Most of the scripts used in StaMPS are NOT executables after installation (.exe files), only a few of them (calamp.exe, cpxsum.exe, pscdem.exe, psclonlat.exe, pscphase.exe, selpsc_patch.exe,selsbc_patch.exe, selsbc_patch_new.exe and showme.exe). mt_prep_gamma is not an executable but a script and it is necessary to change the file by the one provided by @FeiLiu or myself. Just download it and copy/paste in installation directory, erase the old one and change the name of the new one to mt_prep_gamma. Here there is a screenshot of the folder where I have StaMPS installed.
If the installation worked properly and you have added the path to your system variable, when you type "mt_prep_gamma" on cygwin shell (from any directory) the header of the script with instructions should be printed on the console. If this does not happen it means that the script is not placed where you indicated or the directory is not added properly to the system path variable.
Once you get this to work, the program is installed correctly. Then you should change directory to the folder where you exported SNAP data (a folder with 4 subdirectories: dem,diff0,geo,rslc) and execute mt_prep_gamma from there. Take care using the correct syntaxis to call mt_prep_gamma. It should be something like:
mt_prep_gamma [masterdate in format yyyymmdd] [data directory] [amp_threshold] [rg_patches] [az_patches] [az_overlap] [rg_overlap]
for example for a master 15 october 2016 and data placed in C:/Insardata/Stamps_export. Amplitude threshold 0.4, 5 patches in each direction and 200 pixels of overlapping:
mt_prep_gamma 20161015 /cygdrive/c/Insardata/Stamps_export 0.4 5 5 200 200
I hope you find your problems!