ds004286-mriqc: "ValueError: Out of range float values are not JSON compliant: nan"

[jbwexler]

All subjects produced this error:

INFO:    gocryptfs not found, will not be able to use gocryptfs
/opt/conda/lib/python3.11/site-packages/nilearn/plotting/displays/_slicers.py:420: UserWarning: empty mask
  xmin_, xmax_, ymin_, ymax_, zmin_, zmax_ = get_mask_bounds(
/opt/conda/lib/python3.11/site-packages/numpy/core/fromnumeric.py:3504: RuntimeWarning: Mean of empty slice.
  return _methods._mean(a, axis=axis, dtype=dtype,
/opt/conda/lib/python3.11/site-packages/numpy/core/_methods.py:129: RuntimeWarning: invalid value encountered in scalar divide
  ret = ret.dtype.type(ret / rcount)
Traceback (most recent call last):
  File "/opt/conda/lib/python3.11/site-packages/mriqc/engine/plugin.py", line 579, in _send_procs_to_workers
    self.procs[jobid].run(updatehash=updatehash)
  File "/opt/conda/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
    result = self._run_interface(execute=True)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
    return self._run_command(execute)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.11/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 datasink.

Traceback:
        Traceback (most recent call last):
          File "/opt/conda/lib/python3.11/site-packages/nipype/interfaces/base/core.py", line 397, in run
            runtime = self._run_interface(runtime)
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
          File "/opt/conda/lib/python3.11/site-packages/mriqc/interfaces/bids.py", line 192, in _run_interface
            json.dumps(
          File "/opt/conda/lib/python3.11/site-packages/simplejson/__init__.py", line 395, in dumps
            **kw).encode(obj)
                  ^^^^^^^^^^^
          File "/opt/conda/lib/python3.11/site-packages/simplejson/encoder.py", line 300, in encode
            chunks = list(chunks)
                     ^^^^^^^^^^^^
          File "/opt/conda/lib/python3.11/site-packages/simplejson/encoder.py", line 714, in _iterencode
            for chunk in _iterencode_dict(o, _current_indent_level):
          File "/opt/conda/lib/python3.11/site-packages/simplejson/encoder.py", line 645, in _iterencode_dict
            yield _floatstr(value)
                  ^^^^^^^^^^^^^^^^
          File "/opt/conda/lib/python3.11/site-packages/simplejson/encoder.py", line 351, in floatstr
            raise ValueError(
        ValueError: Out of range float values are not JSON compliant: nan


During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/opt/conda/bin/mriqc", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/opt/conda/lib/python3.11/site-packages/mriqc/cli/run.py", line 178, in main
    mriqc_wf.run(**_plugin)
  File "/opt/conda/lib/python3.11/site-packages/nipype/pipeline/engine/workflows.py", line 638, in run
    runner.run(execgraph, updatehash=updatehash, config=self.config)
  File "/opt/conda/lib/python3.11/site-packages/mriqc/engine/plugin.py", line 214, in run
    self._send_procs_to_workers(updatehash=updatehash, graph=graph)
  File "/opt/conda/lib/python3.11/site-packages/mriqc/engine/plugin.py", line 582, in _send_procs_to_workers
    self._clean_queue(
  File "/opt/conda/lib/python3.11/site-packages/mriqc/engine/plugin.py", line 259, in _clean_queue
    raise RuntimeError(''.join(result['traceback']))
RuntimeError: Traceback (most recent call last):
  File "/opt/conda/lib/python3.11/site-packages/mriqc/engine/plugin.py", line 579, in _send_procs_to_workers
    self.procs[jobid].run(updatehash=updatehash)
  File "/opt/conda/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
    result = self._run_interface(execute=True)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
    return self._run_command(execute)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.11/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 datasink.

Traceback:
        Traceback (most recent call last):
          File "/opt/conda/lib/python3.11/site-packages/nipype/interfaces/base/core.py", line 397, in run
            runtime = self._run_interface(runtime)
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
          File "/opt/conda/lib/python3.11/site-packages/mriqc/interfaces/bids.py", line 192, in _run_interface
            json.dumps(
          File "/opt/conda/lib/python3.11/site-packages/simplejson/__init__.py", line 395, in dumps
            **kw).encode(obj)
                  ^^^^^^^^^^^
          File "/opt/conda/lib/python3.11/site-packages/simplejson/encoder.py", line 300, in encode
            chunks = list(chunks)
                     ^^^^^^^^^^^^
          File "/opt/conda/lib/python3.11/site-packages/simplejson/encoder.py", line 714, in _iterencode
            for chunk in _iterencode_dict(o, _current_indent_level):
          File "/opt/conda/lib/python3.11/site-packages/simplejson/encoder.py", line 645, in _iterencode_dict
            yield _floatstr(value)
                  ^^^^^^^^^^^^^^^^
          File "/opt/conda/lib/python3.11/site-packages/simplejson/encoder.py", line 351, in floatstr
            raise ValueError(
        ValueError: Out of range float values are not JSON compliant: nan