Hi Kevin
(a) what is the output of creating a correlation matrix?
The output when you calculate correlation matrix include:
1) The correlation matrix was the same prefix name with your subject
folder, *.txt.
2) Also the fisher-z transformation matrix with z_*.txt.
3) The averaged time courses, TimeCourse_*.txt
4) If you download the latest developing version from github,
the sliding window correlation matrices would be estimated and the
output would be W-All*.txt
(b) how can you change the parcellation scheme being used from AAL 90,
and are you able to import your own parcellation scheme?
We set a Label mask to change the parcellation. For example,
if you have a AAL 90 parcellation, the identifiers for ROIs are
1, 2, 3,...,90. Then GRETNA would extract the averaged time courses
and calculated the correlation matrix. The first position of matrix
is ROI 1 and the last position of matrix is ROI 90.
If you want to use your own parcellation, you need obtain your own
label mask first.
(c) how do you visualize the correlation matrix with labels?
You could import the output from Preprocess GUI to Network Metrics
GUI, then double-click the correlation matrix to visualize the
matrix.

Hope it will help you:)

Best,
Sandy