<div dir="ltr">Hi Alfredo,<div><br></div><div>it is possible that some fields in the session are not populated and that is why you do not see the images. Can you run the following query on one session that was created by the BIDS import script?</div><div><br></div><div>SELECT CandID, Visit_label, Active, Scan_done, CenterID, ProjectID, SubprojectID FROM session WHERE Visit_label = 'screening';   # (I make the assumption that screening is the MRI visit that was inserted here) </div><div><br></div><div>Let me know what you get from that query. My guess is that the Active field is NULL and should be set to 'Y' for you to be able to see it in the imaging browser.</div><div><br></div><div>Cécile</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sun, Jun 6, 2021 at 4:48 PM Morales Pinzon, Alfredo <<a href="mailto:AMORALESPINZON@bwh.harvard.edu">AMORALESPINZON@bwh.harvard.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">



<div style="overflow-wrap: break-word;">
Hi Cécile,
<div><br>
</div>
<div>We managed to insert the candidates and the visits, and create the specific file names for BIDS before actually launching the BIDS script. The script finally worked, however I don’t see the images in LORIS. I am adding down below the bids log
 insertion. Is there something additional I need to do to be able to see the images? In the web site I see the candidate and the visit but the column “Imaging Scan Done” is marked with a question mark (see attachment).</div>
<div><br>
</div>
<div>===</div>
<div>
<div>/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.</div>
<div>  warnings.warn("The ability to pass arguments to BIDSLayout that control "</div>
<div><br>
</div>
<div>Connecting to:</div>
<div>        database: DATABASE</div>
<div>        username: USERNAME</div>
<div>        hostname: 111.222.333440</div>
<div>        port    : 1234</div>
<div><br>
</div>
<div><br>
</div>
<div>Executing query:</div>
<div>        SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = %s);</div>
<div><br>
</div>
<div>With arguments:</div>
<div>        ('default_bids_vl',)</div>
<div><br>
</div>
<div><br>
</div>
<div>Executing query:</div>
<div>        SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = %s);</div>
<div><br>
</div>
<div>With arguments:</div>
<div>        ('dataDirBasepath',)</div>
<div><br>
</div>
<div>AMP::bids_dir: /DATA/CAND_A/bids</div>
<div>Loading the BIDS dataset with BIDS layout library...</div>
<div><br>
</div>
<div>AMP::bids_config: /PROJECT/bin/mri/python/lib/bids.json</div>
<div>root: /DATA/CAND_A/bids</div>
<div>target:: /DATA/CAND_A/bids/dataset_description.json</div>
<div>        => BIDS dataset loaded with BIDS layout</div>
<div><br>
</div>
<div>Grepping candidates from the BIDS layout...</div>
<div>Validating the list of participants...</div>
<div>subjects: ['207019']</div>
<div>        => Passed validation of the list of participants</div>
<div><br>
</div>
<div>        => List of participants found:</div>
<div>                207019</div>
<div><br>
</div>
<div><br>
</div>
<div>Grepping list of sessions from the BIDS layout...</div>
<div>        => List of sessions found:</div>
<div><br>
</div>
<div>                207019: screening</div>
<div><br>
</div>
<div><br>
</div>
<div>Grepping the different modalities from the BIDS layout...</div>
<div>        => Done grepping the different modalities from the BIDS layout</div>
<div><br>
</div>
<div><br>
</div>
<div>Executing query:</div>
<div>        SELECT * FROM candidate WHERE PSCID = %s</div>
<div><br>
</div>
<div>With arguments:</div>
<div>        ('207019',)</div>
<div>Executing query:</div>
<div>        SELECT SubprojectID FROM subproject WHERE title = %s</div>
<div><br>
</div>
<div>With arguments:</div>
<div>        ['Experimental']</div>
<div><br>
</div>
<div><br>
</div>
<div>Executing query:</div>
<div>        SELECT * FROM session WHERE CandID = %s AND Visit_label = %s</div>
<div><br>
</div>
<div>With arguments:</div>
<div>        ('622350', 'screening')</div>
<div><br>
</div>
<div><br>
</div>
<div>Executing query:</div>
<div>        SELECT * FROM candidate WHERE PSCID = %s</div>
<div><br>
</div>
<div>With arguments:</div>
<div>        ('207019',)</div>
<div><br>
</div>
<div><br>
</div>
<div>Executing query:</div>
<div>        SELECT SubprojectID FROM subproject WHERE title = %s</div>
