The easiest way to create a subset of an image in ENVI is by using Basic Tools > Resize Data (Spatial/Spectral), and in the file selection dialog, after selecting your file, click the Spatial Subset button. It sounds like you are trying to use the Segmentaiton Image tool to make your subset. The Segmentation Image tool doesn't create subsets of your original image. Instead, it assigns the pixels in the image into a set of segments, based on their DN values.
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