NiPreps Roundup (bi-monthly)

Date: Feburary 22, 2023
Time: 6.00pm CEST / 5.00pm UTC / 12.00pm EDT / 9.00am PDT
Zoom link: please request to be added to the event messaging to <nipreps@gmail.com>

Agenda

  1. Finally, official introduction of Elodie Savary, Ph.D.
    Elodie has been recently hired as a Research Engineer to lead the development of cross-NiPreps infrastructure, taking the governance documents and their approval to the finish line, centralize the communications flow, and, in general, be responsible for all the action items regarding the CZI funding.

  2. CZI EOSS5 award
    We will walk through the aspects that have been requested for funding, see what is funded by this grant and what is covered by the R01 that started in June 2021, etc.
    Elodie is transferring the action items from the project proposal into this GH project: https://github.com/orgs/nipreps/projects/4/views/1

    In broad terms, the R01 focuses on individual -Preps (fMRIPrep, dMRIPrep, ASLPrep, PETPrep, MRIQC) and underlying neuroimaging developments (e.g., SDCFlows) while the EOSS5 focuses on community building and scientific software engineering aspects.

  3. Reactivating the adoption of a governance model
    Elodie has already resumed the development of governance documents (https://github.com/nipreps/GOVERNANCE).
    One of the main blockers that have held the governance model at a stall is that we had to designate MAINTAINERS for as many projects as possible in the NiPreps organization.
    From those MAINTAINERS, an overal STEERING COMMITTEE would then be selected.
    It would be ideal if we could kick off some sort of election process with this meeting, and close the process by the next meeting (April 19th, 2023).

    The plan is to nominate an acting NiPreps Steering Committee to ensure the MAINTAINERS of the following projects are nominated:

    • fMRIPrep
    • MRIQC
    • dMRIPrep
    • SDCFlows
    • Niworkflows
    • sMRIPrep
    • eddymotion
    • fMRIPrep-rodents
    • NiBabies & fMRIPrep-infants
    • TemplateFlow
    • PETPrep (if Martin is present, and agrees)
    • ASLPrep (Taylor Salo will discuss with Ted Satterthwaite)

    The MAINTAINERS list of these projects should be filled in within six (6) weeks, to allow two weeks before the next Roundup on April 19.
    During these two final weeks, the acting NiPreps Steering Committee will propose the first NiPreps Steering Committee with three (3) members or five (5), drawn from the MAINTAINERS of the projects.
    The election process will also defined, proposed, and organized by the acting NiPreps Steering Committee.

    Before jumping into the next point, we will bring up the proposal by CJM about SDCFlows listed below.

  4. Organization of workshops
    With the R01 we committed to organizing several workshops.
    Under this point we could briefly summarize what came out of the first workshop held at OHBM 2022 (Glasgow, UK), and initiate conversations regarding ISMRM 2023 (Toronto) and OHBM 2023 (Montreal).
    Members of the community based in Toronto and Montreal are very welcome to offer themselves for organization 🙏

  5. NiPreps Logo
    Within the EOSS5 grant, the design of a logo was included. OE went ahead and requested a first proposal with four options of logo + typography.
    During the meeting, we will share a link to a PDF file so that you can see the different options.
    We will then open a period of ten days to vote your preferred designs – for any information on this, please contact Elodie.

  6. Technical update (if time permits)
    We will show where the latest efforts have been directed towards. At the time of writing, the following comes to mind:

    • SDCFlows: where the new API wants to get, and why it is being so painful.
    • MIGAS (by Mathias Goncalves): our own telemetry (i.e., we want to discontinue Sentry)
    • Most active projects update (fMRIPrep – by Chris Markiewicz–, MRIQC – by Celine Provins–, eddymotion – by Ariel Rokem–)

Suggestions / TBD

Please add here topics you want to bring up or that you feel we missed in the list above.

  • [CJM] Potential collaborators for sdcflows; the value is highly limited if not adopted outside nipreps (the data/file structures at minimum). Additional stakeholders will be important for long-term benefits. From discussions with C-PAC, any assistance will be short-lived as they lack particular fieldmap expertise. It could be worth approaching AFNI and other tools to target our intermediate representation to take the load off of one tool to get everything right.

    • [OE] This is a good idea and I overall agree. I'm not sure how much we can outsource:

      • AFNI: this is one of the largest gaps in AFNI (IMHO). The 3dQWarp would need some improvement to generate B-Spline coefficients fields, not just the field. That is a hairy problem, because we will fall into the compatibility issue (unless they accept NiTransforms/SDCFlows conventions, which is unlikely given their LPS coordinate system among other factors.
      • FSL: this is the most obvious package where help could come from, but they are not going to change (for many reasons, some more legitimate than others, but overall all justifiable).
      • ANTs: this could be the best option for expansion, perhaps reaching out to Nick could help. On the downside list there is the lack for s-forms support, and some of the interpolation features of NiTransforms are missing in ITK. Nonetheless, there's been talks with Russ about a TOPUP implementation with ANTs which would make a lot of sense.
      • An agreement on the internal representation could be placed under the NiTransforms' responsibility - this suggestion solves nothing, but indicates that we need to also understand/acknowledge searching for this idea trascends SDCFlows' domain.

    • [OE2] Operatively speaking, I believe we want to set a MAINTAINERS list for SDCFlows (point 3 of the agenda) and then, ask from the community/steering-committee that the new MAINTAINERS implement this idea (i.e., try to talk to other projects, see what they think about the initiative, etc.) This is likely the same situation as right now, but at least we start using the new governance structure more formally, WDYT?

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