[Loris-dev] BIDS participants tvf and json file

Tue Apr 27 17:26:32 EDT 2021

Right. But it will use what is in the sub-<PSCID> to create the new PSCID,
so in your case, the script will try to create a candidate with
PSCID=CFTY720D2306.0102.00001

Sorry for the confusion.

Cécile

On Tue, Apr 27, 2021 at 4:40 PM Morales Pinzon, Alfredo <
AMORALESPINZON at bwh.harvard.edu> wrote:

> Hi Cecile,
>
> 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.
>
> I thought the option “-c, --createcandidate: to create BIDS candidates in
> LORIS (optional)” would take care of this.
>
> Regarding the visits/sessions, do they need to be created in advance as
> well?
>
> Best,
> Alfredo.
>
> On Apr 27, 2021, at 4:23 PM, Cecile Madjar <cecile.madjar at mcin.ca> wrote:
>
>         External Email - Use Caution
>
> 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
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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
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> the sender and properly dispose of the e-mail.
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