UPDATE- (sorry for two accounts, my school computer is logged on to my school email)
Re-ran it, still got an error. It won’t let me upload the .html but it says “qform matrix overwritten” a bunch of times at the top and then gives me that same error at the bottom.
My command to run it:
singularity run --cleanenv -B /data2/users/liz/MLINDIV/fmriPrep:/work ~/fmriprep-1.2.6.simg /work/dataBids /work/processed participant -w /work/workDir --fs-license-file /work/license.txt --skip_bids_validation --ignore fieldmaps
And the end of the output
…
return super(SubjectSummary, self)._run_interface(runtime)
File “/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/interfaces/reports.py”, line 63, in _run_interface
segment = self._generate_segment()
File “/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/interfaces/reports.py”, line 123, in _generate_segment
for series in bold_series)
File “/usr/local/miniconda/lib/python3.7/collections/init.py”, line 566, in init
self.update(*args, **kwds)
File “/usr/local/miniconda/lib/python3.7/collections/init.py”, line 653, in update
_count_elements(self, iterable)
File “/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/interfaces/reports.py”, line 123, in
for series in bold_series)
TypeError: ‘NoneType’ object is not subscriptable
190123-20:35:25,400 nipype.workflow WARNING:
[Node] Error on “fmriprep_wf.single_subject_020_wf.summary” (/work/workDir/fmriprep_wf/single_subject_020_wf/summary)
190123-20:35:25,402 nipype.workflow ERROR:
Node summary failed to run on host hopper.
190123-20:35:25,411 nipype.workflow ERROR:
Saving crash info to /work/processed/fmriprep/sub-020/log/20190123-201548_ab833868-4d9f-4c48-8582-986252f05b5b/crash-20190123-203525-jsmith-summary-121c01d5-ae8a-418f-a57b-2b014e82b960.txt
Traceback (most recent call last):
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py”, line 316, in _send_procs_to_workers
self.procs[jobid].run(updatehash=updatehash)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 473, in run
result = self._run_interface(execute=True)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 557, in _run_interface
return self._run_command(execute)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 637, in _run_command
result = self._interface.run(cwd=outdir)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py”, line 369, in run
runtime = self._run_interface(runtime)
File “/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/interfaces/reports.py”, line 96, in _run_interface
return super(SubjectSummary, self)._run_interface(runtime)
File “/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/interfaces/reports.py”, line 63, in _run_interface
segment = self._generate_segment()
File “/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/interfaces/reports.py”, line 123, in _generate_segment
for series in bold_series)
File “/usr/local/miniconda/lib/python3.7/collections/init.py”, line 566, in init
self.update(*args, **kwds)
File “/usr/local/miniconda/lib/python3.7/collections/init.py”, line 653, in update
_count_elements(self, iterable)
File “/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/interfaces/reports.py”, line 123, in
for series in bold_series)
TypeError: ‘NoneType’ object is not subscriptable
Preprocessing did not finish successfully. Errors occurred while processing data from participants: 020 (1), 024 (1), 025 (1), 027 (1), 031 (1), 032 (1), 034 (1), 038 (1), 041 (1), 043 (1). Check the HTML reports for details.
Sentry is attempting to send 9 pending error messages
Waiting up to 2.0 seconds
Press Ctrl-C to quit
Captured warning (<class ‘ResourceWarning’>): unclosed <socket.socket fd=12, family=AddressFamily.AF_INET, type=SocketKind.SOCK_STREAM, proto=6, laddr=(‘128.111.106.39’, 59414), raddr=(‘35.188.42.15’, 443)>