Hey guys:
I had gotten through a lengthy run of FMRIPREP when I got an error saying:
could not run node: fmriprep_wf.single_subject_S04V1A_wf.func_preproc_task_compound_run_01_wf.bold_confounds_wf.tcompcor
With the following traceback:
Traceback (most recent call last):
File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/plugins/multiproc.py”, line 69, in run_node
result[‘result’] = node.run(updatehash=updatehash)
File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py”, line 471, in run
result = self._run_interface(execute=True)
File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py”, line 555, in _run_interface
return self._run_command(execute)
File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py”, line 635, in _run_command
result = self._interface.run(cwd=outdir)
File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/base/core.py”, line 521, in run
runtime = self._run_interface(runtime)
File “/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/interfaces/patches.py”, line 51, in _run_interface
runtime = super(RobustTCompCor, self)._run_interface(runtime)
File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/algorithms/confounds.py”, line 539, in _run_interface
self.inputs.pre_filter, degree, self.inputs.high_pass_cutoff, TR)
File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/algorithms/confounds.py”, line 1189, in compute_noise_components
u, _, _ = linalg.svd(M, full_matrices=False)
File “/usr/local/miniconda/lib/python3.6/site-packages/scipy/linalg/decomp_svd.py”, line 132, in svd
raise LinAlgError(“SVD did not converge”)
numpy.linalg.linalg.LinAlgError: SVD did not converge
I checked out this issue that seems to indicate its a memory problem and that cleaning up the working directory fixes the issue.
I am saving files to both a working and output directory. Does this mean I need to erase the whole working directory and start over? I’m mostly asking because this error popped up after 12 hours of processing and I’ll start from scratch if necessary but I’m not sure what’ll keep it from happening again if I do. Can any of the work to this point be salvaged?
Thanks!
Lauren