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Dear Cecile,
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<div class="">I am running Loris 23.0.2. If I upload a BIDS dataset in this version, what project will be used to link the Candidates? I believe a project with the name of the dataset, taken from the “dataset_description.json”, will be created and the Candidates
will be inserted under this project, is this correct?</div>
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<div class="">Best regards,</div>
<div class="">Alfredo.<br class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On Apr 26, 2021, at 9:12 AM, Cecile Madjar <<a href="mailto:cecile.madjar@mcin.ca" class="">cecile.madjar@mcin.ca</a>> wrote:</div>
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<p class=""><span style="padding: 3px 10px; border-radius: 5px; color: #ffffff; font-weight: bold; display: inline-block; background-color: #ff0000;" class=""> External Email - Use Caution </span></p>
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<div dir="ltr" class="">Dear Alfredo,
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<div class="">Indeed, the participants.tsv file is required for LORIS since this is the file being read to create participants when they need to be created (this way LORIS can populate some additional information like site, sex, date of birth and age). We thought
this file was required in BIDS, which is probably why it was not documented. </div>
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</div>
<div class="">Ideal structure of the participants.tsv file:</div>
<div class="">participant_id sex date_of_birth site</div>
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<div class="">Note: in release 24.0, a 'project' column will be added so that upon creation of a candidate, a project can be associated with it.</div>
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<div class="">We will definitely update the documentation. Thank you for letting us know!<br class="">
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<div class="">Hope this helps,</div>
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<div class="">Cécile</div>
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<div dir="ltr" class="gmail_attr">On Sat, Apr 24, 2021 at 11:10 AM Morales Pinzon, Alfredo <<a href="mailto:AMORALESPINZON@bwh.harvard.edu" class="">AMORALESPINZON@bwh.harvard.edu</a>> wrote:<br class="">
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<div style="overflow-wrap: break-word;" class="">Dear LorisDev team,
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<div class="">I am launching the insertion pipeline in LORIS of a dataset in BIDS format. I am getting the following error:</div>
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<div class="">Loading the BIDS dataset with BIDS layout library...</div>
<div class=""> => BIDS dataset loaded with BIDS layout</div>
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</div>
<div class="">Grepping candidates from the BIDS layout...</div>
<div class="">Validating the list of participants...</div>
<div class="">Traceback (most recent call last):</div>
<div class=""> File "bids_import.py", line 431, in <module></div>
<div class=""> main()</div>
<div class=""> File "bids_import.py", line 75, in main</div>
<div class=""> read_and_insert_bids(bids_dir, config_file, verbose, createcand, createvisit)</div>
<div class=""> File "bids_import.py", line 157, in read_and_insert_bids</div>
<div class=""> bids_reader = BidsReader(bids_dir, verbose)</div>
<div class=""> File "/data_/ipmsa/loris_data/IPMSA/bin/mri/python/lib/bidsreader.py", line 62, in __init__</div>
<div class=""> self.participants_info = self.load_candidates_from_bids()</div>
<div class=""> File "/data_/ipmsa/loris_data/IPMSA/bin/mri/python/lib/bidsreader.py", line 114, in load_candidates_from_bids</div>
<div class=""> self.candidates_list_validation(participants_info)</div>
<div class=""> File "/data_/ipmsa/loris_data/IPMSA/bin/mri/python/lib/bidsreader.py", line 142, in candidates_list_validation</div>
<div class=""> for row in participants_info:</div>
<div class="">TypeError: 'NoneType' object is not iterable</div>
</div>
<div class="">===</div>
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</div>
<div class="">It looks like the file “participants.tsv” is required in LORIS, is this correct? In the BIDS specification this file is not required (<a href="https://secure-web.cisco.com/1FkPVQKx5OdH5N-uQcoP67Q4hJ2IGMbxqdqMTNHhzlomIH9oPTTZmuS_uW90xN5z6nWSf5cgN7yWLsXSuqxvgr-8BRujVvx3NiarjVql4H1FcL0Pl9keF6enV-6v6Hxw41wTLtG525Uf3caL5A6INeunnZMb_SLZtu7jQqMWGwAkCSgWdI1J1_q9H1I-DNRZnQRjJERe1abnF7ZzVnS4QMY_rfFcRLb2JWdxg3xUkruusRB3g1XPLtbAQ9Mbo_SwTZITvtEXs1PJEJmMpFiIwuw/https%3A%2F%2Fbids-specification.readthedocs.io%2Fen%2Fstable%2F03-modality-agnostic-files.html%23participants-file" target="_blank" class="">https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#participants-file</a>)
and there is no mention in LORIS documentation (<a href="https://secure-web.cisco.com/1SJdJkp532xdhMmyZnfObS0kR8gPjV3Gsyw2P6zXjNwBA9mn_d9jMtS-zQVNrBUq98-2_fViHxGkfKyp4Q5Erreluijztt80yo5SatnXCgFvlp7rEC_v3QT8KAkKq-m1hyArddk6HXvFK_uR46w-zouOXCp5A39ib9g067eyXbygGi7uCfdAYf4qWOmNtPHFgUDtAxCjT2mJfzNs42ZeUaTj7sREJ1L7WjVL67QOXbf5OlxTNfJdmh6785uwipnvKilqd6QsMvlKSZpsAjXNfOA/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fblob%2Fmain%2Fdocs%2F05-PipelineLaunchOptions.md%2352---pipeline-launch-for-bids-datasets" target="_blank" class="">https://github.com/aces/Loris-MRI/blob/main/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets</a>).</div>
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<div class="">Thank you in advance for your help.</div>
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</div>
<div class="">Best regards,</div>
<div class="">Alfredo.</div>
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