Emergent session: Developing a community-driven standard file format for brain tractography

[arokem]

Francois Rheault (@frheault)¹ Anibal Solon (@anibalsolon)², Chris Roorden (@neurolabusc)³ Franco Pestilli (@francopestilli)², Ariel Rokem (@arokem) ⁴

1. Sherbrooke University
2. University of Texas, Austin,
3. University of South Carolina
4. University of Washington

Recording and streaming volunteer: Francois Rheault, Sherbrooke University (@frheault)

Short description and the goals for the session

TRX (pronounced “tee ar ex”) is an emerging tractography file format designed to facilitate dataset exchange, interoperability, and state-of-the-art analyses, acting as a community-driven replacement for the myriad existing file formats.

File formats that store the results of computational tractography were typically developed within specific software packages. This approach has facilitated a myriad of applications, but this development approach has also generated insularity within software packages, and has limited standardization. Moreover, because tractography file formats were developed to solve immediate challenges, only a limited breadth of applications within a single software package was envisioned, sometimes also neglecting computational performance. Given the growing interest in tractography methods and applications, and the increasing size and complexity of datasets, a community-driven standardization of tractography has become a priority. To address these challenges, our community initiated a discussion to design a new file format and agreed to participate in its conception, development, and, if successful, its adoption.

The goal of TRX is to become the first community-driven standard amongst tractography file formats. As with other file formats like NiFTI, we believe that TRX will serve the community well and the growing computational needs of our field. We encourage community members to consider early contributions to our proposal so as to ensure the new standard will cover the needs of the wider audience of software developers, toolboxes, and scientists. Our long-term plan is to integrate TRX within the Brain Imaging Data Structure (BIDS) ecosystem.

TRX was first presented at the OHBM 2022 conference (abstract, poster) with 27 authors from 26 different institutions who are participating in the effort. In this emergent session, we propose to give an update on TRX development over the passing year, including consolidation of Python and JavaScript software for TRX, and integration into existing analysis pipelines and visualization software. We will open the floor to a broad discussion of the development milestones that we hope to achieve in the coming year. We are hoping to engage stakeholders from across the community towards development of software tools that support use of TRX.

Tagging @ValHayot, @Lestropie, @jdtournier, @Garyfallidis, @frankyeh, @effigies, @matthew-brett, @bjeurissen, @mrneont, @baranaydogan, @dPys, @skoudoro, @soichih, @haehn, @pieper, @DanNBullock, @emanuele, @jchoude, @MarcCote, @mdesco, @BennettLandman, who all were involved in the OHBM submission last year (in addition to some others whose GitHub handles I could not determine).

[slugtmeijer]

Hi there, this sounds like an interesting session. Thanks for submitting. We have allocated emergent session 2, Monday 24th 10:30-11:30, to this topic. If you send me an email I can provide you with more information: slugtmeijer@brocku.ca. Looking forward to meet you in Montreal. Best, Selma

[Remi-Gau]

I am including a link to this issue in the public google cal I am creating for ohbm.

https://twitter.com/RemiGau/status/1680754650830471168

[rgbayrak]

Here is the streaming link to your emergent session, distribute it widely 🤓
https://www.crowdcast.io/e/osr-2023-emergent-2

[arokem]

The slides for today's session are here: https://docs.google.com/presentation/d/1ap3L2vxsDiO8AljFRW__-5xsh5dxMKSBIDGgYPFt6-M/edit?usp=sharing

[slugtmeijer]

Thank you!

…

________________________________ Van: Ariel Rokem ***@***.***> Verzonden: dinsdag 25 juli 2023 02:58 Aan: ohbm/osr2023 ***@***.***> CC: slugtmeijer ***@***.***>; Comment ***@***.***> Onderwerp: Re: [ohbm/osr2023] Emergent session: Developing a community-driven standard file format for brain tractography (Issue #6) The slides for today's session are here: https://docs.google.com/presentation/d/1ap3L2vxsDiO8AljFRW__-5xsh5dxMKSBIDGgYPFt6-M/edit?usp=sharing — Reply to this email directly, view it on GitHub<#6 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A77F2TSUV5LGQDZI5UA5RILXR4Y3XANCNFSM6AAAAAAZQ5G3Y4>. You are receiving this because you commented.Message ID: ***@***.***>