Dear AFNI experts,
The output from 3dNetCorr includes a “graph dataset” of .niml.dset, which can be used for SUMA visualization of the connectivity matrix. However, my connectome includes a lot of ROIs that I want to filter out in this SUMA visualization. I am wondering if there is a convenient AFNI command to filter the .niml.dset, only keeping connectivity measures across a specified subset of ROIs.
Hi, Zhihao-
There isn’t a direct way to pare down those datasets. The best way to do that would be to re-run 3dNetCorr with a subset of the ROIs in the “-in_rois …” dset. That could be done with subbrick selectors, for example: -in_rois DSET_ROIS"[0…10,12,17,21…$]"
As a side benefit, that will also mean that the corresponding *.netcc file with the associated matrix values will be pared down similarly, which would be useful for quantitative comparisons.
–pt
Thank you Paul for this prompt response! It’s very helpful.
If not using 3dNetCorr, could you point me to the documentation of how to construct a .niml.dset? Suppose someone has just given you two regions’ MNI coordinates and their connection value, how would you visualize them in SUMA with two balls and a stick?
Hi, Zhihao-
You can create a set of spheres with stick connections as described here in the sphere tutorials:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/rois_corr_vis/suma_spheres.html#spheres-from-graph-views
Please let us know if that doesn’t work.
–pt