As mentioned above the default behavior for this operation is to store the processed images as a temporary document, with the following segment generating operations using these images to generate the objects but storing the resulting objects on the original image. There are two very important aspects to this:

1. Temporary documents are stored on the hard disk and used for the segmentation but are automatically deleted when the pipeline is finished.
2. Since the segmented objects are normally stored on the original image data it means that intensity measurements are made on the original data and not on the processed image.

So first, some notes on the temporary documents. The default location for temporary documents can be set in the Analysis preferences.

Note that for optimum performance it best to ensure that the location for temporary documents is on a fast local storage device. Avoid network drives or removable storage. It is also very important that there is ample free space in the selected destination to hold the temporary images. We typically recommend at least 5x as much free space and the size of the file being processed.