Hi,
I got an inconsistant error from the docker bids validator, while the online version of the bids validator does not give any error nor warning for the the same dataset.
Output of the docker BIDS-validator (pulled today, December 18th 2018):
1: [ERR] A json sidecar file was found without a corresponding data file (code: 90 - SIDECAR_WITHOUT_DATAFILE)
./sub-11/func/sub-11_task-random_run-01_recording-cardiac_physio.json
A json sidecar file was found without a corresponding data file
./sub-11/func/sub-11_task-random_run-01_recording-respiratory_physio.json
A json sidecar file was found without a corresponding data file
1: [WARN] Tabular file contains custom columns not described in a data dictionary (code: 82 - CUSTOM_COLUMN_WITHOUT_DESCRIPTION)
./sub-11/func/sub-11_task-random_run-01_events.tsv
Tabular file contains custom columns not described in a data dictionary not defined, please define in: /sub-11/func/sub-11_events.json, /sub-11/func/sub-11_task-random_events.json,/sub-11/sub-11_events.json,/sub-11/sub-11_task-random_events.json,/events.json,/task-random_events.json,/sub-11/func/sub-11_task-random_run-01_events.json
Summary: Available Tasks: Available Modalities:
16 Files, 284.73MB random bold
1 - Subject sbref
Here is a screenshot of the output of the online validator (same dataset)
Yes it does contain both:
./sub-11/func/sub-11_task-random_run-01_recording-cardiac_physio.tsv.gz
and
./sub-11/func/sub-11_task-random_run-01_recording-respiratory_physio.tsv.gz
Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a β.bidsignoreβ file in your dataset (see https://github.com/bids-standard/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.
Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a β.bidsignoreβ file in your dataset (see https://github.com/bids-standard/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.
Thank you for your message! The naming looks good (I presume your bold file is named: sub-01_task-ecriture_run-01_bold.nii.gz?) - perhaps @rwblair may see something?
I was able to replicate. Doesnβt look like the recording key word was used in our example datasets. Iβll fix the regex, add a test, and make a new release.
Also, using the bids validator singularity and running Bids-validator 1.5.2, on the same directory, this error doesnβt occur and the project passes the BIDS validator!
With the version 1.5.7 of the web browser of the bids validator, I found my answer: the json file related to the physiological files was not correctly formatted: The value for βColumnsβ must be an array: "Columns": [
βcardiacβ ]
and not a single value:
"Columns": βcardiacβ
Thanks to a better description of the error message, my problem is solved. Thanks!
cool that you caught the issue. We also updated the BIDS spec a couple of weeks ago so that tables include a column on how a field is to be formatted in terms of its datatype.
Youβll see that Columns needs to be an array of strings. So hopefully this relatively new feature of the BIDS specification will prevent issues like yours in the future.
