Hi @LiuYuchen,
Correct: SIFT is fundamentally not applicable to seed-based tractography, only to whole-brain tractography. I’m hoping that my (updated) preprint adequately explains why this is the case (this is one of many threads on this forum that motivated writing it).
I was doing a similar research to generate tracks seeded from VTA to whole GM, thus can get a connection map of GM for VTA. … Is there any problem with this pipeline?
What you’re doing there seems to be fundamentally different to the original question in this topic. The original question related to wanting to quantify connection strength from one region to others, which is the context in which SIFT2 is applicable. In your case, you’re simply generating an image of the density of streamlines terminations, where the streamlines were seeded from a specific region. There’s nothing intrinsically wrong with this, as long as the result is interpreted in accordance with the way in which they were generated. However if you are aiming for these to have an alternative quantitative interpretation to that I just described, then you would need to go about the experiment in a different way:
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Just seeding from one (ideally very small) region of interest, and seeing where the streamlines propagate to, would typically be interpreted as representing the probability that that region is structurally connected to any other region of the brain;
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Performing whole-brain tracking, applying a method such as SIFT2, isolating those streamlines connecting to your region of interest, and seeing the density of streamlines traversing from there to other regions, would typically be interpreted as representing the density of structural connections from the region of interest to any other region of the brain.
Obviously both of these have caveats. Unfortunately I’ve on multiple occasions seen people start talking cross-purposes because each did not realise that the other party was implicitly applying the converse interpretation to “probabilistic streamlines”. But I thought I’d elucidate here given there’s a reasonable chance that it’s related to your uncertainty here, and my publication where I explain this is still not out yet so I couldn’t just refer you to it…
Rob