Error running fmriprep 23.x using Docker

Software Support
1

Summary of what happened:

I have been running fmriprep 22.x using the docker images. I recently commenced a reanalysis of some of my data along with some new data and thought I would reprocess all the data using the latest fmriprep version 23.1.3. Docker versions of fmriprep beginning 23.x are not working for some reason.

Command used (and if a helper script was used, a link to the helper script or the command generated):

docker run -ti --rm -v /home/jeff/license.txt:/opt/freesurfer/license.txt:ro -v /neuro/labs/grantlab/research/moyamoya/data:/data:ro -v /home/jeff/moyamoya/derivatives:/out -v /home/jeff/moyamoya/work:/work nipreps/fmriprep:23.0.1 /data /out participant --participant-label minc008 minc011 minc017 minc021 minc028 minc029 minc030 --write-graph --output-spaces T1w func MNI152NLin2009cAsym -w /work --output-layout legacy
This command causes the error.
docker run -ti --rm -v /home/jeff/license.txt:/opt/freesurfer/license.txt:ro -v /neuro/labs/grantlab/research/moyamoya/data:/data:ro -v /home/jeff/moyamoya/derivatives:/out -v /home/jeff/moyamoya/work:/work nipreps/fmriprep:22.0.2 /data /out participant --participant-label minc008 minc011 minc017 minc021 minc028 minc029 minc030 --write-graph --output-spaces T1w func MNI152NLin2009cAsym -w /work --output-layout legacy
This was the previous command to process my data that ran just fine. The only difference is in the fmriprep version.

Version:

23.x

Environment (Docker, Singularity, custom installation):

Docker

Data formatted according to a validatable standard? Please provide the output of the validator:

BIDS check performed on my data with only warning related to not having identical files for all runs.

Relevant log outputs (up to 20 lines):

node[9]: ../../src/node_platform.cc:61:std::unique_ptr<long unsigned int> node::WorkerThreadsTaskRunner::DelayedTaskScheduler::Start(): Assertion `(0) == (uv_thread_create(t.get(), start_thread, this))' failed.
 1: 0x7f15aac1f9e9 node::Abort() [/opt/conda/envs/fmriprep/bin/../lib/libnode.so.93]
 2: 0x7f15aac1fa7b  [/opt/conda/envs/fmriprep/bin/../lib/libnode.so.93]
 3: 0x7f15aac9472d node::WorkerThreadsTaskRunner::WorkerThreadsTaskRunner(int) [/opt/conda/envs/fmriprep/bin/../lib/libnode.so.93]
 4: 0x7f15aac94816 node::NodePlatform::NodePlatform(int, v8::TracingController*) [/opt/conda/envs/fmriprep/bin/../lib/libnode.so.93]
 5: 0x7f15aabe2c65  [/opt/conda/envs/fmriprep/bin/../lib/libnode.so.93]
 6: 0x7f15aabe3697 node::InitializeOncePerProcess(int, char**, node::InitializationSettingsFlags, node::ProcessFlags::Flags) [/opt/conda/envs/fmriprep/bin/../lib/libnode.so.93]
 7: 0x7f15aabe383a node::InitializeOncePerProcess(int, char**) [/opt/conda/envs/fmriprep/bin/../lib/libnode.so.93]
 8: 0x7f15aabe3897 node::Start(int, char**) [/opt/conda/envs/fmriprep/bin/../lib/libnode.so.93]
 9: 0x7f15aa21ed90  [/usr/lib/x86_64-linux-gnu/libc.so.6]
10: 0x7f15aa21ee40 __libc_start_main [/usr/lib/x86_64-linux-gnu/libc.so.6]
11: 0x55f8dddd2145  [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 43, in main
    parse_args()
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/fmriprep/cli/parser.py", line 812, 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 185, 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/tmp74fpj_y3.json']' died with <Signals.SIGABRT: 6>.

Screenshots / relevant information:

Seeing the bid-validator command in the last line of the error I tried the skip bids validation flag and that has no effect. I still get an error.

