[Loris-dev] BIDS upload in LORIS - Participants file

Mon Apr 26 10:18:09 EDT 2021

Dear Cecile,

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?

Best regards,
Alfredo.

On Apr 26, 2021, at 9:12 AM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:

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Dear Alfredo,

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.

Ideal structure of the participants.tsv file:
participant_id  sex  date_of_birth  site

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.

We will definitely update the documentation. Thank you for letting us know!

Hope this helps,

Cécile

On Sat, Apr 24, 2021 at 11:10 AM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Dear LorisDev team,

I am launching the insertion pipeline in LORIS of a dataset in BIDS format. I am getting the following error:

===
Loading the BIDS dataset with BIDS layout library...
        => BIDS dataset loaded with BIDS layout

Grepping candidates from the BIDS layout...
Validating the list of participants...
Traceback (most recent call last):
  File "bids_import.py", line 431, in <module>
    main()
  File "bids_import.py", line 75, in main
    read_and_insert_bids(bids_dir, config_file, verbose, createcand, createvisit)
  File "bids_import.py", line 157, in read_and_insert_bids
    bids_reader = BidsReader(bids_dir, verbose)
  File "/data_/ipmsa/loris_data/IPMSA/bin/mri/python/lib/bidsreader.py", line 62, in __init__
    self.participants_info = self.load_candidates_from_bids()
  File "/data_/ipmsa/loris_data/IPMSA/bin/mri/python/lib/bidsreader.py", line 114, in load_candidates_from_bids
    self.candidates_list_validation(participants_info)
  File "/data_/ipmsa/loris_data/IPMSA/bin/mri/python/lib/bidsreader.py", line 142, in candidates_list_validation
    for row in participants_info:
TypeError: 'NoneType' object is not iterable
===

It looks like the file “participants.tsv” is required in LORIS, is this correct? In the BIDS specification this file is not required (https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#participants-file<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>) and there is no mention in LORIS documentation (https://github.com/aces/Loris-MRI/blob/main/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets<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>).

Thank you in advance for your help.

Best regards,
Alfredo.
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