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

[Cecile Madjar]

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> 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)
> 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
> ).
>
> Thank you in advance for your help.
>
> Best regards,
> Alfredo.
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