2

Hi @dittothat,

You might want to check out this thread? fmriPrep error codes? - #5 by Justin_Smith1. Looks like the user had the same error as you.

Best,
Steven

3

Thanks for the idea, but that user seemed to have issues with BIDS compliance and computer memory. As I described, my data is BIDS compliant with only an immaterial warning. I don’t think this is memory related given docker version 22.0.1 runs fine. Only 23.x won’t run. Have the 23.x docker images been used mostly without issue?

4

Just to be clear this is the result of the BIDS validation when I run the 22.0.2 version of the fmriprep command:

	1: [WARN] The recommended file /README is missing. See Section 03 (Modality agnostic files) of the BIDS specification. (code: 101 - README_FILE_MISSING)

	Please visit https://neurostars.org/search?q=README_FILE_MISSING for existing conversations about this issue.


        Summary:                 Available Tasks:        Available Modalities: 
        179 Files, 2.46GB        cvr                     MRI                   
        25 - Subjects                                                          
        2 - Sessions
5

What about trying the online validator which is up-to-date? https://bids-standard.github.io/bids-validator/

6

Sorry for the log dump, but I don’t think there is a material issue here. Happy to be corrected on this point:

docker run -ti --rm -v /neuro/labs/grantlab/research/moyamoya/data:/data:ro bids/validator --verbose /data
bids-validator@1.4.2