<div><br>
</div>
<div>With arguments:</div>
<div>        ['Experimental']</div>
<div><br>
</div>
<div><br>
</div>
<div>Executing query:</div>
<div>        SELECT * FROM session WHERE CandID = %s AND Visit_label = %s</div>
<div><br>
</div>
<div>With arguments:</div>
<div>        ('622350', 'screening')</div>
<div><br>
</div>
<div><br>
</div>
<div>Executing query:</div>
<div>        SELECT type FROM ImagingFileTypes</div>
<div><br>
</div>
<div><br>
</div>
<div>Executing query:</div>
<div>        SELECT f.FileID, f.File FROM files AS f JOIN parameter_file USING (FileID) JOIN parameter_type USING (ParameterTypeID) WHERE Value=%s</div>
<div><br>
</div>
<div>With arguments:</div>
<div>        ('248248fb303a762548e0be602b0b6bd6c6f33b4c860898c69faa8273be7a80f6d93b6413ec3bbeaadf22005fac04b07e9c08487e7b0a6690f64c2781d77d69b4',)</div>
<div><br>
</div>
<div><br>
</div>
<div>Executing query:</div>
<div>        SELECT type FROM ImagingFileTypes</div>
<div><br>
</div>
<div><br>
</div>
<div>Executing query:</div>
<div>        SELECT f.FileID, f.File FROM files AS f JOIN parameter_file USING (FileID) JOIN parameter_type USING (ParameterTypeID) WHERE Value=%s</div>
<div><br>
</div>
<div>With arguments:</div>
<div>        ('b16bc029ea1cb8271a0728785d04eddaaa66e4d89c09e990552667b3c5598d17cee045b5b4ee3480dc2b8e08b5b05ca4e53c57f50b13b26f6467b9e4f455d09e',)</div>
<div><br>
</div>
<div><br>
</div>
<div>Executing query:</div>
<div>        SELECT type FROM ImagingFileTypes</div>
<div><br>
</div>
<div><br>
</div>
<div>Executing query:</div>
<div>        SELECT f.FileID, f.File FROM files AS f JOIN parameter_file USING (FileID) JOIN parameter_type USING (ParameterTypeID) WHERE Value=%s</div>
<div><br>
</div>
<div>With arguments:</div>
<div>        ('44346136db049d0faf867a34d57d5714803a320b070013da0e1cf66e064f4dc9db92533f8aa8caaafcb78ce141c5444c5b8f8dc6b1d1c7dac530a4c2375eedcd',)</div>
<div><br>
</div>
<div><br>
</div>
<div>Executing query:</div>
<div>        SELECT type FROM ImagingFileTypes</div>
<div><br>
</div>
<div><br>
</div>
<div>Executing query:</div>
<div>        SELECT f.FileID, f.File FROM files AS f JOIN parameter_file USING (FileID) JOIN parameter_type USING (ParameterTypeID) WHERE Value=%s</div>
<div><br>
</div>
<div>With arguments:</div>
<div>        ('ee91658a67d7d96007f6f0c625cceb700c9fa5bbecf34cea3cae8f1445a6efce5f735b2ab68d26717a6aaa418808b3d8fb30b03e03ae1982b0eeed834429d081',)</div>
<div><br>
</div>
<div><br>
</div>
<div>Executing query:</div>
<div>        SELECT type FROM ImagingFileTypes</div>
<div><br>
</div>
<div><br>
</div>
<div>Executing query:</div>
<div>        SELECT f.FileID, f.File FROM files AS f JOIN parameter_file USING (FileID) JOIN parameter_type USING (ParameterTypeID) WHERE Value=%s</div>
<div><br>
</div>
<div>With arguments:</div>
<div>        ('749c00e5aa64583c91f29672b228b9d89e691cef7d8f3380eefbc1fee466bd3d987fd7178001f0e4f63684a50e139a7bb8ed197981d1588ffc4dfc4eed8278b8',)</div>
</div>
<div>===</div>
<div><br>
</div>
<div>Thank you for your help.</div>
<div><br>
</div>
<div>Best,</div>
<div>Alfredo.</div>
<div><br>
</div>
<div><img id="gmail-m_-6827858577988785114F954AAAD-4C67-42E4-8B66-95E6D7DBD242" src="cid:179e6bcde08ae1fccbe1"><br>
<div><br>
<blockquote type="cite">
<div>On May 13, 2021, at 10:08 AM, Cecile Madjar <<a href="mailto:cecile.madjar@mcin.ca" target="_blank">cecile.madjar@mcin.ca</a>> wrote:</div>
<br>
<div>
<p><span style="padding:3px 10px;border-radius:5px;color:rgb(255,255,255);font-weight:bold;display:inline-block;background-color:rgb(255,0,0)">        External Email - Use Caution        </span></p>
<div><br>
</div>
<div dir="ltr">Hi Alfredo,
<div><br>
</div>
<div>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. </div>
<div><br>
</div>
<div>On the LORIS front: </div>
<div>
<ul>
<li>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).</li><li>the ID used next to ses-<ID> will be used for the visit label field of the session table</li></ul>
<div>There might be another solution for you: modifying the file <a href="https://secure-web.cisco.com/1GvLDW-g8RekA6xfXzTQGS9x-cvm3VJ64Me4gEy4E2Yh3_J_-W9ZJiP9DEv9M9oH_JN3CJGEaRyJUvOCUzrNqMXl0tpX8TJ_Cfrs5JA9p_ICYgDGAU_HcPRpK0aHBkRHCW9mHZTixcIoY9EEim1Tt4JhQWyQlJpaTKY-bd1bc5O1lxwHz6sj4nGQ5bXFiDLYRP4Y8DWJzxYpm8EMaj_QYRiVdUOwHiSGfVGMouhDDMYYwBHrEEdV1Ompf5QRyVkSSAJaGL2Q3tSABSa8USdVkOQ/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fblob%2Fmain%2Fpython%2Flib%2Fbids.json" target="_blank">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. </div>
