[Loris-dev] BIDS Error

Tue May 11 12:01:11 EDT 2021

Sounds like a plan. Let me know once it is uploaded and I will ask Nicolas to give me access.

Thanks!

PS: you can view the diff on the PR and simply copy the code over to your files if easier

> On May 11, 2021, at 11:47 AM, Morales Pinzon, Alfredo <AMORALESPINZON at BWH.HARVARD.EDU> wrote:
> 
> Hi Cecile,
> 
> In my testing dataset I have only one subject, I can share it with you in the LORIS sftp, does that work for you?
> 
> In the mean time I will diff and pull your PR, and then execute it. I’ll send you the output asap.
> 
> Best,
> Alfredo. 
> 
>> On May 11, 2021, at 11:36 AM, Cecile Madjar <cecile.madjar at mcin.ca <mailto:cecile.madjar at mcin.ca>> wrote:
>> 
>>         External Email - Use Caution        
>> 
>> 
>> 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://secure-web.cisco.com/17BHyJzFWfexg2et-D1qxjFw7-MsSpwCyZsKHDjuQa1Iruj-GV8fZRnaNOQe7rTfFaljPkHD9E0Kch6nwzSvbbe_48vUcKT3ozGDvxPfpe248W0Nml3EbqwefqTQo6V0gIBseIrXtJ4qwpUnrLVYpwZQyTPaDCbkm_NqrpLrBeXaHi-m5KCVluJqMYsb1DZBrqFL_XKJiIevFuiValC7eTehDRbTek9A5RvYsPN6hDTzEHFPQfCzzRD6W_iQSp80c_PbAKgxDUVLU2cePcP45pg/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fpull%2F617> 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 <mailto: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://secure-web.cisco.com/1eWQtSLH8tHTpC1qsinKLnr4amf7Vdt1MLFNigX4jKdNz2mAoHV9ejLLcHZh1a0CUaUlzZMYTU9qzLaUEYYpyP1cl5UCR8e02WTmdMZUKXBNDeD8-cV2O5yTv8cgci7szP_MIGsvZ7FCjhqVmibPUnMFYbs6uYHGXZHOB5MsouWYLRHh89rJtQaFS8DOg4jfbwjp1bxwnO4FyuD3aKRv17dw9zoczaaXWnkbXXr87i6NQKYmA1NXhjM570IkyzSKuq-dlKj94vTZIlAChD5aFeg/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fpull%2F558%2Ffiles> ) 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://secure-web.cisco.com/1sAIMc1N1U7sTpJYVEGfljx8iP9AUjxof1GeCQwNPKhd82OAXEZmdHoYu7n3Uq8jLaO-quBK1igoIw9Oo7d5JVNCfb3MNy6u-cvR2KkL-rfKwSOW_ovP_V5YKydvDMoE1ltw4MO29keFq-JiTymIk8Wm8TbXeHKxF2njboK6-6bctzRI-5K2tWwz82zUZyzDxyFdn4zXPqI8AihHeuWQQG3GOGgPSbRP-GOUfwbu2eVmvL_P_ldZetO1qjKowic0Gqnt-a9XN_8GORD5BLNlxTw/https%3A%2F%2Fgithub.com%2Flaemtl%2FLoris-MRI%2Fblob%2F3742522fa46b0ee2b9e384e30650a0c1f425c7af%2Fpython%2Flib%2Fbidsreader.py%23L134>
>>> 
>>> 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
>>> ===
>>> 
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