<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Alfredo,<div class=""><br class=""></div><div class="">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>.)</div><div class=""><br class=""></div><div class="">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.</div><div class=""><br class=""></div><div class="">I created a PR on LORIS-MRI to elaborate the log from the function you just sent: <a href="https://github.com/aces/Loris-MRI/pull/617" class="">https://github.com/aces/Loris-MRI/pull/617</a> 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?</div><div class=""><br class=""></div><div class="">Let me know how it goes,</div><div class=""><br class=""></div><div class="">Cécile</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On May 10, 2021, at 4:15 PM, Morales Pinzon, Alfredo <<a href="mailto:AMORALESPINZON@bwh.harvard.edu" class="">AMORALESPINZON@bwh.harvard.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
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<div class="">Dear LorisDev team.</div>
<div class=""><br class="">
</div>
<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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<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo;" 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>
</div>
<div class="">===</div>
<div class=""><br class="">
</div>
<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>
<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>
<div class=""><br class="">
</div>
<div class="">Best.</div>
<div class="">Alfredo.</div>
<div class=""><br class="">
</div>
<div class="">===</div>
<div class="">
<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo;" 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>
<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> warnings.warn("The ability to pass arguments to BIDSLayout that control "</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; min-height: 16px;" class="">
<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;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">Connecting to:</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> database: DATABASE</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> username: USERDATABASE</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> hostname: 111.222.333.444</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> port : 3306</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; min-height: 16px;" class="">
<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; min-height: 16px;" class="">
<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;" 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;" 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>
<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; min-height: 16px;" class="">
<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;" 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;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> ('default_bids_vl',)</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; min-height: 16px;" class="">
<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; min-height: 16px;" class="">
<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;" 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;" 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>
<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; min-height: 16px;" class="">
<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;" 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;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> ('dataDirBasepath',)</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; min-height: 16px;" class="">
<br class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""></span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">Loading the BIDS dataset with BIDS layout library...</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; min-height: 16px;" class="">
<br class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""></span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> => BIDS dataset loaded with BIDS layout</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; min-height: 16px;" class="">
<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;" 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;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">Validating the list of participants...</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; min-height: 16px;" class="">
<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;" 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>
</div>
<div class="">===</div>
<div class=""><br class="">
</div>
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