<div><br>
</div>
<div>Hope this helps,</div>
<div><br>
</div>
<div>Cécile</div>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Thu, May 13, 2021 at 9:47 AM Morales Pinzon, Alfredo <<a href="mailto:AMORALESPINZON@bwh.harvard.edu" target="_blank">AMORALESPINZON@bwh.harvard.edu</a>> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>Hi Cécile,
<div><br>
</div>
<div>
<blockquote type="cite">
<div dir="ltr">
<div>Is it possible to modify your IDs to be alphanumerical?</div>
</div>
</blockquote>
<div><br>
</div>
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.</div>
<div><br>
</div>
<div>Best,</div>
<div>Alfredo.<br>
<div>
<div><br>
<blockquote type="cite">
<div>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:</div>
<br>
<div>
<p><span style="padding:3px 10px;border-radius:5px;color:rgb(255,255,255);font-weight:bold;display:inline-block;background-color:rgb(255,0,0)">        External Email - Use Caution        </span></p>
<div><br>
</div>
<div dir="ltr">Hi Alfredo,
<div><br>
</div>
<div>It looks like the pybids is not able to read your BIDS dataset, which is why it returns an empty list of subjects.</div>
<div><br>
</div>
<div>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?</div>
<div><br>
</div>
<div>Cécile</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">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:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>Hi Cécile,
<div><br>
</div>
<div>I just shared the dataset in the sftp in the following path: 2021_05_11/caseCecile_BIDS.zip</div>
<div><br>
</div>
<div>Additionally, here is the output of the script after adding the prints in the PR 617:</div>
<div><br>
</div>
<div>===</div>
<div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">/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:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">  warnings.warn("The ability to pass arguments to BIDSLayout that control "</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px">
<span style="font-variant-ligatures:no-common-ligatures"></span><br>
</div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">Connecting to:</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">        database: DATABASE</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">        username: USERDATABASE</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">        hostname: 111.222.333.44</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">        port    : 3306</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px">
<span style="font-variant-ligatures:no-common-ligatures"></span><br>
</div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px">
<span style="font-variant-ligatures:no-common-ligatures"></span><br>
</div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">Executing query:</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">        SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = %s);</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px">
<span style="font-variant-ligatures:no-common-ligatures"></span><br>
</div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">With arguments:</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">        ('default_bids_vl',)</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px">
<span style="font-variant-ligatures:no-common-ligatures"></span><br>
</div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px">
<span style="font-variant-ligatures:no-common-ligatures"></span><br>
</div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">Executing query:</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">        SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = %s);</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px">
<span style="font-variant-ligatures:no-common-ligatures"></span><br>
</div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">With arguments:</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">        ('dataDirBasepath',)</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px">
<br>
