Hi Adam,

In case 1, you may be running out of memory. The -mask option
does not reduce what is read in (the full ~1GB dataset is read).
The advantage of the mask is just to make processing faster, so
that voxels outside the mask are ignored. Also, your errts
output dataset is going to be just as big as the input dataset.
So you will be needing more than 2GB of RAM for that.

How much do you have? ("head /proc/meminfo", if Linux)

Note that since the runs are processed independently, there is
no need to use "allruns" as the input. You could break that
into the first and second half of runs, which would require
only half of the memory.

---

Case 2 may require you to set a couple of environment variables.
Perhaps you need to set AFNI_1D_TIME to "Y", and AFNI_1D_TIME_TR
to whatever your TR is (in seconds).

If you try this, please let us know how it works.

- rick