Hi @GulinOz, thanks for posting! I’m tagging @wclarke here so he sees your question with regard to letting spec2nii handle de-identified files (I imagine it’s quite easy to loosen which fields it expects to be filled).
We plan to present the latest iteration of the NIfTI MRS specification to the community soon, and designate a time window during which community members can submit feedback and suggestions. Once this feedback is incorporated, there shouldn’t be many roadblocks left. Do you have a deadline for making the data available at NDA?
Thanks for the encouragement! I’m optimistic that the specification we have currently is not going to change for the more standard acquisition protocols such as SVS. However, as @admin says, we need a level of community agreement that what we have is fit for purpose - so there is always a chance we’d need to change something.
Is it ready for the prime time? I think the best way to find out is to test it with a real use case - so your timing is good! So far we have 8 software packages agreeing to support the format with maybe half that actually having a working NIfTI MRS import code at the moment.
It’s important to note that you’d be an early adopter and there are bound to be teething issues (thanks for spotting the de-identified data issue!) - however there is a strong will (no pun intended :)) to sort these things out quickly.
Ideally we will try to have just one conversion tool (spec2nii), but in the meantime I have code to perform the conversion for Siemens data and don’t mind taking a look if Will is unable to update spec2nii and you need something ASAP.
It’s great to hear that we already have some interest for this project. As far as the de-identification problem goes, that is an easy fix. I’m currently re-writing the spec2nii code to actually produce data in the provisional standard (rather than something I cobbled together for FSL-MRS). The provisional standard makes nearly all fields optional so it is appropriate that I change the conversion tool to cope with anonymised data. I will have a go at this tomorrow and I think it’s likely that I will push out a new version this week or next week. It will also be possible to try the new version straight from Github even if I don’t get it up on conda-forge yet.
With respect to whether the standard is ready, as Martin says it would be great to have a real world case to try it out on and with that, some feedback on what is important to capture for the data sharing use case. I think that as long as the data is relatively ‘normal’ e.g. 1H SVS/MRSI then I don’t expect the standard to change much. I suspect the issues we are going to have to iron out will be around more exotic data and for some of the meta-data that people may want to carry with it.
@admin, our first NDA deadline is very soon, on January 15, but my plan is to request an exception for submission of the MRS data. The next deadline is in July and it seems we may be ready for submission of MRS data in NIfTI format by then.
@wclarke, we’ll be happy to try your new version as soon as you feel it is ready for testing. Our data is indeed relatively normal SVS, saved in single shots. Please contact me off-line once the new version is ready and I’ll connect you to our data management team. Thank you for your work on this!
So good to see this work happening _ and a lot of thought has gone into it already. I wonder if there is scope to add the MRSinMRS checklist parameters in some fashion to the BIDS .json sidecar? A lot of the parameters are likely already included (field strength, frequency, voxel size etc), but if there is some way to include, or generate the checklist (or most of it) from the .json it would be very useful to authors, and would seem to fit with the intent of BIDS. (IMHO). Still getting to grips with using the MRS hub forum, so don’t quite see how to add a word document with the MRS checklist table to this conversation. @admin any helpful tips Georg?
Agreed, @PGMM. I hope to dedicate some time this month to resurrecting the BIDS MRS Extension Proposal. The MRSinMRS checklist will certainly inform on the specification significantly.
Actually I think @wclarke may already be thinking about this as I shared a preprint of the MRSinMRS paper with him a little while back to make sure the nifti conversion got some if not all, the parameters we included.
Yes, you are right about that. I’d like to cover those parameters that are easily extractable from raw data formats into the NIfTI-MRS standard and spec2nii conversion tool. Plus, those which aren’t so easily to automate we can define the meaning of the standard. The NIfTI-MRS group are having a meeting about this (and other things) next week on Wednesday at 4pm. If you’d like to join you would be very welcome.
@wclarke - I wouyld be happy to join next week - not that I would add much beyond the suggestion I’ve already made about the checklist parameters being in some way incorporated in the BIDS format - but if it would be sueful to ahve me there, happy to join.
@admin thanks Georg, adding the checklist itself as a PDF to this thread, will see about adding it to a seperate post for reference for all users. MRSinMRS_checklist.pdf (62.1 KB)
For those interested, the next annual BIDS Town Hall will take place next Monday, June 21st at 10 pm CEST / 4 pm ET / 1 pm PT during the Open Science Room program. OSR is a part of the OHBM Annual Meeting.
