I'm not sure that anyone on this forum is going to be able to explain the FLAASH equations any better than they are explained in the published articles that it sounds like you already have.
Maybe your main confusion, though, is that you don't understand that the input image to FLAASH is the radiance data that FLAASH requires. Your image must be calibrated to radiance before you choose it as the input file for FLAASH. That radiance image will include both "at-sensor radiance reflected by the target" and "at-sensor radiance scattered into the path by the atmosphere". The point of FLAASH is to take that input radiance image, and convert it to surface reflectance, thereby removing the "at-sensor radiance scattered into the path by the atmosphere", among other things.
In case you do not already have the FLAASH references, here they are:
Adler-Golden, S. M., M. W. Matthew, L. S. Bernstein, R. Y. Levine, A. Berk, S. C. Richtsmeier, P. K. Acharya, G. P. Anderson, G. Felde, J. Gardner, M. Hoke, L. S. Jeong, B. Pukall, A. Ratkowski, and H.-H Burke, 1999. Atmospheric Correction for Short-wave Spectral Imagery Based on MODTRAN4. SPIE Proceedings on Imaging Spectrometry, Vol. 3753, pp. 61-69.
Berk, A., L. S. Bernstein, G. P. Anderson, P. K. Acharya, D. C. Robertson, J.H. Chetwynd, and S. M. Adler-Golden, 1998. MODTRAN Cloud and Multiple Scattering Upgrades with Application to AVIRIS. Remote Sensing of the Environment, Vol. 65, pp. 367-375.
Berk A., L. S. Bernstein, and D. C. Robertson, 1989. MODTRAN: a moderate resolution model for LOWTRAN7. GL-TR-89-0122. Air Force Geophysical Laboratory, Hanscom AFB, MA. p. 38.
Matthew, M. W., S. M. Adler-Golden, A. Berk, S. C. Richtsmeier, R. Y. Levine, L. S. Bernstein, P. K. Acharya, G. P. Anderson, G. W. Felde, M. P. Hoke, A. Ratkowski, H.-H. Burke, R. D. Kaiser, and D. P. Miller, 2000. Status of Atmospheric Correction Using a MODTRAN4-based Algorithm. SPIE Proceedings, Algorithms for Multispectral, Hyperspectral, and Ultraspectral Imagery VI. Vol. 4049, pp. 199-207.
Peg
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