It is almost certainly the case that the EP dataset is byte-swapped relative to the order on your CPU. This fact is recorded in the AFNI header, so that AFNI will silently fix the data as it reads from disk. Matlab does not do this. You can check by looking at the top lines of the 3dinfo output, which will include a line like so:
Byte Order: LSB_FIRST [this CPU native = MSB_FIRST]
In this example, you can see that the dataset is stored on disk in a byte-reversed way relative to the current CPU. Rick Reynolds described how to fix this (2swap and 3drefit).
#18 in the FAQ list has a little more about this subject.
bobcox
