Hi, JW-
The updated 3dNetCorr is now in the distribution, which was just rebuilt this morning. So, if you type
@update.afni.binaries -d
you should be able to get the new version (version number >= AFNI_21.2.06).
There are 2 new options, and I suspect you will want to use both simultaneously for having a "complete" NxN matrix output, even when some of the N ROIs are completely filled with time series that are all zeros:
-allow_roi_zeros :by default, this program will end unhappily if any ROI
contains only time series that are all zeros (which
might occur if you applied a mask to your data that
is smaller than your ROI map). This is because the
correlation with an all-zero time series is undefined.
However, if you want to allow ROIs to have all-zero
time series, use this option; each row and column
element in the Pearson and Fisher-Z transformed
matrices for this ROI will be 0. NB: you cannot
use -part_corr when this option is used, to avoid
of mathematical badness.
See the NOTE about this option, below
-automask_off :if you do not enter a mask, this program will
make an internal automask of where time series are
not uniformly zero. However, if you don't want this
done (e.g., you have a map of N ROIs that has greater
extent than your masked EPI data, and you are using
'-allow_roi_zeros' to get a full NxN matrix, even if
some rows and columns are zero), then use this option.
and this note comments a bit more about it:
[
afni.nimh.nih.gov]
Please let me know how it goes.
--pt
