Hi Paul-

this is really very helpful, thanks! okay i transformed all the maps into the same space and just ran a simpler version to see what would happen with only the freesurfer file (Destrieux 2009 parcellations). the results are terrific and i was able to imagesc the .netcc file in matlab after minimal manual editing. a few more questions:

is there a way to tell 3dNetCorr to ignore some mask values or do i have to change the image mask itself (zeroing out values with 3dcalc for example)?

as for labels i'm a little unclear what to do. i've run @SUMA_Make_Spec_FS on my files so i do have aparc.a2009s+aseg_rank.niml.lt, etc, but i would like to remove/ignore some rows and add others (my masks, for example) so the correlation matrix only includes regions i care about. will doing this manually be a recipe for disaster, even if i'm very careful the 3d file integers and labels line up?

is @MakeLabelTable a new program written for FATCATing?

finally how do i get 3dNetCorr to recognize my labels so they track with the .netcc output? btw i'm using the most updated afni

thanks!!

-Sam