Segmenting white matter tracts for FBA metric computation

[ThijsDhollander]

Hey @Ana_Han,

Hope you’re doing well!

The questions you’re asking are indeed quite broad, and there’s many different ways to go about it. There’s certainly no single way that is best here: it’s about choosing what works best for your data, hypothesis/es and even just practically (or pragmatically).

@Ana_Han

I am interested in studying degeneration of specific white matter tracts and computing FD for each tract.

I understand that the use of an atlas to segment different tracts is required, and looked at this thread: Fixel-based analysis - assign significant fixels to tracks , but I was confused at how to where to obtain the white matter atlases. Is there a specific one recommended for FBA? As well, I am unsure how to manually create the inclusion and exclusion ROIs. Are these ROIs sourced from other publications, or are they derived from one’s subject data using Mrtrix commands?

If indeed you’re looking to get FD per tract “a priori”, you might want go get a fixel masks for each tract of your interest. Note this is a bit different from the post you link to: Remika Mito’s (@rmito) work there performed a whole-brain fixel-based analysis first: i.e. without hypothesising a set of tracts. Once the fixel-wise results were obtained, they were essentially labelled by identifying structures/tracts present in those results. So on an abstract level, it’s a bit the other way around, you could say. I’ll highlight your question to Remika: she might be able to clarify some details of the atlases used. But in the end, this was quite a bit of manual work; it’s not an automated approach combining an existing atlas to get that kind of output.

@Ana_Han

Lastly, I’m assuming that one can use the WM atlas to ‘guide’ categorization of fixels into a specific ROI/tract of interest, as was mentioned in the thread. Is there a command in Mrtrix to do this?

So sadly, no, there’s no simple solution available: it takes some manual work. A PhD student is working on creating a fixel-wise tract atlas that might eventually serve this purpose, but it’s still a ways off.

@jpalm

Potential alternative approach - I’ve had success using TractSeg to derive tract masks by segmenting the FOD template created according to the FBA pipeline instructions(Fibre density and cross-section - Single-tissue CSD — MRtrix3 3.0 documentation). You could then pass the tract masks you’re interested in to fixelcfestats?

Yes, approaches using TractSeg might help you quite a bit along the road to make a few things more automated or simpler. In the end, the challenge will still partially be that the main TractSeg output is voxel-wise maps: so you need to bridge a gap to link it to the fixels in the FOD template (and a tract shouldn’t contain all fixels in each voxel it passes through of course!). These days, TractSeg also outputs “tract orientation maps” ("TOM"s): I can imagine with a slight bit of trickery you could use that output and correspond it with the fixel in your fixel analysis mask, as derived from the FOD template. @jpalm, how did you go about it in practice? (again, I can imagine some alternatives, but would be great to hear some experiences!)

@Ana_Han, there was another recent question on this topic you might’ve missed: see also some of the things I wrote over here, as well as the follow-up replies. That might also inspire a few options. @jpalm, take a look as well: might be interesting to see how it relates to your approach to deal with this!

Cheers & take care,
Thijs