[Loris-dev] BIDS participants tvf and json file

Wed Apr 28 08:30:38 EDT 2021

Hi Alfredo,

Exactly. The same will apply for the visits.

Best,

Cécile

On Tue, Apr 27, 2021 at 5:30 PM Morales Pinzon, Alfredo <
AMORALESPINZON at bwh.harvard.edu> wrote:

> Hi Cécile,
>
> Great! Thank you for the clarification.
>
> I guess the same will apply for the visits/sessions.
>
> Best,
> Alfredo.
>
> On Apr 27, 2021, at 5:26 PM, Cecile Madjar <cecile.madjar at mcin.ca> wrote:
>
>         External Email - Use Caution
>
> 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
>> 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
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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
> to you in error but does not contain patient information, please contact
> the sender and properly dispose of the e-mail.
>
> Please note that this e-mail is not secure (encrypted).  If you do not
> wish to continue communication over unencrypted e-mail, please notify the
> sender of this message immediately.  Continuing to send or respond to
> e-mail after receiving this message means you understand and accept this
> risk and wish to continue to communicate over unencrypted e-mail.
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