Hi, Sondos-

All matrices work the same. Off-diagonal elements apply to connections/WM-ROIs between two separate targets; on-diagonal elements apply to where all tracts through a single target go.

The number of tracts between any pair of targets is given by the off-diagonal elements of the "NT" matrix. You could add up the off-diagonal NT elements for a given target (i.e., sum across its row or column *excluding* the diagonal), but note that, depending on your targets, some tracts could theoretically go through multiple ROIs.

BL is bundle length, yes. You can choose what you want the length to represent with 4 different options, as described here:
[afni.nimh.nih.gov]
and in particular, this figure is probably the most useful part:
[afni.nimh.nih.gov]
Options are:

Default: only the parts of the tract within and between the targets; that is, parts of the initial tract that stick out away from the partner target are ignored.
    -uncut_at_rois: The whole initial tract: parts of the tract within each target, between the targets, and those endparts sticking out away from each target.
    -targ_surf_stop: only parts of the tract between the targets and just one layer into the target volumes; that is, the target surface stops the tracts after they enter.
    -targ_surf_twixt: only parts of the tract between the targets, stopping just just outside of the target volumes; that is, the tracts are only between (= betwixt) the targets, not overlapping at all.

For any of those, NT should still be the same. NT is number of tracts in a bundle, which is unaffected by that choice of endpoint-trimming. What *would* be affected is the bundle length measurement (BL), and things like the physical volume (PV) and number of voxels (NV and fNV)

--pt