Great, glad things are going well.

>> 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)?

3dNetcorr will deal with all ROIs, so those would have to be edited out, either before or after running-- for the former, probably 3dcalc'ing, yes; for the latter, Python/matlab trickery to whittle down the columns/rows.


>> 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?

I think that if you have keys+values in a label table, but no ROIs of some key values in the file, then there's no problem-- the labeltable won't display those unwanted names. Thus, a larger set of keys in the labeltable is not really a problem, I don't believe, unless you re-number labels. However, I don't think you would need to renumber, especially if you are going to use labeltable labels (and 3dNetCorr does not require consecutive numbering of integers for ROIs).

Currently, there is a program for selecting just a single row out of a file; I guess I could generalize that to selecting sub-matrices... That should be doable on a ~shortish time scale.


>> is @MakeLabelTable a new program written for FATCATing?

Nope, it's an old school AFNI script; however, FATCAT has recently learned how to use and include table information.

>> 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

If your '-in_rois' has a labeltable, then the output (data sets and *.netcc files) should automatically include it. And, this excellent question points out that I forgot to include this useful information in the 3dNetCorr helpfile!

--pt