How can I use EEG data as input and target for patternnet?

I have EEG data which is a 513 by n matrices of microvolt values. Each column corresponds to a vector in time that, when plotted looks like a wave. It is this wave object that I want as input and target rather than each individual microvolt value. There are two different conditions- one where the subject felt the stimulus and one where the subject did not and these waves will be different. I have tried using patternnet but I can't help but feel that it thinks that I am interested in the single values instead of the wave pattern. I am lost as well in coding for the targets. The documentation says it should be a matrix/array with 1 for target, 0 otherwise. Again, I run into the problem of not being able to tell Matlab that the entire column is the object of interest so I don't know how/where to put the 1s.

Please help! Thank you! Kim

[Greg Heath]

Words are insufficient

 [ I N ] = size(input)% [ ? ? ]
 [ O N ] = size(target)% [ ? ? ]

CODE???