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<div class="">Dear LorisDev team.</div>
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<div class="">I am running the BIDS uploading functionality of LORIS (from this PR suggested by Cecile:
<a href="https://github.com/aces/Loris-MRI/pull/558/files" class="">https://github.com/aces/Loris-MRI/pull/558/files</a> ) but I’m getting the following error (see all the output below):</div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">ERROR: Participant ID mismatch between participants.tsv and raw data found in the BIDS directory/n</span></div>
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<div class="">After some debugging I saw that the array subjects in the following line is empty:</div>
<a href="https://github.com/laemtl/Loris-MRI/blob/3742522fa46b0ee2b9e384e30650a0c1f425c7af/python/lib/bidsreader.py#L134" class="">https://github.com/laemtl/Loris-MRI/blob/3742522fa46b0ee2b9e384e30650a0c1f425c7af/python/lib/bidsreader.py#L134</a>
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<div class="">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.</div>
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<div class="">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.</div>
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<div class="">Looking forward to hearing from you.</div>
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<div class="">Best.</div>
<div class="">Alfredo.</div>
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<div class="">===</div>
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<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; color: rgb(0, 0, 0);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">/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.</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class=""> warnings.warn("The ability to pass arguments to BIDSLayout that control "</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class=""></span><br class="">
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<span style="font-variant-ligatures: no-common-ligatures" class="">Connecting to:</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class=""> database: DATABASE</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class=""> username: USERDATABASE</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class=""> hostname: 111.222.333.444</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class=""> port : 3306</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">Executing query:</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; color: rgb(0, 0, 0);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = %s);</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">With arguments:</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class=""> ('default_bids_vl',)</span></div>
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<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; color: rgb(0, 0, 0);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">Executing query:</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; color: rgb(0, 0, 0);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = %s);</span></div>
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<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; color: rgb(0, 0, 0);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">With arguments:</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; color: rgb(0, 0, 0);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> ('dataDirBasepath',)</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class=""></span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">Loading the BIDS dataset with BIDS layout library...</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class=""></span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class=""> => BIDS dataset loaded with BIDS layout</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class=""></span><br class="">
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<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; color: rgb(0, 0, 0);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">Grepping candidates from the BIDS layout...</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; color: rgb(0, 0, 0);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">Validating the list of participants...</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class=""></span><br class="">
</div>
<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; color: rgb(0, 0, 0);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">ERROR: Participant ID mismatch between participants.tsv and raw data found in the BIDS directory/n</span></div>
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<div class="">===</div>
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