Hi, Sondos-

When you say that "ROIs are missing", does that refer to the target ROIs or to the WM-connection ROIs? In general, there will be target ROIs without direct connections between them -- that is true physiologically as well as when running tractography.

Please see:
+ Taylor et al 2015: Brain Connectivity Vol. 6, No. 2, "Open Environment for Multimodal Interactive Connectivity Visualization and Analysis" for more about this, specifically the 2nd column of pg 116, in the paragraph starting with "The general implementation ...".
+ THe AFNI Bootcamp presentation: FATCAT_02_dti_tracking_intro.pdf, pg. 37 and the few following it mentioning sparsity
+ The first 11 slides of FATCAT_03_dti_tracking_funcs.pdf, which ends by mentioning specific tools for dealing with this when doing post-tractography group analysis
+ and perhaps most importantly, the FAT-MVM Demo (downloadable with "@Install_FATMVM_DEMO" which has a detailed readme file and scripts for looking at this matter when preparing to run 3dMVM.

---> Not finding connections tractographically doesn't mean they necessarily don't exist. In brief, it is very difficult to interpret them. By default, the MVM-based analysis in AFNI finds just the WM-connections that were found across all subjects and uses those.

Re. inflating target ROIs to white matter-- you can/should look at that in those data sets. Hopefully your target ROIs are close/mostly bordering WM already, before inflation; if they aren't, how were they created? Inflation should be a small effect, in general.

Re.:
<< Also, does that possibly mean that my ROI's don't inflate to the white matter, therefore we are not getting any values? >>
It is hard for me to tell the exact location of those regions in the initial post, because there is no accompanying WM (FA>0.2) image...

You can make a WM skeleton map (FA>0.2) with something like this :

3dcalc -a FA_VOLUME -expr '(a-0.2)' -prefix wm_skel_FA02.nii.gz

... then underlay that beneath your current ROIs and check how/if they border it.

--pt



Edited 1 time(s). Last edit at 10/22/2018 10:28PM by ptaylor.