	1: [WARN] Not all subjects contain the same files. Each subject should contain the same number of files with the same naming unless some files are known to be missing. (code: 38 - INCONSISTENT_SUBJECTS)
		./sub-minc009/ses-01/fmap/sub-minc009_ses-01_dir-PA_epi.json
			This file is missing for subject sub-minc009, but is present for at least one other subject.
			Evidence: Subject: sub-minc009; Missing file: sub-minc009_ses-01_dir-PA_epi.json
		./sub-minc009/ses-01/fmap/sub-minc009_ses-01_dir-PA_epi.nii.gz
			This file is missing for subject sub-minc009, but is present for at least one other subject.
			Evidence: Subject: sub-minc009; Missing file: sub-minc009_ses-01_dir-PA_epi.nii.gz
		./sub-minc009/ses-01/func/sub-minc009_ses-01_task-cvr_bold.json
			This file is missing for subject sub-minc009, but is present for at least one other subject.
			Evidence: Subject: sub-minc009; Missing file: sub-minc009_ses-01_task-cvr_bold.json
		./sub-minc009/ses-01/func/sub-minc009_ses-01_task-cvr_bold.nii.gz
			This file is missing for subject sub-minc009, but is present for at least one other subject.
			Evidence: Subject: sub-minc009; Missing file: sub-minc009_ses-01_task-cvr_bold.nii.gz
		./sub-minc009/ses-01/func/sub-minc009_ses-01_task-cvr_events.tsv
			This file is missing for subject sub-minc009, but is present for at least one other subject.
			Evidence: Subject: sub-minc009; Missing file: sub-minc009_ses-01_task-cvr_events.tsv
		./sub-minc010/ses-01/fmap/sub-minc010_ses-01_dir-PA_epi.json
			This file is missing for subject sub-minc010, but is present for at least one other subject.
			Evidence: Subject: sub-minc010; Missing file: sub-minc010_ses-01_dir-PA_epi.json
		./sub-minc010/ses-01/fmap/sub-minc010_ses-01_dir-PA_epi.nii.gz
			This file is missing for subject sub-minc010, but is present for at least one other subject.
			Evidence: Subject: sub-minc010; Missing file: sub-minc010_ses-01_dir-PA_epi.nii.gz
		./sub-minc021/ses-01/fmap/sub-minc021_ses-01_dir-PA_epi.json
			This file is missing for subject sub-minc021, but is present for at least one other subject.
			Evidence: Subject: sub-minc021; Missing file: sub-minc021_ses-01_dir-PA_epi.json
		./sub-minc021/ses-01/fmap/sub-minc021_ses-01_dir-PA_epi.nii.gz
			This file is missing for subject sub-minc021, but is present for at least one other subject.
			Evidence: Subject: sub-minc021; Missing file: sub-minc021_ses-01_dir-PA_epi.nii.gz
		./sub-mincx01/ses-01/fmap/sub-mincx01_ses-01_dir-PA_epi.json
			This file is missing for subject sub-mincx01, but is present for at least one other subject.
			Evidence: Subject: sub-mincx01; Missing file: sub-mincx01_ses-01_dir-PA_epi.json
		./sub-mincx01/ses-01/fmap/sub-mincx01_ses-01_dir-PA_epi.nii.gz
			This file is missing for subject sub-mincx01, but is present for at least one other subject.
			Evidence: Subject: sub-mincx01; Missing file: sub-mincx01_ses-01_dir-PA_epi.nii.gz
		./sub-mincx01/ses-01/func/sub-mincx01_ses-01_task-cvr_bold.json
			This file is missing for subject sub-mincx01, but is present for at least one other subject.
			Evidence: Subject: sub-mincx01; Missing file: sub-mincx01_ses-01_task-cvr_bold.json
		./sub-mincx01/ses-01/func/sub-mincx01_ses-01_task-cvr_bold.nii.gz
			This file is missing for subject sub-mincx01, but is present for at least one other subject.
			Evidence: Subject: sub-mincx01; Missing file: sub-mincx01_ses-01_task-cvr_bold.nii.gz
		./sub-mincx01/ses-01/func/sub-mincx01_ses-01_task-cvr_events.tsv
			This file is missing for subject sub-mincx01, but is present for at least one other subject.
			Evidence: Subject: sub-mincx01; Missing file: sub-mincx01_ses-01_task-cvr_events.tsv
		./sub-mincx03/ses-01/fmap/sub-mincx03_ses-01_dir-PA_epi.json
			This file is missing for subject sub-mincx03, but is present for at least one other subject.
			Evidence: Subject: sub-mincx03; Missing file: sub-mincx03_ses-01_dir-PA_epi.json
		./sub-mincx03/ses-01/fmap/sub-mincx03_ses-01_dir-PA_epi.nii.gz
			This file is missing for subject sub-mincx03, but is present for at least one other subject.
			Evidence: Subject: sub-mincx03; Missing file: sub-mincx03_ses-01_dir-PA_epi.nii.gz
		./sub-mincx03/ses-01/func/sub-mincx03_ses-01_task-cvr_bold.json
			This file is missing for subject sub-mincx03, but is present for at least one other subject.
			Evidence: Subject: sub-mincx03; Missing file: sub-mincx03_ses-01_task-cvr_bold.json
		./sub-mincx03/ses-01/func/sub-mincx03_ses-01_task-cvr_bold.nii.gz
			This file is missing for subject sub-mincx03, but is present for at least one other subject.
			Evidence: Subject: sub-mincx03; Missing file: sub-mincx03_ses-01_task-cvr_bold.nii.gz
		./sub-mincx03/ses-01/func/sub-mincx03_ses-01_task-cvr_events.tsv
			This file is missing for subject sub-mincx03, but is present for at least one other subject.
			Evidence: Subject: sub-mincx03; Missing file: sub-mincx03_ses-01_task-cvr_events.tsv

	Please visit https://neurostars.org/search?q=INCONSISTENT_SUBJECTS for existing conversations about this issue.

