subprocess.CalledProcessError: Command '['bids-validator', '/data', '-c', '/tmp/tmp3_xycsud.json']' died with <Signals.SIGABRT: 6>.

[m9080212]

What happened?

I tried to preprocess the FMRI dataset and got the following error.

What command did you use?

fmriprep-docker '/media/menglab/Work2/hy/face_imagery/block_design/BIDS' '/media/menglab/Work2/hy/face_imagery/block_design/BIDS/derivatives/fMRIprep' -w '/media/menglab/Work2/hy/face_imagery/block_design/fMRIprep_working_directory' --fs-license-file '/home/menglab/freesurfer/license.txt' --participant-label 1 2 --ignore slicetiming --output-spaces anat MNI152NLin2009cAsym --skull-strip-t1w force

What version of fMRIPrep are you running?

23.2.2

How are you running fMRIPrep?

Docker

Is your data BIDS valid?

Yes

Are you reusing any previously computed results?

No

Please copy and paste any relevant log output.

RUNNING: docker run --rm -e DOCKER_VERSION_8395080871=20.10.7 -it -v /home/menglab/freesurfer/license.txt:/opt/freesurfer/license.txt:ro -v /media/menglab/Work2/hy/face_imagery/block_design/BIDS:/data:ro -v /media/menglab/Work2/hy/face_imagery/block_design/BIDS/derivatives/fMRIprep:/out -v /media/menglab/Work2/hy/face_imagery/block_design/fMRIprep_working_directory:/scratch nipreps/fmriprep:23.2.2 /data /out participant --participant-label 1 2 --ignore slicetiming --skull-strip-t1w force -w /scratch --output-spaces anat MNI152NLin2009cAsym
node[9]: ../../src/node_platform.cc:68:std::unique_ptr<long unsigned int> node::WorkerThreadsTaskRunner::DelayedTaskScheduler::Start(): Assertion `(0) == (uv_thread_create(t.get(), start_thread, this))' failed.
 1: 0x7fe9ec255d69 node::Abort() [/opt/conda/envs/fmriprep/bin/../lib/libnode.so.108]
 2: 0x7fe9ec255dfb  [/opt/conda/envs/fmriprep/bin/../lib/libnode.so.108]
 3: 0x7fe9ec2cd2dd node::WorkerThreadsTaskRunner::WorkerThreadsTaskRunner(int) [/opt/conda/envs/fmriprep/bin/../lib/libnode.so.108]
 4: 0x7fe9ec2cd3e7 node::NodePlatform::NodePlatform(int, v8::TracingController*, v8::PageAllocator*) [/opt/conda/envs/fmriprep/bin/../lib/libnode.so.108]
 5: 0x7fe9ec211fd7  [/opt/conda/envs/fmriprep/bin/../lib/libnode.so.108]
 6: 0x7fe9ec214104 node::InitializeOncePerProcess(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, node::ProcessFlags::Flags) [/opt/conda/envs/fmriprep/bin/../lib/libnode.so.108]
 7: 0x7fe9ec2148d3 node::Start(int, char**) [/opt/conda/envs/fmriprep/bin/../lib/libnode.so.108]
 8: 0x7fe9eb7cad90  [/usr/lib/x86_64-linux-gnu/libc.so.6]
 9: 0x7fe9eb7cae40 __libc_start_main [/usr/lib/x86_64-linux-gnu/libc.so.6]
10: 0x55f8a87f807f  [node]
Traceback (most recent call last):
  File "/opt/conda/envs/fmriprep/bin/fmriprep", line 8, in <module>
    sys.exit(main())
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/fmriprep/cli/run.py", line 40, in main
    parse_args()
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/fmriprep/cli/parser.py", line 828, in parse_args
    validate_input_dir(config.environment.exec_env, opts.bids_dir, opts.participant_label)
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/fmriprep/utils/bids.py", line 237, in validate_input_dir
    subprocess.check_call(['bids-validator', str(bids_dir), '-c', temp.name])
  File "/opt/conda/envs/fmriprep/lib/python3.10/subprocess.py", line 369, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['bids-validator', '/data', '-c', '/tmp/tmpslslstgg.json']' died with <Signals.SIGABRT: 6>.
fMRIPrep: Please report errors to https://github.com/nipreps/fmriprep/issues

Additional information / screenshots

No response

[mgxd]

Looks like you are hitting nodejs/node#43064 - skimming through that thread, updating Docker could help

[Yingjuan]

Hello,
I encountered the same issue. Could you please share how you resolved it? Thank you!

• Mary