fMRIPrep error: "ValueError: dictionary update sequence element #0 has length 4; 2 is required"

[akashkrathi]

Hi there, I am attempting to run fmriprep on singular subjects in my BIDS directory but am getting the following error.

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

SUB=$2
echo $SUB
singularity run --cleanenv -B /projects/b1108:/projects/b1108 \
-B /projects/b1108/studies/RADAR/data/preprocessed/fmriprep:/out \
-B /projects/b1108/studies/RADAR/data/raw/neuroimaging/bids:/data \
-B /projects/b1108/studies/RADAR/data/preprocessed/fmriprep/work:/work \
/projects/b1108/software/singularity_images/fmriprep_23.1.4.sif \
/data /out participant --participant-label ${2} \
--fs-license-file /projects/b1108/software/freesurfer_license/license.txt \
--fs-subjects-dir /projects/b1108/studies/RADAR/data/preprocessed/fmriprep/freesurfer \
--output-spaces MNI152NLin6Asym MNI152NLin2009cAsym \
-w /work --skip_bids_validation --bids-filter-file /projects/b1108/studies/RADAR/scripts/2_quality_check/bids_filter.json

Relevant log outputs (up to 20 lines):

You are using fMRIPrep-23.1.4, and a newer version of fMRIPrep is available: 25.1.3.
Please check out our documentation about how and when to upgrade:
https://fmriprep.readthedocs.io/en/latest/faq.html#upgrading
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 786, in parse_args
    config.from_dict({})
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/fmriprep/config.py", line 678, in from_dict
    execution.load(settings, init=initialize('execution'), ignore=ignore)
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/fmriprep/config.py", line 232, in load
    cls.init()
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/fmriprep/config.py", line 476, in init
    cls._layout = BIDSLayout(
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/bids/layout/layout.py", line 176, in __init__
    indexer(self)
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/bids/layout/index.py", line 150, in __call__
    self._index_metadata()
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/bids/layout/index.py", line 403, in _index_metadata
    file_md.update(pl())
ValueError: dictionary update sequence element #0 has length 4; 2 is required

I am not sure if this is a BIDS compliance issue or a code issue. I have experimented with my bids filter json file with little luck.

Thank you in advance!

[Steven]

Hi @akashkrathi, and welcome to neurostars!

Please try updating, return the BIDS validator output, and provide contents your BIDS filter file.

Best,
Steven

[akashkrathi]

Hi Steven, thanks for the response!

Here is my BIDS filter file

{
    "t1w": {
        "datatype": "anat",
        "session": "1",
        "acquisition": null,
        "suffix": "T1w"
    },
    "bold": {
        "datatype": "func",
        "session": "1",
        "suffix": "bold"
    }
}

Unfortunately, I cannot get my BIDS validator output because the code breaks before validation.

Thanks!

[Steven]

Hi @akashkrathi,

You can run the bids validator separately from fmriprep. GitHub - bids-standard/bids-validator: Validator for the Brain Imaging Data Structure

A tree output from a subject raw data folder might also be helpful.

Best,
Steven

[akashkrathi]

Here is the output from bids-validator. I downloaded a couple subjects and all non-subject folders locally and ran bids-validator.

npm WARN EBADENGINE Unsupported engine {
npm WARN EBADENGINE   package: 'unicode-name@1.0.4',
npm WARN EBADENGINE   required: { node: '>=18.20' },
npm WARN EBADENGINE   current: { node: 'v18.18.2', npm: '9.8.1' }
npm WARN EBADENGINE }
npm WARN deprecated inflight@1.0.6: This module is not supported, and leaks memory. Do not use it. Check out lru-cache if you want a good and tested way to coalesce async requests by a key value, which is much more comprehensive and powerful.
npm WARN deprecated glob@7.2.3: Glob versions prior to v9 are no longer supported
bids-validator@1.15.0
(node:16897) Warning: Closing directory handle on garbage collection
(Use `node --trace-warnings ...` to show where the warning was created)
	1: [WARN] Task scans should have a corresponding events.tsv file. If this is a resting state scan you can ignore this warning or rename the task to include the word "rest". (code: 25 - EVENTS_TSV_MISSING)
		./sub-2200/ses-1/func/sub-2200_ses-1_task-mid_run-01_bold.nii.gz
		./sub-2200/ses-1/func/sub-2200_ses-1_task-mid_run-02_bold.nii.gz
		./sub-2235/ses-1/func/sub-2235_ses-1_task-mid_run-01_bold.nii.gz
		./sub-2235/ses-1/func/sub-2235_ses-1_task-mid_run-02_bold.nii.gz
		./sub-2295/ses-1/func/sub-2295_ses-1_task-mid_run-01_bold.nii.gz
		./sub-2295/ses-1/func/sub-2295_ses-1_task-mid_run-02_bold.nii.gz

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

	2: [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.

