BIDS validation for openneuro takes forever

1

Hi,

I am trying to upload my dataset on the openneuro.

While I already checked my data through BIDS validator (https://bids-standard.github.io/bids-validator/),
the validation process in the openneuro website never ends.

I generated a test dataset with only two participants or tried on a different laptop but it was the same.
(I think it’s a bug on the site API).

Did any of you have the same issue and solve?
Thanks a lot!

June

2

Just tried the site with a couple datasets I had on my local computer and the validator completed for all of them so hopefully isn’t an issue for any and all dataset uploads.

Are there any errors being printed to your browsers javascript console? (Usually Command+Option+J for Mac, or Control+Shift+J for Windows, Linux, best to open before loading the page.)

Is there any other place where you could upload the test dataset you are having issues with if it isn’t too large? I could download it and try to recreate the issue with it.

3

Are there any T1w images in the datasets you tried to upload? Curious if its related to this issue with the latest release:

4

Thanks to your advice, I could find some error messages on the browsers javascript console as follows:

index.js:57924 Uncaught (in promise) TypeError: Cannot set property global of # which has only a getter
at index.js:57924
at Array.map ()
at Object.Sje [as generateMergedSidecarDict] (index.js:57920)
at mGe (index.js:95070)
at index.js:95171
at new Promise ()
at index.js:95170
at index.js:59498
at new Promise ()
at n (index.js:59497)

But sadly, I still have no clue about the error message.
I don’t think it’s caused by T1w images (as I also tried to upload it, deleting T1w). Basically, my dataset with a single image still causes the same error. (I’d like to upload it to somewhere but it’s around 2GB per subject).

Thanks a lot!

5

It’s still not solved but I would just update a bit.

I found that my json files automatically generated by heudiconv have multi-level curly brackets ‘{ }’ and when I deleted large parts of json text, the validation process finished rapidly.

Currently, the files contain too many details, but I am not sure how much (and which) I can manually delete some of them.

6

Thank you for the console output. It does look like an issue parsing the JSON file. Can you post a copy of the file that was failing? Should be able to use that to help the validator fail more gracefully, and see if there is an issue with the JSON that heudiconv generates or if the problem arose from the source material.

7

As I cannot really upload non-image file on this post, I would share the link of it.

I only included anat folder of my BIDS structure (due to the file size). But if you put this into any dataset (or it alone with empty structured directories), I am sure it will reproduce the same problem.

In the end, I erased out the ‘global’ field (and its sub-parameters) of the json files and it passed BIDS validation of openNeuro. So, the problem was indeed in decoding json files.

Hope this helps the other users.

p.s - But, after successful uploading, I have faced another error, for which I need technical support. I am waiting for the response of openNeuro team. It’s really tough to upload, indeed.

Best regards,
June