Hi, Juan-

I can't really advise on @ROI_Corr_Mat.

3dNetCorr can calculate both correlation matrices (all pairwise combinations of correlation coefficients of average time series in a map of ROIs), as well as whole brain (WB) connectivity maps for each ROI's average time series. The correlation matrices are calculated by default, and the WB maps are also generated with a switch. You can calculate WB maps even if you enter just a single ROI (the 1x1 correlation matrix wouldn't be so interesting), but if you have a bunch of ROIs, you can also just get all results at once.

Looking at the help of 3dNetCorr, there is an example for doing what you would want (probably):

      3dNetCorr                                  \
         -inset REST_in_DWI.nii.gz               \
         -in_rois ROI_ICMAP_GM+orig              \
         -fish_z                                 \
         -ts_wb_corr                             \
         -mask mask_DWI+orig                     \
         -prefix FMRI/REST_corr

line by line, this describes:
entering a subject's 4D (time series) data set;
entering a map of ROIs (all voxels with value '1' are in that ROI, all voxels with value '2' in another one, etc.);
asking the program to Fisher Z-transform the correlation matrix;
asking the program to output whole brain correlation maps of each ROI's average time series as a Pearson 'r' value ('-ts_wb_Z' would get you Fisher Z-transformed version of that, if you preferred);
and then you can enter a whole brain map (probably useful if doing a whole brain corr map);
... and last but not least, the output prefix for file names.

You can also output each ROI's average time series into a simple text file, if you wished; if your ROIs are labelled going in, then the output correlation matrices will store those labels, as well.

--pt