Hello!
I am trying to run fmriprep 20.6.2 on an HPC cluster using singularity and have successfully done so with all subjects but one, which gives the following errors:
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 521, in run
result = self._run_interface(execute=True)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 639, in _run_interface
return self._run_command(execute)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 751, in _run_command
f"Exception raised while executing Node {self.name}.\n\n{result.runtime.traceback}"
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node dvars.
Traceback (most recent call last):
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py”, line 398, in run
runtime = self._run_interface(runtime)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/algorithms/confounds.py”, line 170, in _run_interface
intensity_normalization=self.inputs.intensity_normalization,
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/algorithms/confounds.py”, line 1058, in compute_dvars
AR_est_YW, 1, regress_poly(0, mfunc, remove_mean=True)[0].astype(np.float32), 1
File “/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/shape_base.py”, line 380, in apply_along_axis
buff[ind] = asanyarray(func1d(inarr_view[ind], *args, **kwargs))
File “/usr/local/miniconda/lib/python3.7/site-packages/nitime/algorithms/autoregressive.py”, line 96, in AR_est_YW
ak = linalg.solve(Tm, y)
File “/usr/local/miniconda/lib/python3.7/site-packages/scipy/linalg/basic.py”, line 139, in solve
a1 = atleast_2d(_asarray_validated(a, check_finite=check_finite))
File “/usr/local/miniconda/lib/python3.7/site-packages/scipy/_lib/_util.py”, line 238, in _asarray_validated
a = toarray(a)
File “/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/function_base.py”, line 461, in asarray_chkfinite
“array must not contain infs or NaNs”)
ValueError: array must not contain infs or NaNs
This error only happens for the msit task (rest and ssrt run fine) and only happens for this one subject. The msit images have the correct number of volumes and do not appear to have any issues when visually inspected with fsleyes.
Any suggestions on what to do would be greatly appreciated!
Thanks!
Emily