	3: [WARN] The Name field of dataset_description.json is present but empty of visible characters. (code: 115 - EMPTY_DATASET_NAME)

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

        Summary:                Available Tasks:        Available Modalities: 
        93 Files, 8.28GB        mid                     MRI                   
        3 - Subjects            rest                                          
        1 - Session                                                           


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

Here is the tree diagram:

.
├── code
│   └── Protocol_Translator.json
├── dataset_description.json
├── derivatives
├── participants.json
├── participants.tsv
├── sourcedata
│   └── 2374
│       └── 1
├── sub-2200
│   └── ses-1
│       ├── anat
│       ├── dwi
│       ├── fmap
│       └── func
├── sub-2235
│   └── ses-1
│       ├── anat
│       ├── dwi
│       ├── fmap
│       └── func
└── sub-2295
    └── ses-1
        ├── anat
        ├── dwi
        ├── fmap
        └── func

24 directories, 4 files 

Thanks!

Akash

[Steven]

Hi @akashkrathi,

Please make sure the file names are visible as well in the tree output.

Best,
Steven

[akashkrathi]

Here is an updated version

./
├── code/
│   └── Protocol_Translator.json
├── dataset_description.json
├── derivatives/
├── participants.json
├── participants.tsv
├── sourcedata/
└── sub-2295/
    └── ses-1/
        ├── anat/
        │   ├── sub-2295_ses-1_run-1_T1w.json
        │   └── sub-2295_ses-1_run-1_T1w.nii.gz
        ├── dwi/
        │   ├── sub-2295_ses-1_run-1_dwi.bval
        │   ├── sub-2295_ses-1_run-1_dwi.bvec
        │   ├── sub-2295_ses-1_run-1_dwi.json
        │   └── sub-2295_ses-1_run-1_dwi.nii.gz
        ├── fmap/
        │   ├── sub-2295_ses-1_dir-ap_run-1_epi.json
        │   ├── sub-2295_ses-1_dir-ap_run-1_epi.nii.gz
        │   ├── sub-2295_ses-1_dir-ap_run-2_epi.json
        │   ├── sub-2295_ses-1_dir-ap_run-2_epi.nii.gz
        │   ├── sub-2295_ses-1_dir-ap_run-3_epi.json
        │   ├── sub-2295_ses-1_dir-ap_run-3_epi.nii.gz
        │   ├── sub-2295_ses-1_dir-pa_run-1_epi.json
        │   ├── sub-2295_ses-1_dir-pa_run-1_epi.nii.gz
        │   ├── sub-2295_ses-1_dir-pa_run-2_epi.json
        │   ├── sub-2295_ses-1_dir-pa_run-2_epi.nii.gz
        │   ├── sub-2295_ses-1_dir-pa_run-3_epi.json
        │   └── sub-2295_ses-1_dir-pa_run-3_epi.nii.gz
        └── func/
            ├── sub-2295_ses-1_task-mid_run-01_bold.json
            ├── sub-2295_ses-1_task-mid_run-01_bold.nii.gz
            ├── sub-2295_ses-1_task-mid_run-02_bold.json
            ├── sub-2295_ses-1_task-mid_run-02_bold.nii.gz
            ├── sub-2295_ses-1_task-rest_run-01_bold.json
            ├── sub-2295_ses-1_task-rest_run-01_bold.nii.gz
            ├── sub-2295_ses-1_task-rest_run-02_bold.json
            ├── sub-2295_ses-1_task-rest_run-02_bold.nii.gz
            ├── sub-2295_ses-1_task-rest_run-03_bold.json
            ├── sub-2295_ses-1_task-rest_run-03_bold.nii.gz
            ├── sub-2295_ses-1_task-rest_run-04_bold.json
            └── sub-2295_ses-1_task-rest_run-04_bold.nii.gz

10 directories, 34 files

[Steven]

Hi @akashkrathi,

Does fmriprep work locally on this smaller dataset? Did you try updating fmriprep? Can you try the validator on your full dataset?

Best,
Steven

[akashkrathi]

Hi Steven,

Fmriprep does not work on the smaller dataset likely because i used docker to run it locally. The larger dataset is on a computing cluster and on which I am unable to install bids-validator. Fmriprep did not work on the local dataset likely because I used docker to run it.

It seems as though someone else on Neurostars experienced the same issue. Was there ever a resolution to this post?

XCP-D error: ValueError: dictionary update sequence element #0 has length 4; 2 is required due to problem with BIDSLayout

Summary of what happened: I am trying to run the following code and get the following error. The thing is, I have another session, which I’ve derived to the folder iter6s2 and BIDSLayout can load this derivative. Edit: I can load resting states from iter6s2 using .get(subject='avl200', task='rest', extension='nii.gz', suffix='bold', return_type='filename'). But again, iter6s1 does not load at all. Command used (and if a helper script was used, a link to the helper script or the command generat…

Thanks!

[Steven]

Hi @akashkrathi,

@akashkrathi

Fmriprep does not work on the smaller dataset likely because i used docker to run it locally.

What do you mean by this?

Best,
Steven

[akashkrathi]

Hi Steven,

I was able to figure out. My work folder had output from a separate process.

Thanks!