According to their documentation, you are limited to 5000 voxels.
ROIs
must
be
formatted
as
binary
NIfTI
(http://nifti.nimh.nih.gov)
images
with
1x1x1
mm3 resolution,
and
the
ROI
must
not
extend
across
more
than
5000 voxels.
That's not a lot of voxels at anatomical resolution, but it may be useful at EPI data resolution. Consider resampling ROIs to a lower resolution with 3dfractionize or 3dresample. Also "3dAutobox -noclust" can be used to limit the dataset, even the zero voxels, to the smallest box that contains the ROI.
