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I used two 3D input images to do a FAST segmentation with two classes (CSF and brain matter). The input images were 1) a T2-image after BET and 2) an ADC-map with the same BET mask. This is the input: mfast -s 2 -c 2 -os -od adc_t2 t2.hdr adc.hdr The resulting error is: Empty input image. Nothing to do! even though the images were definitely not identical zero. The only reason for that I can imagine is that in the ADC map there are some pixels identical zero which have a non-zero value in the T2 image. May that be the problem? Markus