	2: [WARN] Not all subjects/sessions/runs have the same scanning parameters. (code: 39 - INCONSISTENT_PARAMETERS)
		./sub-minc008/ses-01/func/sub-minc008_ses-01_task-cvr_bold.nii.gz
			 The most common set of dimensions is: 78,78,51,288 (voxels), This file has the dimensions: 78,78,51,317 (voxels).
		./sub-minc010/ses-01/func/sub-minc010_ses-01_task-cvr_bold.nii.gz
			 The most common set of dimensions is: 78,78,51,288 (voxels), This file has the dimensions: 78,78,51,287 (voxels).
		./sub-minc014/ses-02/anat/sub-minc014_ses-02_T1w.nii.gz
			 The most common set of dimensions is: 176,256,256 (voxels), This file has the dimensions: 192,280,256 (voxels). The most common resolution is: 1.00mm x 1.00mm x 1.00mm, This file has the resolution: 0.90mm x 0.86mm x 0.86mm.
		./sub-minc016/ses-01/fmap/sub-minc016_ses-01_dir-PA_epi.nii.gz
			 The most common set of dimensions is: 78,78,51,20 (voxels), This file has the dimensions: 78,78,51,14 (voxels).
		./sub-minc029/ses-01/func/sub-minc029_ses-01_task-cvr_bold.nii.gz
			 The most common set of dimensions is: 78,78,51,288 (voxels), This file has the dimensions: 78,78,51,272 (voxels).
		./sub-mincx01/ses-01/anat/sub-mincx01_ses-01_T1w.nii.gz
			 The most common set of dimensions is: 176,256,256 (voxels), This file has the dimensions: 160,192,192 (voxels). The most common resolution is: 1.00mm x 1.00mm x 1.00mm, This file has the resolution: 1.10mm x 1.15mm x 1.15mm.
		./sub-mincx03/ses-01/anat/sub-mincx03_ses-01_T1w.nii.gz
			 The most common set of dimensions is: 176,256,256 (voxels), This file has the dimensions: 168,224,224 (voxels).
		./sub-mod036/ses-01/anat/sub-mod036_ses-01_T1w.nii.gz
			 The most common set of dimensions is: 176,256,256 (voxels), This file has the dimensions: 160,224,224 (voxels). The most common resolution is: 1.00mm x 1.00mm x 1.00mm, This file has the resolution: 1.10mm x 1.03mm x 1.03mm.
		./sub-mod037/ses-01/anat/sub-mod037_ses-01_T1w.nii.gz
			 The most common set of dimensions is: 176,256,256 (voxels), This file has the dimensions: 216,224,224 (voxels).
		./sub-mod929/ses-01/anat/sub-mod929_ses-01_T1w.nii.gz
			 The most common set of dimensions is: 176,256,256 (voxels), This file has the dimensions: 216,224,224 (voxels).

	Please visit https://neurostars.org/search?q=INCONSISTENT_PARAMETERS for existing conversations about this issue.

	3: [WARN] Tabular file contains custom columns not described in a data dictionary (code: 82 - CUSTOM_COLUMN_WITHOUT_DESCRIPTION)
		./participants.tsv
			Tabular file contains custom columns not described in a data dictionary
			Evidence: Columns: group, date_of_scan, notes not defined, please define in: /participants.json
		./sub-minc008/ses-01/func/sub-minc008_ses-01_task-cvr_events.tsv
			Tabular file contains custom columns not described in a data dictionary
			Evidence: Columns: event not defined, please define in: /task-cvr_events.json, /events.json,/sub-minc008/sub-minc008_task-cvr_events.json,/sub-minc008/sub-minc008_events.json,/sub-minc008/ses-01/sub-minc008_ses-01_task-cvr_events.json,/sub-minc008/ses-01/sub-minc008_ses-01_events.json,/sub-minc008/ses-01/func/sub-minc008_ses-01_task-cvr_events.json,/sub-minc008/ses-01/func/sub-minc008_ses-01_events.json

	Please visit https://neurostars.org/search?q=CUSTOM_COLUMN_WITHOUT_DESCRIPTION for existing conversations about this issue.