<span style="font-variant-ligatures:no-common-ligatures"></span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">Loading the BIDS dataset with BIDS layout library...</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">        => BIDS dataset loaded with BIDS layout</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px">
<span style="font-variant-ligatures:no-common-ligatures"></span><br>
</div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">Grepping candidates from the BIDS layout...</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">Validating the list of participants...</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px">
<span style="font-variant-ligatures:no-common-ligatures"></span><br>
</div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">ERROR: Participant ID mismatch between participants.tsv and raw data found in the BIDS directory/n</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">CFTY720D2306.0102.00001is missing from the BIDS Layout</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px">
<span style="font-variant-ligatures:no-common-ligatures"></span><br>
</div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">List of subjects parsed by the BIDS layout:</span></div>
</div>
<div>===</div>
<div><br>
</div>
<div>Best,</div>
<div>Alfredo.</div>
<div>
<div><br>
<blockquote type="cite">
<div>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:</div>
<br>
<div>
<div>
<p><span style="padding:3px 10px;border-radius:5px;color:rgb(255,255,255);font-weight:bold;display:inline-block;background-color:rgb(255,0,0)">        External Email - Use Caution        </span></p>
<div><br>
</div>
Sounds like a plan. Let me know once it is uploaded and I will ask Nicolas to give me access.
<div><br>
</div>
<div>Thanks!</div>
<div><br>
</div>
<div>PS: you can view the diff on the PR and simply copy the code over to your files if easier<br>
<div><br>
<blockquote type="cite">
<div>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:</div>
<br>
<div>
<div>Hi Cecile,
<div><br>
</div>
<div>In my testing dataset I have only one subject, I can share it with you in the LORIS sftp, does that work for you?</div>
<div><br>
</div>
<div>In the mean time I will diff and pull your PR, and then execute it. I’ll send you the output asap.</div>
<div><br>
</div>
<div>Best,</div>
<div>Alfredo. </div>
<div>
<div><br>
<blockquote type="cite">
<div>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:</div>
<br>
<div>
<p style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
<span style="padding:3px 10px;border-radius:5px;color:rgb(255,255,255);font-weight:bold;display:inline-block;background-color:rgb(255,0,0)">        External Email - Use Caution        </span></p>
<div style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
<br>
</div>
<span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">Hi
 Alfredo,</span>
<div style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
<br>
</div>
<div style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
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 style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
<br>
</div>
<div style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
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 style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
<br>
</div>
<div style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
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?</div>
<div style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
<br>
</div>
<div style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
Let me know how it goes,</div>
<div style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
<br>
</div>
<div style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
Cécile</div>
<div style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none">
<br>
<div><br>
<blockquote type="cite">
<div>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:</div>
<br>
<div>
<div>
<div>Dear LorisDev team.</div>
<div><br>
</div>
<div>I am running the BIDS uploading functionality of LORIS (from this PR suggested by Cecile:<span> </span><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):</div>
<div><br>
</div>
<div>===</div>
<div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">ERROR: Participant ID mismatch between participants.tsv and raw data found in the BIDS directory/n</span></div>
