Hi Ann,
Q2.1: We have waffled a bit regarding X.stim.xmat.1D, between having it full, empty and non-existent (for resting state data). Nothing makes everyone/thing happy. Right now, the file exists, but is empty, and afni (the GUI program itself) is whining about not finding valid contents. There is another similar message from 1dplot that I should change the driver to avoid.
Q2.2: For the collinearity warning, what is the output of:
1d_tool.py -show_cormat_warnings -infile X.xmat.1D
Thanks,
- rick