There will be updates on BIDS in general and the various BIDS Extension Proposals. I’ve been asked to give a 1–2 min update on our MRS BEP.
Now that the NIfTI-MRS data format standard has matured, I will be updating the MRS BEP accordingly. The BEP is a bit out of date with respect to the current version of the BIDS specification (e.g., redundant definitions of general terminology, the inclusion of subject session sidecar files). I will be taking the next week or so to clean up the doc (while trying not to remove any unresolved comments/suggestions already present).
Once things have been updated to fall in line with the current BIDS specification and our NIfTI-MRS initiative, I will post here what I believe our next priorities regarding the BEP are/might be.
As always, community contributions to this effort are most welcome!
I have taken the time to significantly update the draft BIDS Extension Proposal (BEP) for BIDS-MRS so that it complies with the current version of BIDS and covers as much of modern MRS methodology (relevant to data storage) as possible.
But, it is incomplete.
Some (but not all) areas we particularly would need input on from experts are, e.g., how i) MRSI, ii) ultra-high-field, iii) X-nuclei, and iv) preclinical data should be handled by BIDS-MRS. E.g., for MRSI, how do we distinguish between data acquired by different accelerated methods and/or different readouts (I realize, naively, these may be the same technique): Should this be handled by the file name or the sidecar JSON metadata file?
Important note : The BID-MRS BEP assumes that modality-common organizational standards that are not MRS-specific are already understood by users. That is, the BEP does not, and should not, reproduce what is already specified by BIDS. E.g., how participant data should be stored. This makes the inclusion of the MRS-BIDS BEP into the stable version of BIDS much easier further down the line.
I realize that BIDS may not be familiar to some of you, so I encourage you to look through the current specification. It’s likely that something you think of has already been standardized by BIDS.
Any feedback/comments can be provided either on the Google doc itself or on this thread.
Update: I have completed v1.0 of the MRS-BIDS extension proposal. We will be moving towards integration into the greater BIDS standard. Feedback is still welcome.
We have been finalizing the extension proposal and it is near completion.
If you would like to look over the Google doc and suggest any further changes, please do so in the next two weeks as we are due to meet with the BIDS Maintainers to go over the BEP and plan the integration into the BIDS standard. There then will be a final two-week community review (as a pull request on the BIDS specification GitHub repository).
I’m planning to share my SVS MRS dataset on an open database following the BIDS format. Yet, I couldn’t find any guidelines within the existing BIDS specifications for organizing basis sets. I’ve scoured past discussions here but haven’t come across any decision adopted by the community. Additionally, upon reviewing the listed open datasets on MRSHub, I couldn’t find any database mandating BIDS formatting similar to OpenNeuro. Is there any recommendation regarding where to publish the MRS data?
I’m glad you’ll be using BIDS to organize your dataset!
Before I reply to your queries, I want to link a preview of the upcoming update to the BIDS standard that will include the MRS extension. It would be best to refer to this version for now when standardizing your dataset. It’s still under development but contains the most up-to-date guidelines. (Note that it mentions example MRS datasets, but these have yet to be uploaded to the BIDS GitHub repository, but you can find them in my forked repository.)
As my memory serves, when @martin, @wclarke, and I had conversations with the BIDS team about how to deal with basis sets, it was concluded that because basis sets don’t fit neatly into the current BIDS standard, it was best to deal with them in a later version of BIDS.
My recommendation would be to store your basis sets in the sourcedata/ directory (e.g., sourcedata/basissets/...) (as described here). The sourcedata/ directory allows for more flexibility with data/metadata organization with respect to the “hard” requirements of the standard for raw data and derivatives.
As far as I’m aware, OpenNeuro and DANDI are the only repositories that require BIDS-organized datasets. But please refer to our recent paper for other initiatives that have leveraged BIDS.
That said, there’s no reason you couldn’t choose to use any other open data repository (unless they have their own organization requirements). I’ve not tried to upload any data to OpenNeuro yet, but I believe they run validation scripts on your dataset to see if it matches the current BIDS format. The issue is that the MRS extension has not yet been integrated into the format or the validation schema (this is something I’m working on finalizing at this moment ), so you might have issues using OpenNeuro. But it’s worth giving it a try.
Thank you for your detailed explanation. You were right about OpenNeuro. However, I have converted my dataset to BIDS format thanks to your suggestions.
), so you might have issues using OpenNeuro. But it’s worth giving it a try.