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<p class="MsoNormal">Hi Alfredo and Pisti,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">The BIDS specification is here:<o:p></o:p></p>
<p class="MsoNormal"><a href="https://bids-specification.readthedocs.io/en/stable/02-common-principles.html">https://bids-specification.readthedocs.io/en/stable/02-common-principles.html</a><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hyphens are considered alphanumeric characters, and underscores are used to separate entities. Periods are not allowed, so if there are files or directory names containing periods, that may be the issue.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Sridar<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">Cecile Madjar <cecile.madjar@mcin.ca><br>
<b>Date: </b>Thursday, May 13, 2021 at 10:08 AM<br>
<b>To: </b>"Morales Pinzon, Alfredo" <AMORALESPINZON@bwh.harvard.edu><br>
<b>Cc: </b>"loris-dev@bic.mni.mcgill.ca" <loris-dev@bic.mni.mcgill.ca>, "Douglas Arnold, Dr." <douglas.arnold@mcgill.ca>, "Sridar Narayanan, Dr." <sridar.narayanan@mcgill.ca>, Rozie Arnaoutelis <rozie.arnaoutelis@mcgill.ca>, "Guttmann Charles,M.D." <guttmann@bwh.harvard.edu>,
István Ákos Mórocz <istvan.morocz@mcgill.ca>, Samson Antel <samson@neurorx.com><br>
<b>Subject: </b>Re: [Loris-dev] BIDS Error<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
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<div>
<p class="MsoNormal">Hi Alfredo,<o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
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<div>
<p class="MsoNormal">The requirement of not having any special characters in the Participant ID or Session ID comes from BIDS and the libraries used to parse the BIDS dataset before insertion into LORIS. <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">On the LORIS front: <o:p></o:p></p>
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<div>
<ul type="disc">
<li class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level1 lfo1">
the ID used next to sub-<ID> will be used for the PSCID field of the candidate table (the CandID field being automatically generated as 6 random digits by the insertion script).<o:p></o:p></li><li class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level1 lfo1">
the ID used next to ses-<ID> will be used for the visit label field of the session table<o:p></o:p></li></ul>
<div>
<p class="MsoNormal">There might be another solution for you: modifying the file <a href="https://github.com/aces/Loris-MRI/blob/main/python/lib/bids.json">https://github.com/aces/Loris-MRI/blob/main/python/lib/bids.json</a> so that it matches the string used
for your data. You would need to modify the pattern for subject and session in that file to match what you have. In theory, once done, pybids should be able to read your dataset. <o:p></o:p></p>
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<div>
<p class="MsoNormal"><o:p> </o:p></p>
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<div>
<p class="MsoNormal">Hope this helps,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Cécile<o:p></o:p></p>
</div>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<p class="MsoNormal">On Thu, May 13, 2021 at 9:47 AM Morales Pinzon, Alfredo <<a href="mailto:AMORALESPINZON@bwh.harvard.edu">AMORALESPINZON@bwh.harvard.edu</a>> wrote:<o:p></o:p></p>
</div>
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<p class="MsoNormal">Hi Cécile, <o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<div>
<p class="MsoNormal">Is it possible to modify your IDs to be alphanumerical?<o:p></o:p></p>
</div>
</div>
</blockquote>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<p class="MsoNormal">It is possible but puts more burden on our side as every single file now has to be modified. What would be best format for LORIS for the user ids (e.g., six digits) and the visit labels (e.g., alphanumerical without dash)? I just want to
make sure we are compliant with LORIS requirements before modifying the bids files.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Best,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Alfredo.<o:p></o:p></p>
<div>
<div>
<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal">On May 11, 2021, at 6:34 PM, Cecile Madjar <<a href="mailto:cecile.madjar@mcin.ca" target="_blank">cecile.madjar@mcin.ca</a>> wrote:<o:p></o:p></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p><b><span style="color:white;background:red"> External Email - Use Caution </span></b><o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Hi Alfredo, <o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">It looks like the pybids is not able to read your BIDS dataset, which is why it returns an empty list of subjects.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">I just tried on the python terminal to load your dataset on pybids and it does not find any subject or visit. This is probably due to the name of the subject that contains special characters. That will also be problematic for the session
label of your dataset. I guess subjects in BIDS should remain alphanumerical only. Is it possible to modify your IDs to be alphanumerical?<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Cécile<o:p></o:p></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<p class="MsoNormal">On Tue, May 11, 2021 at 5:37 PM Morales Pinzon, Alfredo <<a href="mailto:AMORALESPINZON@bwh.harvard.edu" target="_blank">AMORALESPINZON@bwh.harvard.edu</a>> wrote:<o:p></o:p></p>
</div>
<blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm">
<div>
