I am getting the following error with validator 1.5.8
1: [ERR] Internal error. SOME VALIDATION STEPS MAY NOT HAVE OCCURRED (code: 0 - INTERNAL ERROR)
.undefined
Evidence: RangeError: Maximum call stack size exceeded
at missingSessionFiles (/usr/lib/node_modules/bids-validator/validators/session.js:20:10)
at validateMisc.then.then.then.then.then.then.then.then.eventsIssues (/usr/lib/node_modules/bids-validator/validators/bids/fullTest.js:199:42)
at processTicksAndRejections (internal/process/task_queues.js:86:5)
It seems the error I am experiencing is similar to what’s described in the thread below, but I didn’t find any resolution or workaround mentioned.
Thank you for your message. Can you please share the size of the dataset you are trying to validate? Perhaps one way to reduce the validation size can be to add this flag: --ignoreSubjectConsistency . Another way could be to break down your dataset into a few subsets and validate the subsets.
Thanks so much for responding. Dataset has more than 400 subjects but we started getting the error only after adding an additional modality data to it. Using that flag eliminates the error. I am curious what does it really do and in what way is it helping what appears to be a memory-related issue ? I still get the following warning (which is not an issue as it is a heterogeneous dataset):
[WARN] Not all subjects/sessions/runs have the same scanning parameters. (code: 39 - INCONSISTENT_PARAMETERS)
Thank you for your message. That flag reduces down the validator log and the associated memory needs. That warning can be accounted for (as you also surfaced) by the heterogeneous dataset.
I’m having a similar error when trying to run the bids validator through singularity with the command below, after reading through the threads here and here.
singularity run ../tools/singularity/bids-validator-v1-7-2.simg . --verbose --ignoreSessionConsistency --ignoreSubjectConsistency
bids-validator@1.7.2
Unhandled rejection (
reason: RangeError: Maximum call stack size exceeded
at recursiveMerge (/src/utils/files/readDir.js:264:26)
at async getFilesFromFs (/src/utils/files/readDir.js:283:9)
at async recursiveMerge (/src/utils/files/readDir.js:266:7)
at async getFilesFromFs (/src/utils/files/readDir.js:283:9)
at async recursiveMerge (/src/utils/files/readDir.js:266:7)
at async getFilesFromFs (/src/utils/files/readDir.js:283:9)
at async preprocessNode (/src/utils/files/readDir.js:107:10)
at async Object.readDir (/src/utils/files/readDir.js:25:7)
).
As a note, I don’t believe I had this problem before using heudiconv to convert some more recent scans into this BIDS directory, and encountering this issue, and changing permissions so heudiconv could touch all the files. My /derivatives directory is also now quite large, though, after running more processing, so maybe it’s a size thing?
I can successfully use the bids-validator after I shell into the container, with the commands below. Is there a way to bids-validate outside the container, though? I was also afeared that I messed up some .jsons by killing heudiconv while it was touching all the top-level files a few times while figuring out the heudiconv error.