[Loris-dev] BIDS Error

[Cecile Madjar]

Hi Alfredo,

I do not have access to your dataset but is it possible that there is one or more sub-<ID> in the participants.tsv that are different from the sub-<ID> used in the directory structure? (a.k.a., folders sub-<ID> and filenames that should start with sub-<ID>.)

This function is specifically cross checking the list provided in the participants.tsv file and the information gathered by the BIDSLayout library that read your BIDS dataset.

I created a PR on LORIS-MRI to elaborate the log from the function you just sent: https://github.com/aces/Loris-MRI/pull/617 <https://github.com/aces/Loris-MRI/pull/617> Maybe try adding the print statement in the diff of the PR to your code and rerun to get a better idea of what is going on?

Let me know how it goes,

Cécile


> On May 10, 2021, at 4:15 PM, Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu> wrote:
> 
> Dear LorisDev team.
> 
> I am running the BIDS uploading functionality of LORIS (from this PR suggested by Cecile: https://github.com/aces/Loris-MRI/pull/558/files <https://github.com/aces/Loris-MRI/pull/558/files> ) but I’m getting the following error (see all the output below):
> 
> ===
> ERROR: Participant ID mismatch between participants.tsv and raw data found in the BIDS directory/n
> ===
> 
> After some debugging I saw that the array subjects in the following line is empty:
> https://github.com/laemtl/Loris-MRI/blob/3742522fa46b0ee2b9e384e30650a0c1f425c7af/python/lib/bidsreader.py#L134 <https://github.com/laemtl/Loris-MRI/blob/3742522fa46b0ee2b9e384e30650a0c1f425c7af/python/lib/bidsreader.py#L134>
> 
> I thought the issue was that we have symbolic links in our folder structure but after setting a testing example I am getting the same exact error.
> 
> Any ideas why this is happening? The error does not help much. I’m happy to share the testing case, with all the BIDS structure to a LORIS developer, if this is helpful.
> 
> Looking forward to hearing from you.
> 
> Best.
> Alfredo.
> 
> ===
> /PROJECT/bin/mri/python_virtualenvs/loris-mri-python/lib/python3.6/site-packages/bids/layout/validation.py:46: UserWarning: The ability to pass arguments to BIDSLayout that control indexing is likely to be removed in future; possibly as early as PyBIDS 0.14. This includes the `config_filename`, `ignore`, `force_index`, and `index_metadata` arguments. The recommended usage pattern is to initialize a new BIDSLayoutIndexer with these arguments, and pass it to the BIDSLayout via the `indexer` argument.
>   warnings.warn("The ability to pass arguments to BIDSLayout that control "
> 
> Connecting to:
>         database: DATABASE
>         username: USERDATABASE
>         hostname: 111.222.333.444
>         port    : 3306
> 
> 
> Executing query:
>         SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = %s);
> 
> With arguments:
>         ('default_bids_vl',)
> 
> 
> Executing query:
>         SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = %s);
> 
> With arguments:
>         ('dataDirBasepath',)
> 
> Loading the BIDS dataset with BIDS layout library...
> 
>         => BIDS dataset loaded with BIDS layout
> 
> Grepping candidates from the BIDS layout...
> Validating the list of participants...
> 
> ERROR: Participant ID mismatch between participants.tsv and raw data found in the BIDS directory/n
> ===
> 
> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
> 
> Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. 
> 
> _______________________________________________
> Loris-dev mailing list
> Loris-dev at bic.mni.mcgill.ca
> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20210511/9894c761/attachment.html>