<p class="MsoNormal">Hi Cécile, <o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">I just shared the dataset in the sftp in the following path: 2021_05_11/caseCecile_BIDS.zip<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Additionally, here is the output of the script after adding the prints in the PR 617:<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">===<o:p></o:p></p>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo">/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.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo"> warnings.warn("The ability to pass arguments to BIDSLayout that control "<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo">Connecting to:<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo"> database: DATABASE<o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo"> username: USERDATABASE<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo"> hostname: 111.222.333.44<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo"> port : 3306<o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo"><o:p> </o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo">Executing query:<o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo"> SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = %s);<o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo">With arguments:<o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo"> ('default_bids_vl',)<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo">Executing query:<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo"> SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = %s);<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo">With arguments:<o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo"> ('dataDirBasepath',)<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo"><br>
<br>
<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo">Loading the BIDS dataset with BIDS layout library...<o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo"> => BIDS dataset loaded with BIDS layout<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo">Grepping candidates from the BIDS layout...<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo">Validating the list of participants...<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo">ERROR: Participant ID mismatch between participants.tsv and raw data found in the BIDS directory/n<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo">CFTY720D2306.0102.00001is missing from the BIDS Layout<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo"><o:p> </o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo">List of subjects parsed by the BIDS layout:<o:p></o:p></span></p>
</div>
</div>
<div>
<p class="MsoNormal">===<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
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<div>
<p class="MsoNormal">Best,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Alfredo.<o:p></o:p></p>
</div>
<div>
<div>
<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal">On May 11, 2021, at 12:01 PM, Cécile Madjar <<a href="mailto:cecile.madjar@mcin.ca" target="_blank">cecile.madjar@mcin.ca</a>> wrote:<o:p></o:p></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<p><b><span style="color:white;background:red"> External Email - Use Caution </span></b><o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<p class="MsoNormal">Sounds like a plan. Let me know once it is uploaded and I will ask Nicolas to give me access.
<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
</div>
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<p class="MsoNormal">Thanks!<o:p></o:p></p>
</div>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">PS: you can view the diff on the PR and simply copy the code over to your files if easier<o:p></o:p></p>
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<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
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<p class="MsoNormal">On May 11, 2021, at 11:47 AM, Morales Pinzon, Alfredo <<a href="mailto:AMORALESPINZON@BWH.HARVARD.EDU" target="_blank">AMORALESPINZON@BWH.HARVARD.EDU</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<p class="MsoNormal">Hi Cecile, <o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">In my testing dataset I have only one subject, I can share it with you in the LORIS sftp, does that work for you?<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">In the mean time I will diff and pull your PR, and then execute it. I’ll send you the output asap.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<div>
<p class="MsoNormal">Best,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Alfredo. <o:p></o:p></p>
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<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal">On May 11, 2021, at 11:36 AM, Cecile Madjar <<a href="mailto:cecile.madjar@mcin.ca" target="_blank">cecile.madjar@mcin.ca</a>> wrote:<o:p></o:p></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p style="font-variant-caps:normal;text-align:start;word-spacing:0px"><b><span style="font-size:9.0pt;font-family:Helvetica;color:white;background:red"> External Email - Use Caution </span></b><span style="font-size:9.0pt;font-family:Helvetica"><o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica">Hi Alfredo,</span>
<o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica">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>.)<o:p></o:p></span></p>
</div>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica"><o:p> </o:p></span></p>
