[Loris-dev] BIDS participants tvf and json file

Tue Apr 27 16:23:30 EDT 2021

Hi Alfredo,

Indeed, the sites will need to be created in advance.

Regarding the BIDS subject ID, they do need to be sub-<PSCID> other LORIS
will not know to which subject the images should be attached to. Sorry.

Cécile

On Tue, Apr 27, 2021 at 3:48 PM Morales Pinzon, Alfredo <
AMORALESPINZON at bwh.harvard.edu> wrote:

> Hi Cécile,
>
> Thank you for your response and the documentation. We are modifying our
> participants tsv and json file accordingly. I will pull to the PR you sent
> and test as soon as possible. I’ll keep you posted.
>
> In the mean time, I have two questions:
>
> 1. I assume that I have to create the sites in advance if I want them to
> be used in the BIDS importing script, right?
>
> 2. Our subject Ids do not follow the CandID of LORIS, for instance one
> subject folder is named “sub-CFTY720D2306.0102.00001”, is this okay for
> LORIS?. I saw in the documentation that the participant ID is the PSCID of
> the candidate. However having the PSCID here won’t make much sense as that
> would imply that all the BIDS files having the subjectID will have to be
> renamed.
>
> Best,
> Alfredo.
>
> On Apr 26, 2021, at 1:14 PM, Cecile Madjar <cecile.madjar at mcin.ca> wrote:
>
>         External Email - Use Caution
>
> Hi Alfredo,
>
> we are writing the documentation at the same time we are communicating. I
> created a PR with a detailed instruction and it contains answers to your
> questions: https://github.com/aces/Loris-MRI/pull/615/files
> <https://secure-web.cisco.com/1LYhiti2WmTM-2nhE7RMmvGsJO8YhxJJkTL3yNcudsFVZgRxKbH2hRDDtPIwcXz5zZHmnGfft9aik-0UCKzjojqhagkZ_T7p5ZZstuh4g9Y8Olr0k43DntX3a-b-GSXk2-Lcu17daBslxK3f9T2VW-QmtM2lwqcpBWxdtnOvMwYoGwz1W7AjD9t3rQsNahaUAAwX8ZYEoDQBf2-cK1jxAMAQmyq-yQvGezOYA3uarFPyuc5ujioMzxCQ8J_onOctQrE1tBn66KvEk-llDbkquiQ/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fpull%2F615%2Ffiles>
>
> In short:
> - for sex: any of M, F, female, male works (case insensitive so m, f,
> Female and Male works as well)
> - for date of birth: format = YYYY-MM-DD
> - for the participants.json, see the example given in the description of
> https://github.com/aces/Loris-MRI/pull/615/files
> <https://secure-web.cisco.com/1LYhiti2WmTM-2nhE7RMmvGsJO8YhxJJkTL3yNcudsFVZgRxKbH2hRDDtPIwcXz5zZHmnGfft9aik-0UCKzjojqhagkZ_T7p5ZZstuh4g9Y8Olr0k43DntX3a-b-GSXk2-Lcu17daBslxK3f9T2VW-QmtM2lwqcpBWxdtnOvMwYoGwz1W7AjD9t3rQsNahaUAAwX8ZYEoDQBf2-cK1jxAMAQmyq-yQvGezOYA3uarFPyuc5ujioMzxCQ8J_onOctQrE1tBn66KvEk-llDbkquiQ/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fpull%2F615%2Ffiles>
>
> Note: the support of the project is new and will be part of release
> LORIS-MRI 24 but there is no release scheduled soon. In the meantime, two
> solutions:
> - manually populate the project after the script has been run (not sure
> how realistic that is depending on your projects' need)
> - pull the code from this PR:
> https://github.com/aces/Loris-MRI/pull/558/files
> <https://secure-web.cisco.com/1SeC5rj4ftibokIYqslvNVOQX0yELRiZqrCAn8Ns25dXnyiVDtSgl2M627NuVbiFk-JpzN5VyQdSDtRJ5zYcsaQLu4puhk4xHqmRzVUZE5lxqblUAIyfrDVyXw-XftgvOyELswWIIHomEBkN5dHPUiF4zMHXeaSW8SfyuvZA1FxI-mx2znto5YBooqfW9RjrSo5YwlOWpEQSqyDSNN-GXeVl5F88m1YKGiQl2g83Tn-LyLS1AcICOaY11rqw0LL6bnriDLZQjiO7RFA6MuDTy6g/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fpull%2F558%2Ffiles>
> that adds the support for the project insertion in the candidate and
> session tables
>
> Hope this helps,
>
> Cécile
>
> On Mon, Apr 26, 2021 at 12:40 PM Morales Pinzon, Alfredo <
> AMORALESPINZON at bwh.harvard.edu> wrote:
>
>> Dear LorisDev Team,
>>
>> I have three questions regarding the BIDS participants files for LORIS:
>>
>> 1. What is the format that LORIS will be expecting for the column
>> date_of_birth in the participants.json file?
>>
>> 2. What are the values expected for the column sex in the
>> participants.json file? M,F or Male, Female?
>>
>> 3. Does LORIS need the participants.json file?
>>
>> Best regards,
>> Alfredo.
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>
> 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
> http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent
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> the sender and properly dispose of the e-mail.
>
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> wish to continue communication over unencrypted e-mail, please notify the
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