[ENH]: BEP046, diffusion tractography#2333
[ENH]: BEP046, diffusion tractography#2333arokem wants to merge 1 commit intobids-standard:masterfrom
Conversation
Starting to port over information from https://docs.google.com/document/d/1ubDQ2RhgjnfGqoeukzEkPV9YEHhfYMERrj7-3b0c2HI/edit?tab=t.0
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## master #2333 +/- ##
=======================================
Coverage 82.81% 82.81%
=======================================
Files 22 22
Lines 1693 1693
=======================================
Hits 1402 1402
Misses 291 291 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
|
|
Hi @arokem and @francopestilli, I hope you are well. We are getting ready to release data from our NIH BRAIN CONNECTS UM1 and are reviewing BEP046. Prior to reviewing BEP046, our plan was to release the tractography data as TRK files since that is the format we use throughout most of our processing pipelines. I see that the plan for BEP046 is to only support TRX files. We would like you to reconsider also supporting TRK files. From our perspective, TRK and TCK represent the most widely used tractography formats. We believe BEP046 would benefit from supporting these established formats, similar to how the BIDS microscopy spec supports multiple formats (PNG, TIFF, OME-TIFF, and OME-Zarr), even through OME-Zarr appears to be the most cutting-edge option. Presumably the choice of the NIfTI format for neuroimaging data in the BIDS spec was much easier as that had been the most commonly used format for many years. Perhaps once the microscopy and tractography worlds settle on their respective formats the BIDS spec could support a single format, but in the meantime it would be beneficial to support the most commonly used formats. Additionally, I am unclear as to why the need to use TRK version 2 as outlined in the Google Doc is a 'non-starter' and would appreciate clarification on this point. Thanks for considering and I would be happy to join your working group meetings to discuss further. |
|
Hi @kabilar: thanks for contributing to this discussion! I would also suggest to read this discussion that led to the development of TRX: nipy/nibabel#942 and the document that laid out the initial plans for its specification: https://docs.google.com/document/d/1GOOlG42rB7dlJizu2RfaF5XNj_pIaVl_6rtBSUhsgbE/edit?tab=t.0#heading=h.c6igqydj1hrf. For obvious reasons, BIDS has traditionally been quite resistant to proliferation of file formats, where that can be avoided. I believe that it can be avoided here, while TRX offers a good set of features for the community to work with and growing software support (now in Python, C++, Javascript, and even Pascal!). In the meanwhile, I will separately send you information about the meetings of the IST Standardization Unit, so you can join the conversation there. |
|
Surfice already supports TRX (though it seems to be a while since a release was made.) DSI Studio and MRTRIX will both be supporting trx in the near future (e.g., see PR and PR). MI-Brain eventually too, according to my understanding, but I don't exactly know what the status of support for TRX is there. Niivue opens up the possibility to relatively easily design a variety of tools for specific uses. I think that brainlife uses niivue for some of their tools, so it's possible that they already have some tools for editing tractograms in TRX (@francopestilli, can you comment?) I realize that I forgot to cc @bids-standard/bep046 when posting this PR originally. I hope that others in that team can chime in as well. |
|
What are the tools that users you are referring to currently using with trk and tck files? I forgot to mention that @mattcieslak has already implemented TRX reading for ITK (PR), so I believe that should cover some more tools (e.g., 3D slicer, I think? Maybe also Freeview? There's also a browser-based freeview that should already read/write TRX thanks to niivue) |
|
You'd be able to do this in DSI Studio after frankyeh/DSI-Studio#114 is approved |
|
@ayendiki Is this repository helpful? https://github.com/tee-ar-ex/trx-python |
5 participants
Starting to port over information from https://docs.google.com/document/d/1ubDQ2RhgjnfGqoeukzEkPV9YEHhfYMERrj7-3b0c2HI/edit?tab=t.0
Note
We meet regularly to discuss this BEP at the IST Standardization Unit
Please reach out to @arokem ([email protected]) if you would like to join these meetings, which usually occur on the last Friday of each month at 7:30 AM PT.