	4: [WARN] Not all subjects contain the same sessions. (code: 97 - MISSING_SESSION)
		./sub-minc008/ses-02
			A session is missing from one subject that is present in at least one other subject
			Evidence: Subject: sub-minc008; Missing session: ses-02
		./sub-minc009/ses-02
			A session is missing from one subject that is present in at least one other subject
			Evidence: Subject: sub-minc009; Missing session: ses-02
		./sub-minc010/ses-02
			A session is missing from one subject that is present in at least one other subject
			Evidence: Subject: sub-minc010; Missing session: ses-02
		./sub-minc012/ses-02
			A session is missing from one subject that is present in at least one other subject
			Evidence: Subject: sub-minc012; Missing session: ses-02
		./sub-minc013/ses-02
			A session is missing from one subject that is present in at least one other subject
			Evidence: Subject: sub-minc013; Missing session: ses-02
		./sub-minc015/ses-02
			A session is missing from one subject that is present in at least one other subject
			Evidence: Subject: sub-minc015; Missing session: ses-02
		./sub-minc017/ses-02
			A session is missing from one subject that is present in at least one other subject
			Evidence: Subject: sub-minc017; Missing session: ses-02
		./sub-minc019/ses-02
			A session is missing from one subject that is present in at least one other subject
			Evidence: Subject: sub-minc019; Missing session: ses-02
		./sub-minc020/ses-02
			A session is missing from one subject that is present in at least one other subject
			Evidence: Subject: sub-minc020; Missing session: ses-02
		./sub-minc021/ses-02
			A session is missing from one subject that is present in at least one other subject
			Evidence: Subject: sub-minc021; Missing session: ses-02
		./sub-minc022/ses-02
			A session is missing from one subject that is present in at least one other subject
			Evidence: Subject: sub-minc022; Missing session: ses-02
		./sub-minc023/ses-02
			A session is missing from one subject that is present in at least one other subject
			Evidence: Subject: sub-minc023; Missing session: ses-02
		./sub-minc024/ses-02
			A session is missing from one subject that is present in at least one other subject
			Evidence: Subject: sub-minc024; Missing session: ses-02
		./sub-minc028/ses-02
			A session is missing from one subject that is present in at least one other subject
			Evidence: Subject: sub-minc028; Missing session: ses-02
		./sub-minc029/ses-02
			A session is missing from one subject that is present in at least one other subject
			Evidence: Subject: sub-minc029; Missing session: ses-02
		./sub-minc030/ses-02
			A session is missing from one subject that is present in at least one other subject
			Evidence: Subject: sub-minc030; Missing session: ses-02
		./sub-mincx01/ses-02
			A session is missing from one subject that is present in at least one other subject
			Evidence: Subject: sub-mincx01; Missing session: ses-02
		./sub-mincx02/ses-02
			A session is missing from one subject that is present in at least one other subject
			Evidence: Subject: sub-mincx02; Missing session: ses-02
		./sub-mincx03/ses-02
			A session is missing from one subject that is present in at least one other subject
			Evidence: Subject: sub-mincx03; Missing session: ses-02
		./sub-mod036/ses-02
			A session is missing from one subject that is present in at least one other subject
			Evidence: Subject: sub-mod036; Missing session: ses-02
		./sub-mod037/ses-02
			A session is missing from one subject that is present in at least one other subject
			Evidence: Subject: sub-mod037; Missing session: ses-02
		./sub-mod929/ses-02
			A session is missing from one subject that is present in at least one other subject
			Evidence: Subject: sub-mod929; Missing session: ses-02

	Please visit https://neurostars.org/search?q=MISSING_SESSION for existing conversations about this issue.

	5: [WARN] The recommended file /README is missing. See Section 03 (Modality agnostic files) of the BIDS specification. (code: 101 - README_FILE_MISSING)

	Please visit https://neurostars.org/search?q=README_FILE_MISSING for existing conversations about this issue.


        Summary:                 Available Tasks:        Available Modalities: 
        179 Files, 2.46GB        cvr                     T1w                   
        25 - Subjects                                    bold                  
        2 - Sessions                                     events                
                                                         fieldmap              


	If you have any questions, please post on https://neurostars.org/tags/bids.
7

And the web result which apparently is a few versions newer in the BIDS standard. Same result.
data_errors.txt (15.1 KB)

8

I upgraded to docker to 24.0.5 from docker 20.10.6 (for Ubuntu 20.04.5), and now things work like they had for me in the past. If you are getting weird error messages trying a newer version of the fmriprep docker image whilst everything else remains constant and worked in the past, try upgrading docker. Maybe the developers could incorporate a docker version check to save future users from this issue.

2 Likes