Can you supply some sample data? In the meantime, you can use findpeaks if you have the toolbox that it's in. Otherwise threshold and send the result into find() and start scanning for gaps of 3 seconds. It's all a lot easier if you have the Image Processing Toolbox where you can use functions like bwdist() and bwlabel() and regionprops() to find data separated by certain distances and of certain sizes.
Finally, define exactly what you mean by "isolate" since this is somewhat vague and ambiguous. Do you want to know the location of these peaks, or do you want to extract them out into their own submatrix? What exactly does "isolate" mean to you?
