OK, looking at the data, the reason that PC calculations run into trouble---note that this runtime warning appears as another sign of it:
*+ WARNING: Badness in partial correlation calculation.
Normalizing factor is <=0 (how to take sqrt?)!
-> making all zeros.
---is that the number of ROIs in the "-inset ." is greater than the number of time points in the input data; this is especially true when the weight is applied, because here that is censoring time points out. This leads to collinearity within the matrix, making the denominator calc for the 'partial correlation' impossible mathematically. Here, there are 57 time points after censoring; when the number of ROIs is >=57, this badness should be expected for partial correlation (here, it actually happens when the number of ROIs is 55; I think that might be because the matrix is diagonal, so there would be 56 indep columns, and the one extra for... a reason I don't know).
Anyways, that appears to be the issue: the time series are too short (or the number of ROIs in the corr matrix too large) for the matrix to be invertible.
--pt
