Error validating very large dataset (web) about bids-validator HOT 10 CLOSED

Hey, is it possible for you to share this dataset or even a file tree description? If it's from a set of test data that Chris has shared I may already have a copy. Otherwise I can do some testing by creating some large datasets to try to reproduce this.

Also do you know if this fails with the command line version?

from bids-validator.

Command line:

/home/oesteban/.nvm/v5.9.0/lib/node_modules/bids-validator/validators/nii.js:74
        var repetitionUnit = header.xyzt_units[3];
                                              ^

TypeError: Cannot read property '3' of undefined
    at NIFTI (/home/oesteban/.nvm/v5.9.0/lib/node_modules/bids-validator/validators/nii.js:74:47)
    at /home/oesteban/.nvm/v5.9.0/lib/node_modules/bids-validator/validators/bids.js:178:29
    at Gunzip.<anonymous> (/home/oesteban/.nvm/v5.9.0/lib/node_modules/bids-validator/utils/files.js:126:21)
    at emitOne (events.js:90:13)
    at Gunzip.emit (events.js:182:7)
    at readableAddChunk (_stream_readable.js:153:18)
    at Gunzip.Readable.push (_stream_readable.js:111:10)
    at Gunzip.Transform.push (_stream_transform.js:128:32)
    at Zlib.callback (zlib.js:572:14)

from bids-validator.

For the dataset, I can email a link to download it.

from bids-validator.

Thanks @oesteban the command line error should be enough info to replicate this. It looks like we're not seeing if xyzt units are present in the header before trying to act on them.

from bids-validator.

Ok, if it helps, it is very common that the field is empty. Maybe issuing a warning is fine.

from bids-validator.

Ok there's a PR open now. It turns out we already had an issue defined for repetition units not being defined is either seconds, milliseconds or microseconds. So cases in which it is undefined will now fall under the same issue which is currently set as an error.

Let me know if you're able to test if the above branch works with your dataset and loop Chris in if you think we should switch this case from an error to a warning.

from bids-validator.

@oesteban The fix for what I believe was your issue is now merged in and deployed to the gh-pages web interface. Please test it when you have a chance and close the issue if it's resolved.

from bids-validator.

Ok, should I go to http://incf.github.io/bids-validator/ ?

EDIT: worked for me!

from bids-validator.

Yes - it's updated automatically.

On Tue, Mar 22, 2016 at 11:45 AM, Oscar Esteban [email protected]
wrote:

Ok, should I go to http://incf.github.io/bids-validator/ ?

—
You are receiving this because you are subscribed to this thread.
Reply to this email directly or view it on GitHub
https://github.com/INCF/bids-validator/issues/104#issuecomment-199958013

from bids-validator.

Looks like this is resolved.

from bids-validator.