Thanks, Oscar and James! Sorry I missed that other post. I ran the suggested command and it seemed to resolve that issue for that subject. However, when I ran it on a different subject, I encountered a new error (which I don’t think has been mentioned on NeuroStars):
[Node] Running "ica_aroma_confound_extraction" ("fmriprep.interfaces.confounds.ICAConfounds")
180502-07:17:39,469 workflow WARNING:
[Node] Error on "fmriprep_wf.single_subject_104_wf.func_preproc_task_rest_run_08_wf.ica_aroma_wf.ica_aroma_confound_extraction" (/root/src/fmriprep/work/fmriprep_wf/single_subject_104_wf/func_preproc_task_rest_run_08_wf/ica_aroma_wf/ica_aroma_confound_extraction)
Traceback (most recent call last):
File "/usr/local/miniconda/bin/fmriprep", line 11, in <module>
load_entry_point('fmriprep==1.0.12.dev0', 'console_scripts', 'fmriprep')()
File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/cli/run.py", line 280, in main
fmriprep_wf.run(**plugin_settings)
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/workflows.py", line 595, in run
runner.run(execgraph, updatehash=updatehash, config=self.config)
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/base.py", line 168, in run
self._clean_queue(jobid, graph, result=result))
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/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/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/multiproc.py", line 68, in run_node
result['result'] = node.run(updatehash=updatehash)
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 479, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 563, in _run_interface
return self._run_command(execute)
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 643, in _run_command
result = self._interface.run(cwd=outdir)
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base/core.py", line 516, in run
runtime = self._run_interface(runtime)
File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/interfaces/confounds.py", line 112, in _run_interface
self.inputs.in_directory, newpath=runtime.cwd)
File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/interfaces/confounds.py", line 239, in _get_ica_confounds
aggr_confounds = np.asarray([melodic_mix_arr.T[x] for x in motion_ic_indices])
TypeError: 'numpy.int64' object is not iterable
I’m not sure if it’s related, but I’ve noticed the masking fails for some of these data (seems to happen when “prescan normalization” is turned on during acquisition). The recent fix seemed to prevent crashes for the subject here (fmriprep output here: https://osf.io/876pn/), but for this other subject it seems to still be failing – but with this new error.