[Loris-dev] BIDS Error
Morales Pinzon, Alfredo
AMORALESPINZON at BWH.HARVARD.EDU
Tue May 11 17:37:24 EDT 2021
Hi Cécile,
I just shared the dataset in the sftp in the following path: 2021_05_11/caseCecile_BIDS.zip
Additionally, here is the output of the script after adding the prints in the PR 617:
===
/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: 111.222.333.44
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
CFTY720D2306.0102.00001is missing from the BIDS Layout
List of subjects parsed by the BIDS layout:
===
Best,
Alfredo.
On May 11, 2021, at 12:01 PM, Cécile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:
External Email - Use Caution
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<mailto: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:
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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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