</div>
<div>===</div>
<div><br>
</div>
<div>After some debugging I saw that the array subjects in the following line is empty:</div>
<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>
<div><br>
</div>
<div>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>
<div><br>
</div>
<div>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>
<div><br>
</div>
<div>Looking forward to hearing from you.</div>
<div><br>
</div>
<div>Best.</div>
<div>Alfredo.</div>
<div><br>
</div>
<div>===</div>
<div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">/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">
<span style="font-variant-ligatures:no-common-ligatures">  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">
<span style="font-variant-ligatures:no-common-ligatures"></span><br>
</div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">Connecting to:</span></div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">        database: DATABASE</span></div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">        username: USERDATABASE</span></div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">        hostname: 111.222.333.444</span></div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">        port    : 3306</span></div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;min-height:16px">
<span style="font-variant-ligatures:no-common-ligatures"></span><br>
</div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;min-height:16px">
<span style="font-variant-ligatures:no-common-ligatures"></span><br>
</div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">Executing query:</span></div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">        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">
<span style="font-variant-ligatures:no-common-ligatures"></span><br>
</div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">With arguments:</span></div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">        ('default_bids_vl',)</span></div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;min-height:16px">
<span style="font-variant-ligatures:no-common-ligatures"></span><br>
</div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;min-height:16px">
<span style="font-variant-ligatures:no-common-ligatures"></span><br>
</div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">Executing query:</span></div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">        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">
<span style="font-variant-ligatures:no-common-ligatures"></span><br>
</div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">With arguments:</span></div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">        ('dataDirBasepath',)</span></div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;min-height:16px">
<br>
<span style="font-variant-ligatures:no-common-ligatures"></span></div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">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">
<br>
<span style="font-variant-ligatures:no-common-ligatures"></span></div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">        => 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">
<span style="font-variant-ligatures:no-common-ligatures"></span><br>
</div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">Grepping candidates from the BIDS layout...</span></div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">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">
<span style="font-variant-ligatures:no-common-ligatures"></span><br>
</div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">ERROR: Participant ID mismatch between participants.tsv and raw data found in the BIDS directory/n</span></div>
</div>
<div>===</div>
<div><br>
</div>
<div>The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine
 at<span> </span><a href="http://secure-web.cisco.com/1qM_d-YnL441NX1CgLDc0-4p5P74OBrZe4qz8DQn4NKFJlMAA7HiKjibIOLkeFbmot5sDXcFfxupjvo_jX8vC9aYNvFDnADUwQFAF2ETaANXw3yIZaf8bb7_SvUXAkTxwK31eivXt_HlY2DxnGsZ739ls6VersNRKPQN2plxFNbqAzR65ZCFC8YSBrs5Vrcr1GWNsx7YN7RWdCvcDN1j8l1v9uD8Je4NlxsZBp9G86xq4w2ATmf4ENiL-6RShyNpajtkjZKD6TUD0FKl1yu9EdA/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline" target="_blank">http://www.massgeneralbrigham.org/complianceline</a><span> </span>.
