Re: [bids-discussion] BEP for allow phantom data into BIDS?
Cyril Pernet
Hi Everyone,based on some recent discussions in the niQC SIG regarding phantom data in QA and beyond (see the video below), we feel there might need to a be a BEP to include phantom data directly into BIDSOne main reason is to get around the limitation of not being able to share dates to help match between subjects and the corresponding phantom data (e.g. from the day of subject's scanning). It appears to me that packaging them together while sharing, if possible, would get around that limitation while retaining the correspondence. Does that make sense?If some or all of this functionality exists already, let us know. Or if we need to consider a new BEP to achieve it?PS: we have an exciting meeting today in an hour (tuesday 11am EDT) focused on phantoms: tinyurl.com/QualityConvs (and other exciting talks in the future).. join us if you are interested!Thanks,Pradeep--
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Dr Cyril, Pernet
yes I think we should try to build a repo as for humans and use
the updated common principles from that PR (to be merged?) -- and
see how it goes from there
Ha I see.
If I am understanding correctly, my gut feeling is that there is a PR in the pipeline that might help formalize reference to BIDS dataset outside of the current dataset: https://github.com/bids-standard/bids-specification/pull/820
But I can see that there will be an issue if you want to:
- keep the acquisition date of the phantom "as is" in a standalone dataset,
- keep track when each scan was acquired respective to the phantom,
- AND anonymize the acquisition dates
On 27/08/2021 11:04, Dr Cyril, Pernet wrote:
The issue is that one phantom BIDS dataset can fit many human/animal BIDS dataset, so we don't want to store many times the same data inside other datserts with specific subjects - while Robert suggestion works that is too cumbersome - also fMRI phantom is not on a daily basis (mote like once a week).
We would therefore rather create BIDS phantom datasets and human datasets can refer to it and conversely (while the later might not be needed, depends if we want to keep bidirectionality) - using interpolation of data (say a sine overtime) QC from phantom can be regressed out on group analyses.
Was trying to think of where this could fit in a BIDS dataset but Robert's suggestions seems a good starting point.
Not sure this requires a full fledged BEP if a pull-request will do, but this may be because I am not seeing the specifics issues.
If dates in the scans.tsv or sessions.tsv have to "anonymised" then I suspect they should be offsetted by the same amount for phantom and the subject data.
@+
On 27/08/2021 10:05, Robert Oostenveld wrote:
Hi Pradeep,
Although not exactly "phantom data", for MEG the specification includes instructions how to organize "empty room” recordings. See https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/02-magnetoencephalography.html#empty-room-meg-recordings. These are organized by sessions corresponding to dates, so that it is possible to find an empty room recording (which are often done once every morning) that matches an experimental recording with a subject later that day. This has similarities to organizing https://bids-specification.readthedocs.io/en/stable/06-longitudinal-and-multi-site-studies.html. If you would have different phantoms (e.g. bottle, belong, cauliflower), I would code their identity as the subject identifier.
Hope this helpsRobert
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On 24 Aug 2021, at 15:58, Open MINDS Lab at Pitt, PI Pradeep Raamana <openmi...@gmail.com> wrote:
Hi Everyone,
based on some recent discussions in the niQC SIG regarding phantom data in QA and beyond (see the video below), we feel there might need to a be a BEP to include phantom data directly into BIDS
One main reason is to get around the limitation of not being able to share dates to help match between subjects and the corresponding phantom data (e.g. from the day of subject's scanning). It appears to me that packaging them together while sharing, if possible, would get around that limitation while retaining the correspondence. Does that make sense?
If some or all of this functionality exists already, let us know. Or if we need to consider a new BEP to achieve it?
PS: we have an exciting meeting today in an hour (tuesday 11am EDT) focused on phantoms: tinyurl.com/QualityConvs (and other exciting talks in the future).. join us if you are interested!
Thanks,Pradeep
--
We are all colleagues working together to shape brain imaging for tomorrow, please be respectful, gracious, and patient with your fellow group members.
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Rémi Gau
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-- Dr Cyril Pernet, PhD, OHBM fellow, SSI fellow Neurobiology Research Unit, Building 8057, Blegdamsvej 9 Copenhagen University Hospital, Rigshospitalet DK-2100 Copenhagen, Denmark wamc...@gmail.com https://cpernet.github.io/ https://orcid.org/0000-0003-4010-4632--
Rémi Gau
-- Dr Cyril Pernet, PhD, OHBM fellow, SSI fellow Neurobiology Research Unit, Building 8057, Blegdamsvej 9 Copenhagen University Hospital, Rigshospitalet DK-2100 Copenhagen, Denmark wamc...@gmail.com https://cpernet.github.io/ https://orcid.org/0000-0003-4010-4632