I have a similar problem. I have a file with a set of monthly SST images, each band on the file represents a month of the year with temperature values ranging from 1 to 40 and a null value of -999999. I need to calculate mean temperature from each pixel but ignoring the null data values. File header has -999999 defined as the ignore value but despite of that, calculating the mean of the data gives me negative values on each pixel that have a null on any of the images. Masking null values to give them any value wont help since they will affect the calculations. Is there any way to calculate the mean of several bands ignoring the null values in the calculation? any help would be appreciated

ENVI does not have a concept of a 'null value' and -9999 is as valid as any other value. What you have to do is create a mask of the pixels you want to exclude in processing and statistics. Then, when you go to calculate the statistics on the file, you can also select the mask band you created to exclude the values that are masked. The mask band is selected in the same dialog as the spatial/spectral subset option.