Hi, Sondos-

No, it is definitely not "wrong" to have 0 tracts between 2 target ROIs. That means that *the tracking program* found no tracts between those targets. How that relates to physiology could be in two ways:
1) matching physiology-- there are no real direct tracts between the two targets, or
2) mismatching physiology-- there *are* some tracts connecting the targets, gosh darnit!

The second case can happen for many reasons, such as: the tracts are subtle, the data are noisy and/or distorted, voxel size is large, tracking algorithms aren't perfect. And mostly likely due to some combination of all of those. As you note, as well, if the targets are *not* bordering on DTI-defined WM (which would be wherever the FA threshold is, typically, and which is often at FA>0.2 for adult humans), then that would also be a reason tracts aren't found.

As to what to do about not havign tracts found-- well, there are tradeoffs to inflating the ROIs a lot. The main reason for ROI inflation is to not be penalized by smoothing/interpolation effects in transforming/regridding data, or to not be penalized by partial voluming in data sets, or somewhat practical reasons like that. Where are your ROIs coming from? A template atlas, or functional data ROIs, or parcellation like FreeSurfer, or ...? Inflating ROIs a large amount can lead to an increase in false positives, so I don't think it should be done a huge amount.

Interpreting results when no tracts are found is difficult, because *many* factors could lead to their not being tracts found-- and it might be hard/impossible to say which, definitively. It is first good to check that there are no obvious practical missteps or processing errors that lead to it (e.g., a bad alignment procedure or something). Once those kinds of things are checked, at present, I don't think there is more to say other than "the tracts weren't found"-- deciding on the cause being practical with the data or physiological with the brain does not seem possible.

The BL matrix gives the average lengths of all tracts found in that bundle. In "pairwise" connections between distinct ROIs, that can be interpreted as the average length of connections between the targets. The "individual ROI" connections (whose properties are listed on the diagonal) are just the set of *all* tracts that went through the ROI-- the aren't connections to/from anything, just ones *through* that ROI. I don't know a situation where those are really useful in an analysis, but htey are output in case they are. In most studies I have seen, it is the pairwise connections only that are used. (Someone *may* find a use for those-- great! It's just that, at present, that seems to be a rarity.)

--pt