Ah, okay thank you for providing that very insightful and clear explanation as to what's going on.
I was using functional ROI's at the 3dMatch step, and the majority of my ROI's are already quite large. I can see how it might be problematic to inflate too much.

Oh, I also noticed that for the 3dTrackID step I was inputting the alg_Thresh_Frac to 0.1(now I can't seem to find the afni link that had done that earlier).
When I was reading the FATCAT documentation for this argument that are typically set it says: "-alg_Thresh_Frac G: default = 0.001; for higher specificity, a value of 0.01-0.05 would be used". It makes me think this may be another reason for the 0 values in my data. I could try to tweak this value and see if anything changes. Because the value I picked seems awfully high.


As a follow up question though, when you said: "The "individual ROI" connections (whose properties are listed on the diagonal) are just the set of *all* tracts that went through the ROI"
Does that logic apply when we are looking at the #NT (number of tracts)? Do the diagonal values involve all the tracts that leave ROI1 (for example)?

If not, how would I get the total number of streamlines leaving ROI1 (to all other ROIs)?

An additional question I have is: I know the default tract control options is to get tracts within and between targets.
However, if I'm interested in getting the distance between ROIs ...which I assume to be the #BL (bundle length). Should I instead use the argument -targ_surf_stop? Because the default value will give us a wrong distance(since it includes the distance within the target).
And then let's say I use targ_surf_stop. If I do that will the number of tracts leaving ROI1 for example, using "default tract control" decrease when I use the targ_surf_stop? Are only the outer voxels considered when tracing the tracts? or does this argument only affect the distance (aka bundle length) outputted only but not the number of tracts leaving the ROI?

I hope what I said makes sense. If something I said wasn't very clear please let me know and I'll clarify.

Thank you so much for your time.

Best wishes



Edited 3 time(s). Last edit at 12/10/2018 11:16AM by sondosayyash.