Hello,
First off, I want to say thank you for making such comprehensive software! I’m new to comp neuro, so it was really helpful to have a package that can do most of the things I needed, and give guides to where else I can go 
I’m currently working on with a monkey dataset, where I have tracts generated from tract-tracing in .tck files, and injection sites that specify where the tract-tracing was done from in a Nifti .nii.gz format. I also have an atlas for different regions of the brain I want to explore, which is in a .nii file. My question is, if I want to study the connection strength from each injection site to each ROI site, is there any way for me to do this? I know the tck2connectome command exists, but that’s typically used with a single atlas to make a square connectivity matrix, and I’m more so wondering if there was any way or command I can use to pass in both an atlas and the injection sites (as a mask with all of the injection sites, or something), and get the connectivity strength between injection site ↔ ROI rather than between atlas ROI ↔ ROI.
I hope this makes sense! The only way I can think of doing this is to maybe create a mask of each injection site with each atlas ROI and pass that to the tck2connectome command, and then repeat that for every combination (which would take a long time), or make a mask of all injection sites and the atlas, then passing that to tck2connectome (which would also take a long time, and I believe give a much bigger matrix than I want).
Thank you for help!
Hana