</div>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica">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.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica"><o:p> </o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica">I created a PR on LORIS-MRI to elaborate the log from the function you just sent: <a href="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" target="_blank">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?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica">Let me know how it goes,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica">Cécile<o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica"><br>
<br>
<o:p></o:p></span></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica">On May 10, 2021, at 4:15 PM, Morales Pinzon, Alfredo <<a href="mailto:AMORALESPINZON@bwh.harvard.edu" target="_blank">AMORALESPINZON@bwh.harvard.edu</a>> wrote:<o:p></o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica"><o:p> </o:p></span></p>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica">Dear LorisDev team.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica">I am running the BIDS uploading functionality of LORIS (from this PR suggested by Cecile: <a href="https://secure-web.cisco.com/1eWQtSLH8tHTpC1qsinKLnr4amf7Vdt1MLFNigX4jKdNz2mAoHV9ejLLcHZh1a0CUaUlzZMYTU9qzLaUEYYpyP1cl5UCR8e02WTmdMZUKXBNDeD8-cV2O5yTv8cgci7szP_MIGsvZ7FCjhqVmibPUnMFYbs6uYHGXZHOB5MsouWYLRHh89rJtQaFS8DOg4jfbwjp1bxwnO4FyuD3aKRv17dw9zoczaaXWnkbXXr87i6NQKYmA1NXhjM570IkyzSKuq-dlKj94vTZIlAChD5aFeg/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fpull%2F558%2Ffiles" target="_blank">https://github.com/aces/Loris-MRI/pull/558/files</a> )
but I’m getting the following error (see all the output below):<o:p></o:p></span></p>
</div>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica"><o:p> </o:p></span></p>
</div>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica">===<o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Menlo">ERROR: Participant ID mismatch between participants.tsv and raw data found in the BIDS directory/n<o:p></o:p></span></p>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica">===<o:p></o:p></span></p>
</div>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica">After some debugging I saw that the array subjects in the following line is empty:<o:p></o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica"><a href="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" target="_blank">https://github.com/laemtl/Loris-MRI/blob/3742522fa46b0ee2b9e384e30650a0c1f425c7af/python/lib/bidsreader.py#L134</a>
<o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica">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.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica">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.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica">Looking forward to hearing from you.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica"><o:p> </o:p></span></p>
</div>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica">Best.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica">Alfredo.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica">===<o:p></o:p></span></p>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Menlo">/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.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Menlo"> warnings.warn("The ability to pass arguments to BIDSLayout that control "<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Menlo"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Menlo">Connecting to:<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Menlo"> database: DATABASE<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Menlo"> username: USERDATABASE<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Menlo"> hostname: 111.222.333.444<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Menlo"> port : 3306<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Menlo"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Menlo"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Menlo">Executing query:<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Menlo"> SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = %s);<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Menlo"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Menlo">With arguments:<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Menlo"> ('default_bids_vl',)<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Menlo"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Menlo"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Menlo">Executing query:<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Menlo"> SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = %s);<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Menlo"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Menlo">With arguments:<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Menlo"> ('dataDirBasepath',)<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Menlo"><br>
<br>
<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Menlo">Loading the BIDS dataset with BIDS layout library...<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Menlo"><br>
<br>
<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Menlo"> => BIDS dataset loaded with BIDS layout<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Menlo"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Menlo">Grepping candidates from the BIDS layout...<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Menlo">Validating the list of participants...<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Menlo"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Menlo">ERROR: Participant ID mismatch between participants.tsv and raw data found in the BIDS directory/n<o:p></o:p></span></p>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica">===<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica"><o:p> </o:p></span></p>
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