, graph, result=result)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/base.py", line 227, in _clean_queue
raise RuntimeError("".join(result["traceback"]))
RuntimeError: Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
return self._run_command(execute)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
result = self._interface.run(cwd=outdir)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 397, in run
runtime = self._run_interface(runtime)
File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/interfaces/anatomical.py", line 113, in _run_interface
stats = summary_stats(inudata, pvmdata, airdata, erode=erode)
File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/qc/anatomical.py", line 602, in summary_stats
"p95": float(np.percentile(img[mask == 1], 95)),
File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/function_base.py", line 3540, in percentile
a, q, axis, out, overwrite_input, interpolation, keepdims)
File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/function_base.py", line 3652, in _quantile_unchecked
interpolation=interpolation)
File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/function_base.py", line 3250, in _ureduce
r = func(a, **kwargs)
File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/function_base.py", line 3767, in _quantile_ureduce_func
x1 = take(ap, indices_below, axis=axis) * weights_below
File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/core/fromnumeric.py", line 181, in take
return _wrapfunc(a, 'take', indices, axis=axis, out=out, mode=mode)
File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/core/fromnumeric.py", line 51, in _wrapfunc
return getattr(obj, method)(*args, **kwds)
IndexError: cannot do a non-empty take from an empty axes.