Welcome to the forum. I’ll try and answer some of the questions. I think it is indeed a good way of figuring out what we need.
On the topic of having an MRS NIfTI standard.
Perusing data e.g. from a publication
I think that this is an important application. We don’t often share much data in our publications, and those data we do share are sometimes liable to be “typical” spectra.
I think some of the reasons we don’t is that there isn’t a standard way to do so. Much of our analysis happens once data is loaded into memory. From there it never again emerges except as either fitting specific formats (e.g. .RAW files), downstream summary statistics or as publication type plots.
If there was an obvious choice of format to share and selection of programs to view it in then I think most of the hurdles would be removed.
Recreate an entire processing pipeline
A data standard will help with this, removing some of the format dependent steps. However, there are other issues that must also be solved to make this a reality.
Single data format for software packages
Currently every software package must reimplement the same functions for data I/O from many different formats. This is done to varying standards as each developer generally has experience with only a subset of the formats. This is a large overhead for any developer. If there was a single format typically handled, we could pool our knowledge and experience in creating a single point of conversion.
Having a single format means that users can use software packages in a much more modular way. Users could pick and choose the best or most relevant pipelines from a collection of toolboxes. In the neuroimaging community people often mix steps from FSL, SPM, Freesurfer and AFNI, this is enabled by them all reading a single format.
DICOM doesn’t achieve this currently mostly because of insufficient vendor reconstruction pipelines. Uncombined coils, or even resolved averages aren’t available in DICOM format on many scanners. In the absence of this the default reconstruction software can apply some very non-optimal steps.
Whilst efforts to solve this on the reconstruction side in either proprietary environments or third-party ones (Gadgetron) might work for the technical research community, I don’t foresee great uptake elsewhere.
Interfacing with imaging tools
To interpret our data fully we are generally reliant on accurately aligning low resolution spectroscopy data with higher resolution imaging data. If we adopt the de facto neuroimaging data standard registration and visualisation become a somewhat solved problem.
I realise that this is a neuroimaging centric view though, NIfTI is not a standard for other anatomies.
On the topic of having an MRS BIDs standard.
I’m not so rehearsed in the arguments for BIDs, and I’ve run out of time for now. I’ll have a think and reply later.