 If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.</div>
<br>
<p class="MsoNormal">Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving
 this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. <span> </span></p>
</div>
_______________________________________________<br>
Loris-dev mailing list<br>
<a href="mailto:Loris-dev@bic.mni.mcgill.ca" target="_blank">Loris-dev@bic.mni.mcgill.ca</a><br>
<a href="https://secure-web.cisco.com/1nZGLPRvHAc4QXkbuPkDbTk6X7cLRpZjuKhOBth4NO62r205kfGQbnAX-YD9BjpSJaYX2q-XFXkB_JSF0s5z2ahDn5jCwO30vrTUlIZlEANwK8y3vIbbTS3OKeQl5HWbDL3FviFQTAC2JkKwXTysKFx31cF_fdj3Ldph7SeZSr25P3BOdkNzQM7CwOgGsZ74Icj-bh17DcnTl_TpfPBvtKvWdT9JJgzhO4xgU1diPaWsF1-yCLwXh4xN8u993AJYONV8vaXR3KRoKV8-QxssqZw/https%3A%2F%2Fmailman.bic.mni.mcgill.ca%2Fmailman%2Flistinfo%2Floris-dev" target="_blank">https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev</a></div>
</blockquote>
</div>
</div>
</div>
</blockquote>
</div>
<br>
</div>
<div>The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine
 at <a href="http://secure-web.cisco.com/1AhAU1QrkHn5uAqLbnmi1HyXx_kpI9yR6ZBTDEz2E2EH9ZJ8W5lI94E700CC6tH7ISW-FmwwtetLtDvUs671_9WDXfhJBJZUlAUiC75p9k2iniolB83RMn1vpjTql7mdvGqhQFlpZCisj05nFxy4_7JaawBv-2YfBcGJkgmL4k4UTe3OZ3Q6CU-jPPmqEDNyFt7jVXNncRMqUUg9ZiUWmhABUAHol2wVTYpBugXYIZfYMj79LvUy54oxCyOtX5FCW00-m4IAVrvYB_EhkHxI5Qw/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline" target="_blank">
http://www.massgeneralbrigham.org/complianceline</a> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.</div>
<br>
<p class="MsoNormal">Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving
 this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. 
</p>
</div>
</div>
</blockquote>
</div>
<br>
</div>
</div>
</div>
</blockquote>
</div>
<br>
</div>
<div>The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine
 at <a href="http://secure-web.cisco.com/1Vs76oaBwBuqLoMP4tDeksrqcCgDkogMEbBScJ4ejcwSa6gekqJpFoL6YNIznACwU31BdOoVLyr1lD6sf6FJ0bhDvv_VDNM4ihqPNDRpk_MBie2PPM8xVjhZzqKoCHhcAwaJVO6JrBb8QVg0k78kxRXH7d0wKdNPAHrs292D3K2KcEskKWx2YgQ-McThsXUDOsdj4Y99wDiDj5fzeT-glwFo2ZGa6-7cdKO2jHZVoiG8_XlvkoA76TtLIZxN04JfUn5UFQZ0p3J-jLf5RR8u_7A/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline" target="_blank">
http://www.massgeneralbrigham.org/complianceline</a> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.</div>
<br>
<p class="MsoNormal">Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving
 this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. 
</p>
</div>
</blockquote>
</div>
</div>
</blockquote>
</div>
<br>
</div>
</div>
<div>The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine
 at <a href="http://secure-web.cisco.com/1n2UbpIP1Hiy1wedtWg9s-6NXBNM5GXQsk4yul5KQtRtD-fpCcwhqxfc9xPmkoXTkvQiEilB7x5cMjoMnEfP7sVBe6N4BZFTL6lnTA5ZoU6_eL-QZrxz4bet8uKLeH8lFWIbsg3Tq1FqZpdjEzQ9aSVMRC-CNrE0-CJn7xfPqJefF9I1-_5OZcKb9QkXl2Rg_xjO8CfyirontcnUgEOHlJ5anCG65dp3TNqKwXi_HsVUusIi9c6KJxpEoiY-xH-7k_UAsbpirJkzRosIoJNyevA/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline" target="_blank">
http://www.massgeneralbrigham.org/complianceline</a> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.</div>
<br>
<p class="MsoNormal">Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving
 this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. 
</p>
</div>
</blockquote>
</div>
</div>
</blockquote>
</div>
<br>
</div>
<div>The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at <a href="http://www.massgeneralbrigham.org/complianceline" target="_blank">http://www.massgeneralbrigham.org/complianceline</a> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.</div><br>
<p class="MsoNormal">Please note that this e-mail is not secure
(encrypted).  If you do not wish to continue communication over
unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you
understand and accept this risk and wish to continue to communicate over
unencrypted e-mail.  </p></div>

</blockquote></div>