Error when trying to run fmriprep

I am running fmriprep on data that passed BIDS-validator but I get:

raceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/", line 51, in run_node
    result['result'] =
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/", line 407, in run
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/", line 517, in _run_interface
    self._result = self._run_command(execute)
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/", line 650, in _run_command
    result =
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/", line 1088, in run
    runtime = self._run_interface(runtime)
  File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/interfaces/", line 321, in _run_interface
    normalized = normalize_xform(reoriented)
  File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/interfaces/", line 507, in normalize_xform
    if all((np.allclose(qform, xform), np.allclose(sform, xform),
  File "/usr/local/miniconda/lib/python3.6/site-packages/numpy/core/", line 2478, in allclose
    res = all(isclose(a, b, rtol=rtol, atol=atol, equal_nan=equal_nan))
  File "/usr/local/miniconda/lib/python3.6/site-packages/numpy/core/", line 2557, in isclose
    xfin = isfinite(x)
TypeError: ufunc 'isfinite' not supported for the input types, and the inputs could not be safely coerced to any supported types according to the casting rule ''safe''

Any idea why?

So we can better help, can you please describe:

  1. How you are running fMRIPrep (version, OS, python vs. singularity vs docker etc)
  2. Your fmriprep command
  3. Your memory/cpu devoted to the job


I am using docker, via the command:
fmriprep-docker bids_dir our_dir --fs-license-file <license_path>
I am not sure how to check memory/cpu but are you sure it should be relevant, given the error occurs from every single subject (starting from the first one)?


Don’t you also need to add participant to the command, after out_dir?

@Steven I added this now but still got the same error