Pull request BEP-001 into main BIDS specification: support for quantitative MRI in BIDS

Dear BIDS-community,

We are lucky to work in a field where rapid progress is made, both in knowledge about the brain, as well as in new techniques to gain that very knowledge. As you probably know, the field of anatomical MRI has recently seen a bloom of techniques that allow us to characterize brain tissue in new ways and visualize brain structure that remained invisible before. This new set of techniques has become known as quantitative MRI (qMRI), offering the possibility of quantifying brain tissue in physical units, such as T1, T2 and T2* in seconds.

Quantitative MRI provides numerous novel applications to the neuroimaging community: it allows the delineation of specific subcortical nuclei in the subcortex, parcellation of the visual system based on laminar myeloarchitecture and measuring the myelination of white matter bundles on an absolute scale, just to count a few.

Unfortunately, these data are not easily collected and need computational modelling to come to full bloom. Of course, BIDS could offer some amazing tools to help researchers make both qMRI data and software more easily accessible. However, Currently BIDS cannot accommodate qMRI data as it confines the description of anatomical images to grayscale T1- or T2-“weighted” images.

Therefore, after dozens of people contributed over the course of 3 years, we are very happy to make an “official” pull request for our BIDS extension proposal 001 that introduces support for a range of anatomical MRI applications. This will facilitate 1/ the dissemination of these advanced imaging techniques in the research community as well as 2/ the development of accessible software to process these data.

To make this possible, we propose to extend the concept of “suffix”, in the domain of anat(omical) data. Specifically, anatomical images can now be described with (1) “traditional” weighted suffixes like “_T1w” and _T2w", (2) “grouped scan collections” suffixes like “_MP2RAGE” and “_MPM”, and (3) quantitative maps suffixes like “_T1map”, “T2_map” and “_Chimap”.

Finally, we also release 8 open data sets using a plethora of qMRI methods that fit in this new scheme. You can find these data sets at https://osf.io/k4bs5/

Now it is your turn: we would very much like a final round of feedback on the pull request, before it can be merged into the main specification.

There are many ways to contribute your feedback: first, and foremost, you can review the pull request at https://github.com/bids-standard/bids-specification/pull/508, but please also feel free to ping one of us, respond to this Neurostars topic or come to the Emergent session in the Open Science room at the upcoming OHBM conference. It will take place in the Open Science Room on Monday the 29th of June, at 8pm CET (2pm NY; 11am LA).

A rendered version of our draft can be found at http://bep001.readthedocs.io/en/dev/

Kind regards,
Gilles de Hollander, Agah Karakuzu, Alberto Lazari, Christophe Phillips, Kirstie Whitaker

1 Like