Hi Dane,

Problem #1 is my fault. Problem #2 is presumably
because of your change for problem #1 (changing
1dcat to 'cat' is not the correct way to go,
adding "-set_run_lengths $tr_counts" is).

That 1d_tool.py command (above 1dcat) does indeed
not take varying run lengths into account. To fix
that, add "-set_run_lengths $tr_counts" to the
1d_tool.py command.

Since the fix for this is in, you could alternatively
wait for updated AFNI binaries tonight. Or if time is
important, I could start an early build or even give
you a single file to update in your AFNI binaries
directory.

Just let me know what you prefer.

Thanks for bringing this up.

- rick