Tract-of-interest segmentation following FBA pipeline completion

[Charly]

Hi,

Those choices might depend on the tracts you are interested in and on the precision you’re looking for, or how many you want to analyse. TractSeg might be the simplest and most convenient if it already provides the tracts you are looking for with successful segmentation. But it may not let you segment all tracts/fibres you’d like to look at. TractSeg’s Tracking function will get tracks from the TOMs and tck2fixel will return a fixel mask in the same space as the FOD template.

If you’re looking to deal with many tracts and have an atlas, you could also warp it to your FOD template and play with tck2connectome/connectome2tck, which allows you to extract tracks connecting specific combinations of regions.

@rsmith did a summary of various ways to build bundle of interest and I think they should also work for a FOD template:

Reconstruction of bundles of interest

When a researcher is interested specifically in one or a small number of pathways of interest, there are multiple strategies that can be employed to reconstruct and interrogate such. Each has their pros and cons. “Targeted tracking” Conventional approach Constraints based on the pathway of interest are applied during streamline generation, ie. tckgen Typically define a seed region from which to commence streamlines, a target inclusion region that they must reach, and potentially additi…