Dear MRTrix team!
I am fairly new to the forum and would like to get some feedback on our pipeline. I’ve read a lot on the forum and in the latest Smith 2020 preprint, but am still unsure what applies to my exact problem.
I am wondering whether SIFT can be applied to non-targeted but seed-based tractography? I’ve read in several posts that it can only be applied to whole-brain tractography and not targeted tractography - but I am uncertain where a seed-based tractography without target would fall into)
If SIFT cannot be applied - how to properly normalize for differences in starting seed volume?
In more detail, we’ve ran a seed-based tractography (i.e. starting seed point but no traget) with the aim to correlate the resulting streamline densities with behavioral measures. The tractography was run with a fixed number of streamlines to select for the output (100.000 - due to comparability to an older project). We’ve now been wondering how to properly normalize for the differences in initial seed volume. So far, we’ve included either cortical thickness or surface area (the initial seeds where projected from GM on the GM/WM boundary) as a covariate when doing the correlations to behavioral measures.
What I’ve got from the forum (mostly this post) is that the ideal approach would to be to run a whole-brain tractography, create a whole-brain connectome and then filter for the streamlines connecting to our ROI. Due to comparability to an older project, if possible, we’d like to stay as close as possible to that older pipeline which did a seed-based approach.
So, in case of not using SIFT and a whole-brain tractography, do you have any recommendations on how to threshold the obtained streamline density map? I see that there is probably no easy answer to that and that it highly depends on the context. I’ve found this paper comparing the required number of streamlines while thresholding at 0.001 x streamline count and at 0.01 x the maximum trackmap intensity and wondered what you think of this approach.
Thank you very much in advance!